------------------------------------------------------------------------
-r451 | lh3lh3 | 2009-09-02 10:44:48 +0100 (Wed, 02 Sep 2009) | 4 lines
+r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-22 (r509)
+ * forget to fix a similar problem in glfgen
+
+------------------------------------------------------------------------
+r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.6-21 (r508)
+ * fixed a potential bug in the indel caller towards the end of a chromosome
+
+------------------------------------------------------------------------
+r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.6-19 (r494)
+ * allow to convert Illumina quality (64 based) to the BAM quality
+
+------------------------------------------------------------------------
+r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam_header.c
+
+ * samtools-0.1.6-18 (r493)
+ * fixed the bugs due to improperly incorporating Petr's header parser
+ * a little code clean up in sam_header.c
+
+------------------------------------------------------------------------
+r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+
+Added sam_header_line_free call for sam_header_parse2
+------------------------------------------------------------------------
+r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/sam_view.c
+
+ * BUGGY VERSION
+ * fixed a minor bug
+
+------------------------------------------------------------------------
+r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/sam.c
+
+ * BUGGY VERSION
+ * improved the interface a bit
+ * bug unfixed
+
+------------------------------------------------------------------------
+r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/sam_header.c
+ M /trunk/samtools/sam_header.h
+
+ * BUGGY VERSION. Please NOT use it.
+ * Fixed a minor bug, but the major bug is still there.
+
+------------------------------------------------------------------------
+r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/kaln.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam_header.c
+ M /trunk/samtools/sam_header.h
+ M /trunk/samtools/sam_view.c
+
+ * This revision is SERIOUSLY BUGGY. Please NOT use it.
+ * Start to incorporate header parsing from Petr Danecek
+
+------------------------------------------------------------------------
+r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+ M /trunk/samtools/sam_header.h
+
+Now possible to merge multiple HeaderDict dictionaries
+------------------------------------------------------------------------
+r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+
+
+------------------------------------------------------------------------
+r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
+Changed paths:
+ A /trunk/samtools/sam_header.c
+ A /trunk/samtools/sam_header.h
+
+
+------------------------------------------------------------------------
+r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/examples/Makefile
+
+ * samtools-0.1.6-17 (r484)
+ * fixed a memory leak in rmdupse
+ * fixed a bug in parsing @RG header lines
+ * test rmdup in examples/
+
+------------------------------------------------------------------------
+r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-16 (r483)
+ * unify the interface of rmdup and rmdupse
+ * a new bug found in rg2lib(). Have not been fixed yet.
+
+------------------------------------------------------------------------
+r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/bamtk.c
+ A /trunk/samtools/klist.h
+
+ * samtools-0.1.6-15 (r482)
+ * rewrite rmdupse
+ * rmdupse is now library aware
+
+------------------------------------------------------------------------
+r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-14 (r480)
+ * rmdup is now RG aware
+
+------------------------------------------------------------------------
+r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+added a small unitity to parse SRA XML files
+
+------------------------------------------------------------------------
+r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_maqcns.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-13 (r479)
+ * merge: optionally use file names as RG tags
+
+------------------------------------------------------------------------
+r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/kaln.c
+
+ * samtools-0.1.6-12 (r478)
+ * fixed a bug in the indel caller
+
+------------------------------------------------------------------------
+r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-11 (r477)
+ * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
+
+------------------------------------------------------------------------
+r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
+Changed paths:
+ A /trunk/samtools/misc/sam2vcf.pl
+
+Added the sam2vcf.pl script.
+------------------------------------------------------------------------
+r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+ A /trunk/samtools/kaln.c
+ A /trunk/samtools/kaln.h
+
+Unfinished modification. Please do not use this revision...
+
+------------------------------------------------------------------------
+r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/knetfile.c
+
+Removed the offending knet_seek message.
+------------------------------------------------------------------------
+r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/razf.c
+
+Bug fix - faidx on RAZF compressed files now working.
+------------------------------------------------------------------------
+r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/samtools.1
+
+Clarify the meaning of a region like "chr2:1,000,000".
+
+------------------------------------------------------------------------
+r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/novo2sam.pl
+
+Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
+
+------------------------------------------------------------------------
+r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile.mingw
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/knetfile.h
+
+ * samtools-0.1.6-9 (r470)
+ * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
+
+------------------------------------------------------------------------
+r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-9 (r469)
+ * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
+
+------------------------------------------------------------------------
+r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools-0.1.6-7 (r468)
+ * make merge stable
+
+------------------------------------------------------------------------
+r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/bgzf.c
+ M /trunk/samtools/bgzip.c
+ M /trunk/samtools/razf.c
+ M /trunk/samtools/razip.c
+
+Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
+------------------------------------------------------------------------
+r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-6 (r466)
+ * do not crash calmd when some sequences are absent from the reference.
+
+------------------------------------------------------------------------
+r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/knetfile.c
+
+Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
+no way to seek on a pipe and the messages always appear.
+
+------------------------------------------------------------------------
+r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/razf.c
+
+A bug fix, "samtools view" is now working again.
+------------------------------------------------------------------------
+r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/faidx.c
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/knetfile.h
+ M /trunk/samtools/razf.c
+ M /trunk/samtools/razf.h
+
+ * samtools-0.1.6-5 (r462)
+ * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
+
+------------------------------------------------------------------------
+r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/samtools.1
+
+fixed a formatting issue
+
+------------------------------------------------------------------------
+r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-4 (r459)
+ * make sort output the result to stdout when -o is in use
+
+------------------------------------------------------------------------
+r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/faidx.c
+ M /trunk/samtools/faidx.h
+ M /trunk/samtools/samtools.1
+
+ * samtools-0.1.6-2 (r458)
+ * added more interface to faidx (by Nils)
+ * updated documentation
+
+------------------------------------------------------------------------
+r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-2 (r457)
+ * get rid of three assert() in bam_sort.c
+
+------------------------------------------------------------------------
+r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/razf.c
+
+Return NULL from _razf_open() (and hence razf_open()/razf_open2())
+when opening the file fails.
+
+------------------------------------------------------------------------
+r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+ D /trunk/samtools/source.dot
+
+Release samtools-0.1.6
+
+------------------------------------------------------------------------
+r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
Changed paths:
M /trunk/samtools/bam_md.c
M /trunk/samtools/bam_rmdup.c
* improved the help message a little bit
------------------------------------------------------------------------
-r450 | lh3lh3 | 2009-09-02 09:55:55 +0100 (Wed, 02 Sep 2009) | 3 lines
+r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_color.c
M /trunk/samtools/bamtk.c
* fixed a bug in bam_color.c (on behalf of Nils Homer)
------------------------------------------------------------------------
-r449 | lh3lh3 | 2009-08-29 20:36:41 +0100 (Sat, 29 Aug 2009) | 4 lines
+r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
Changed paths:
M /trunk/samtools/bam_import.c
M /trunk/samtools/bam_md.c
* in import, give a warning if the read is aligned but there is no CIGAR.
------------------------------------------------------------------------
-r448 | lh3lh3 | 2009-08-19 09:44:28 +0100 (Wed, 19 Aug 2009) | 3 lines
+r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/bam_pileup.c
* fixed an issue when the last CIGAR is I or D
------------------------------------------------------------------------
-r447 | lh3lh3 | 2009-08-17 09:34:57 +0100 (Mon, 17 Aug 2009) | 3 lines
+r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_aux.c
M /trunk/samtools/bamtk.c
* fixed a bug in bam_aux_get(): 'A' is not checked
------------------------------------------------------------------------
-r446 | lh3lh3 | 2009-08-17 09:33:17 +0100 (Mon, 17 Aug 2009) | 2 lines
+r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
Changed paths:
M /trunk/samtools/bam_aux.c
M /trunk/samtools/bamtk.c
*
------------------------------------------------------------------------
-r444 | lh3lh3 | 2009-08-11 10:02:36 +0100 (Tue, 11 Aug 2009) | 3 lines
+r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_sort.c
M /trunk/samtools/bamtk.c
* bug in "merge -n"
------------------------------------------------------------------------
-r443 | lh3lh3 | 2009-08-11 09:29:11 +0100 (Tue, 11 Aug 2009) | 4 lines
+r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
Changed paths:
M /trunk/samtools/bam.c
M /trunk/samtools/bam_import.c
* parse CIGAR "=" and "X" as "M"
------------------------------------------------------------------------
-r442 | lh3lh3 | 2009-08-07 21:56:38 +0100 (Fri, 07 Aug 2009) | 4 lines
+r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
Changed paths:
M /trunk/samtools/bam_pileup.c
M /trunk/samtools/bamtk.c
* fixed a bug in detecting unsorted bam in pileup
------------------------------------------------------------------------
-r441 | bhandsaker | 2009-08-05 14:41:28 +0100 (Wed, 05 Aug 2009) | 2 lines
+r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
Changed paths:
M /trunk/samtools/bgzf.c
M /trunk/samtools/bgzf.h
Change copyright notices now that MIT has approved open source distribution.
------------------------------------------------------------------------
-r440 | lh3lh3 | 2009-08-05 10:44:24 +0100 (Wed, 05 Aug 2009) | 3 lines
+r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_stat.c
M /trunk/samtools/bamtk.c
* in flagstats, do not report singletons if both ends are unmapped
------------------------------------------------------------------------
-r439 | lh3lh3 | 2009-08-04 22:16:51 +0100 (Tue, 04 Aug 2009) | 2 lines
+r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
Changed paths:
M /trunk/samtools/misc/maq2sam.c
fixed a SERIOUS bug in setting 0x20 flag
------------------------------------------------------------------------
-r438 | lh3lh3 | 2009-08-04 21:50:43 +0100 (Tue, 04 Aug 2009) | 2 lines
+r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
fixed two minor bugs (suggested by Tim M Storm)
------------------------------------------------------------------------
-r437 | lh3lh3 | 2009-08-04 09:13:24 +0100 (Tue, 04 Aug 2009) | 3 lines
+r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/misc/samtools.pl
* fixed a typo
------------------------------------------------------------------------
-r434 | lh3lh3 | 2009-08-03 10:40:42 +0100 (Mon, 03 Aug 2009) | 3 lines
+r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_tview.c
M /trunk/samtools/bamtk.c
* in tview, press 'r' to show read names rather than sequences
------------------------------------------------------------------------
-r433 | lh3lh3 | 2009-08-02 19:13:35 +0100 (Sun, 02 Aug 2009) | 3 lines
+r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
Changed paths:
M /trunk/samtools/knetfile.c
* anyway, MinGW seems to have problem with "%lld".
------------------------------------------------------------------------
-r432 | lh3lh3 | 2009-08-02 00:32:07 +0100 (Sun, 02 Aug 2009) | 5 lines
+r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
Changed paths:
M /trunk/samtools/Makefile.mingw
M /trunk/samtools/bamtk.c
* PDCurses support in Windows
------------------------------------------------------------------------
-r431 | lh3lh3 | 2009-08-01 23:34:54 +0100 (Sat, 01 Aug 2009) | 2 lines
+r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
Changed paths:
M /trunk/samtools/win32/libz.a
replace the GnuWin32 version of libz.a with my own build with MinGW.
------------------------------------------------------------------------
-r430 | lh3lh3 | 2009-08-01 23:21:07 +0100 (Sat, 01 Aug 2009) | 2 lines
+r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
Changed paths:
M /trunk/samtools/knetfile.c
add comments
------------------------------------------------------------------------
-r429 | lh3lh3 | 2009-08-01 22:41:19 +0100 (Sat, 01 Aug 2009) | 3 lines
+r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
Changed paths:
M /trunk/samtools/Makefile.mingw
M /trunk/samtools/bamtk.c
* knetfile.c is now compatible with mingw-winsock
------------------------------------------------------------------------
-r428 | lh3lh3 | 2009-08-01 00:39:07 +0100 (Sat, 01 Aug 2009) | 2 lines
+r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/Makefile.mingw
simplify MinGW Makefile
------------------------------------------------------------------------
-r427 | lh3lh3 | 2009-08-01 00:30:54 +0100 (Sat, 01 Aug 2009) | 5 lines
+r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
Changed paths:
A /trunk/samtools/Makefile.mingw
M /trunk/samtools/bam_import.c
* zlib headers and Windows version of libz.a are included in win32/
------------------------------------------------------------------------
-r426 | lh3lh3 | 2009-07-31 23:32:09 +0100 (Fri, 31 Jul 2009) | 3 lines
+r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/sam_view.c
* fixed a bug caused by recent modifications. Sorry.
------------------------------------------------------------------------
-r425 | lh3lh3 | 2009-07-31 23:23:51 +0100 (Fri, 31 Jul 2009) | 2 lines
+r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/bgzf.c
compatible with Windows binary files
------------------------------------------------------------------------
-r424 | lh3lh3 | 2009-07-31 10:19:59 +0100 (Fri, 31 Jul 2009) | 5 lines
+r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
Changed paths:
M /trunk/samtools/bam_maqcns.c
M /trunk/samtools/bam_maqcns.h
* in tview, optionally allow to treat reference skip as deletion
------------------------------------------------------------------------
-r423 | lh3lh3 | 2009-07-30 22:00:36 +0100 (Thu, 30 Jul 2009) | 2 lines
+r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
Changed paths:
A /trunk/samtools/misc/psl2sam.pl
convert BLAT psl to SAM.
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-r422 | lh3lh3 | 2009-07-30 11:24:39 +0100 (Thu, 30 Jul 2009) | 6 lines
+r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/bam.c
* update ChangeLog
------------------------------------------------------------------------
-r421 | lh3lh3 | 2009-07-30 10:03:39 +0100 (Thu, 30 Jul 2009) | 3 lines
+r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_import.c
M /trunk/samtools/bam_plcmd.c
* in view and pileup, load header from FASTA index if the input is SAM.
------------------------------------------------------------------------
-r420 | lh3lh3 | 2009-07-29 09:18:55 +0100 (Wed, 29 Jul 2009) | 2 lines
+r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/misc/maq2sam.c
do not set "read 1" if reads are not mapped in the PE mode of maq
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-r419 | lh3lh3 | 2009-07-28 09:52:33 +0100 (Tue, 28 Jul 2009) | 5 lines
+r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
Changed paths:
M /trunk/samtools/bam_import.c
M /trunk/samtools/bamtk.c
* add "unique" command to samtools.pl
------------------------------------------------------------------------
-r418 | lh3lh3 | 2009-07-24 14:04:19 +0100 (Fri, 24 Jul 2009) | 2 lines
+r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/misc/wgsim_eval.pl
skip @header lines in SAM
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-r417 | lh3lh3 | 2009-07-24 12:42:38 +0100 (Fri, 24 Jul 2009) | 3 lines
+r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/sam_view.c
* more help in "samtools view" due to the recent changes.
------------------------------------------------------------------------
-r416 | lh3lh3 | 2009-07-24 12:34:30 +0100 (Fri, 24 Jul 2009) | 3 lines
+r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam.c
M /trunk/samtools/bam.h
* support import/export SAM with string tags
------------------------------------------------------------------------
-r415 | lh3lh3 | 2009-07-24 11:39:26 +0100 (Fri, 24 Jul 2009) | 3 lines
+r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam.c
M /trunk/samtools/bam.h
* FLAG now can be in HEX
------------------------------------------------------------------------
-r414 | lh3lh3 | 2009-07-22 22:03:49 +0100 (Wed, 22 Jul 2009) | 2 lines
+r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/kstring.h
fixed a compiling error (thank Ken for fixing it)
------------------------------------------------------------------------
-r412 | lh3lh3 | 2009-07-21 22:19:40 +0100 (Tue, 21 Jul 2009) | 2 lines
+r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/kstring.c
M /trunk/samtools/kstring.h
Implemented Boyer-Moore search in the kstring library.
------------------------------------------------------------------------
-r409 | lh3lh3 | 2009-07-17 17:10:20 +0100 (Fri, 17 Jul 2009) | 2 lines
+r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/bam_index.c
do not include knetfile.h when _USE_KNETFILE is not defined
------------------------------------------------------------------------
-r408 | lh3lh3 | 2009-07-17 15:29:21 +0100 (Fri, 17 Jul 2009) | 5 lines
+r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
Changed paths:
M /trunk/samtools/bam_md.c
M /trunk/samtools/bam_tview.c
* bgzf.c: improved the compatibility with Windows headers
------------------------------------------------------------------------
-r407 | lh3lh3 | 2009-07-17 14:46:56 +0100 (Fri, 17 Jul 2009) | 5 lines
+r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
Changed paths:
M /trunk/samtools/bam.h
M /trunk/samtools/bam_aux.c
* fillmd: cmd interface improvement
------------------------------------------------------------------------
-r406 | lh3lh3 | 2009-07-16 23:30:40 +0100 (Thu, 16 Jul 2009) | 2 lines
+r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/Makefile
Sorry. The old Makefile is for PDCurses...
------------------------------------------------------------------------
-r405 | lh3lh3 | 2009-07-16 23:30:11 +0100 (Thu, 16 Jul 2009) | 3 lines
+r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/bam_tview.c
* improved the compatibility with PDCurses a little bit
------------------------------------------------------------------------
-r404 | lh3lh3 | 2009-07-16 23:23:52 +0100 (Thu, 16 Jul 2009) | 3 lines
+r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/bam_tview.c
* compatible with PDCurses
------------------------------------------------------------------------
-r403 | lh3lh3 | 2009-07-16 22:39:39 +0100 (Thu, 16 Jul 2009) | 3 lines
+r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/kseq.h
* fixed a bug in kseq.h for binary files (text files are fine)
------------------------------------------------------------------------
-r402 | lh3lh3 | 2009-07-16 11:49:53 +0100 (Thu, 16 Jul 2009) | 4 lines
+r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
Changed paths:
M /trunk/samtools/bam_import.c
M /trunk/samtools/bam_index.c
* improve portability to MinGW
------------------------------------------------------------------------
-r398 | lh3lh3 | 2009-07-13 10:21:36 +0100 (Mon, 13 Jul 2009) | 3 lines
+r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
Changed paths:
A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
* copy bam.h to bam-lite
------------------------------------------------------------------------
-r395 | lh3lh3 | 2009-07-13 10:12:57 +0100 (Mon, 13 Jul 2009) | 3 lines
+r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam.h
M /trunk/samtools/bam_lite.c
* added bam_pileup_file() and removed bam_lpileup_file()
------------------------------------------------------------------------
-r394 | lh3lh3 | 2009-07-13 00:35:10 +0100 (Mon, 13 Jul 2009) | 3 lines
+r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/knetfile.c
* http_proxy support in knetfile library (check http_proxy ENV)
------------------------------------------------------------------------
-r393 | lh3lh3 | 2009-07-12 23:57:07 +0100 (Sun, 12 Jul 2009) | 5 lines
+r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
Changed paths:
M /trunk/samtools/bam_index.c
M /trunk/samtools/bam_tview.c
not seen the sideeffect so far.
------------------------------------------------------------------------
-r392 | lh3lh3 | 2009-07-12 18:50:55 +0100 (Sun, 12 Jul 2009) | 2 lines
+r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/samtools.1
Remove the warning in tview
------------------------------------------------------------------------
-r391 | lh3lh3 | 2009-07-12 18:42:43 +0100 (Sun, 12 Jul 2009) | 3 lines
+r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_tview.c
M /trunk/samtools/bamtk.c
* do not show a blank screen when no reads mapped
------------------------------------------------------------------------
-r390 | lh3lh3 | 2009-07-09 14:01:42 +0100 (Thu, 09 Jul 2009) | 4 lines
+r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
Changed paths:
M /trunk/samtools/bam.h
A /trunk/samtools/bam_lite.c
* added bam_lite.c for light-weight BAM reading
------------------------------------------------------------------------
-r385 | lh3lh3 | 2009-07-07 16:53:29 +0100 (Tue, 07 Jul 2009) | 2 lines
+r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/knetfile.c
Release samtools-0.1.5c (fixed a bug in piping)
------------------------------------------------------------------------
-r383 | lh3lh3 | 2009-07-07 11:39:55 +0100 (Tue, 07 Jul 2009) | 2 lines
+r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/sam.c
Release samtools-0.1.5b (BUG! so embarrassing!)
------------------------------------------------------------------------
-r381 | lh3lh3 | 2009-07-07 11:20:06 +0100 (Tue, 07 Jul 2009) | 2 lines
+r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/bam.h
Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
------------------------------------------------------------------------
-r373 | lh3lh3 | 2009-07-07 10:26:57 +0100 (Tue, 07 Jul 2009) | 2 lines
+r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/NEWS
Release samtools-0.1.5
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-r372 | lh3lh3 | 2009-07-07 09:49:27 +0100 (Tue, 07 Jul 2009) | 3 lines
+r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/sam.c
* keep header text if "view -t" is used (by Gerton)
------------------------------------------------------------------------
-r371 | lh3lh3 | 2009-07-07 01:13:32 +0100 (Tue, 07 Jul 2009) | 2 lines
+r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/samtools.1
update documentation
------------------------------------------------------------------------
-r370 | bhandsaker | 2009-07-02 22:24:34 +0100 (Thu, 02 Jul 2009) | 2 lines
+r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
Changed paths:
M /trunk/samtools/Makefile
Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
------------------------------------------------------------------------
-r369 | lh3lh3 | 2009-07-02 13:36:53 +0100 (Thu, 02 Jul 2009) | 4 lines
+r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/bam_aux.c
* remove the debugging code in bam_aux_get() (Drat!)
------------------------------------------------------------------------
-r368 | lh3lh3 | 2009-07-02 11:32:26 +0100 (Thu, 02 Jul 2009) | 6 lines
+r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
Changed paths:
M /trunk/samtools/bam.c
M /trunk/samtools/bam.h
* small memory leak may be present on failure, though
------------------------------------------------------------------------
-r367 | lh3lh3 | 2009-06-30 16:18:42 +0100 (Tue, 30 Jun 2009) | 2 lines
+r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/knetfile.c
reduce the chance of blocking in FTP connection
------------------------------------------------------------------------
-r366 | lh3lh3 | 2009-06-30 15:35:21 +0100 (Tue, 30 Jun 2009) | 2 lines
+r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/knetfile.c
minor changes to knetfile: invalid fd equals -1 rather than 0
------------------------------------------------------------------------
-r365 | lh3lh3 | 2009-06-30 14:04:30 +0100 (Tue, 30 Jun 2009) | 3 lines
+r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_index.c
M /trunk/samtools/bamtk.c
* download the BAM index file if it is not found in the current working directory.
------------------------------------------------------------------------
-r364 | lh3lh3 | 2009-06-30 12:39:07 +0100 (Tue, 30 Jun 2009) | 3 lines
+r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/knetfile.c
* knetfile: report error when the file is not present on FTP
------------------------------------------------------------------------
-r363 | lh3lh3 | 2009-06-29 23:23:32 +0100 (Mon, 29 Jun 2009) | 4 lines
+r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
Changed paths:
M /trunk/samtools/bam_tview.c
M /trunk/samtools/bamtk.c
* bgzf: cache recent blocks (disabled by default)
------------------------------------------------------------------------
-r362 | lh3lh3 | 2009-06-25 21:04:34 +0100 (Thu, 25 Jun 2009) | 2 lines
+r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/bgzf.c
write changelog
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-r361 | lh3lh3 | 2009-06-25 21:03:10 +0100 (Thu, 25 Jun 2009) | 3 lines
+r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_index.c
M /trunk/samtools/bamtk.c
* if a file is given on FTP, search locally for the BAM index
------------------------------------------------------------------------
-r360 | lh3lh3 | 2009-06-25 20:44:52 +0100 (Thu, 25 Jun 2009) | 5 lines
+r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/bam_import.c
* support knetfile library in BGZF
------------------------------------------------------------------------
-r359 | lh3lh3 | 2009-06-25 17:10:55 +0100 (Thu, 25 Jun 2009) | 2 lines
+r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/knetfile.c
M /trunk/samtools/knetfile.h
fixed bugs in knetfile.*
------------------------------------------------------------------------
-r358 | lh3lh3 | 2009-06-25 13:53:19 +0100 (Thu, 25 Jun 2009) | 2 lines
+r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
Changed paths:
A /trunk/samtools/knetfile.h
this is the header file
------------------------------------------------------------------------
-r357 | lh3lh3 | 2009-06-25 13:52:03 +0100 (Thu, 25 Jun 2009) | 3 lines
+r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
Changed paths:
A /trunk/samtools/knetfile.c
* preliminary version
------------------------------------------------------------------------
-r354 | lh3lh3 | 2009-06-24 14:02:25 +0100 (Wed, 24 Jun 2009) | 3 lines
+r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam.c
M /trunk/samtools/bamtk.c
* fixed a memory leak in bam_view1(), although samtools is not using this routine.
------------------------------------------------------------------------
-r351 | lh3lh3 | 2009-06-18 00:16:26 +0100 (Thu, 18 Jun 2009) | 4 lines
+r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/faidx.c
* hope this does not introduce new bugs...
------------------------------------------------------------------------
-r350 | lh3lh3 | 2009-06-16 14:37:01 +0100 (Tue, 16 Jun 2009) | 3 lines
+r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* fixed a small memory leak in pileup, caused by recent modifications
------------------------------------------------------------------------
-r347 | lh3lh3 | 2009-06-13 21:20:49 +0100 (Sat, 13 Jun 2009) | 3 lines
+r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* added `-S' to pileup, similar to `view -S'
------------------------------------------------------------------------
-r346 | lh3lh3 | 2009-06-13 17:52:31 +0100 (Sat, 13 Jun 2009) | 3 lines
+r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/bamtk.c
* allow to select a read group at view command-line
------------------------------------------------------------------------
-r344 | lh3lh3 | 2009-06-13 14:06:24 +0100 (Sat, 13 Jun 2009) | 2 lines
+r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/examples/calDepth.c
added more comments
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-r343 | lh3lh3 | 2009-06-13 14:01:22 +0100 (Sat, 13 Jun 2009) | 2 lines
+r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/examples/calDepth.c
nothing really
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-r342 | lh3lh3 | 2009-06-13 13:58:48 +0100 (Sat, 13 Jun 2009) | 2 lines
+r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/examples/Makefile
A /trunk/samtools/examples/calDepth.c
added an example of calculating read depth
------------------------------------------------------------------------
-r341 | lh3lh3 | 2009-06-13 13:00:08 +0100 (Sat, 13 Jun 2009) | 6 lines
+r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/bam.h
* remove the support of -q in pileup
------------------------------------------------------------------------
-r340 | lh3lh3 | 2009-06-13 11:17:14 +0100 (Sat, 13 Jun 2009) | 6 lines
+r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
Changed paths:
M /trunk/samtools/INSTALL
M /trunk/samtools/Makefile
* detect NCURSES in bam_tview.c
------------------------------------------------------------------------
-r339 | lh3lh3 | 2009-06-13 10:35:19 +0100 (Sat, 13 Jun 2009) | 2 lines
+r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/INSTALL
update INSTALL
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-r338 | lh3lh3 | 2009-06-13 00:15:24 +0100 (Sat, 13 Jun 2009) | 4 lines
+r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
Changed paths:
M /trunk/samtools/bam.c
M /trunk/samtools/bam.h
command line
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-r337 | lh3lh3 | 2009-06-12 21:25:50 +0100 (Fri, 12 Jun 2009) | 4 lines
+r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/bgzf.c
* "samtools view" support "-u" command-line option
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-r336 | lh3lh3 | 2009-06-12 17:20:12 +0100 (Fri, 12 Jun 2009) | 5 lines
+r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/misc/Makefile
* on old version of zlib, writing is not available
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-r335 | lh3lh3 | 2009-06-12 16:47:33 +0100 (Fri, 12 Jun 2009) | 2 lines
+r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
D /trunk/samtools/zlib
remove zlib for simplification...
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-r334 | lh3lh3 | 2009-06-12 15:43:36 +0100 (Fri, 12 Jun 2009) | 5 lines
+r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
Changed paths:
M /trunk/samtools/bam.h
M /trunk/samtools/bam_aux.c
* this version works with the latest Bio::DB::Sam (20090612)
------------------------------------------------------------------------
-r333 | lh3lh3 | 2009-06-12 15:33:42 +0100 (Fri, 12 Jun 2009) | 2 lines
+r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
update ChangeLog
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-r332 | lh3lh3 | 2009-06-12 15:21:21 +0100 (Fri, 12 Jun 2009) | 2 lines
+r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/AUTHORS
M /trunk/samtools/Makefile
fixed minor things in Makefile
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-r331 | lh3lh3 | 2009-06-12 15:07:05 +0100 (Fri, 12 Jun 2009) | 4 lines
+r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
Changed paths:
M /trunk/samtools/bamtk.c
changes in the Makefile building system.
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-r330 | lh3lh3 | 2009-06-12 15:03:38 +0100 (Fri, 12 Jun 2009) | 2 lines
+r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/AUTHORS
D /trunk/samtools/README
update information...
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-r329 | lh3lh3 | 2009-06-12 14:52:21 +0100 (Fri, 12 Jun 2009) | 3 lines
+r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/novo2sam.pl
* this version works with indels
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-r328 | lh3lh3 | 2009-06-12 14:50:53 +0100 (Fri, 12 Jun 2009) | 3 lines
+r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/INSTALL
M /trunk/samtools/Makefile
* update INSTALL instruction
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-r327 | lh3lh3 | 2009-06-12 14:18:29 +0100 (Fri, 12 Jun 2009) | 4 lines
+r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
Changed paths:
A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
D /trunk/samtools/Makefile.am
* unfinished! (will be soon)
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-r326 | lh3lh3 | 2009-06-12 14:12:03 +0100 (Fri, 12 Jun 2009) | 2 lines
+r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
Unfinished
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-r325 | lh3lh3 | 2009-06-10 16:27:59 +0100 (Wed, 10 Jun 2009) | 3 lines
+r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_maqcns.c
M /trunk/samtools/bamtk.c
* further avoid wrong consensus calls in repetitive regions.
------------------------------------------------------------------------
-r324 | lh3lh3 | 2009-06-10 15:56:17 +0100 (Wed, 10 Jun 2009) | 4 lines
+r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
Changed paths:
M /trunk/samtools/bam_maqcns.c
M /trunk/samtools/bam_plcmd.c
* allow filtering on mapQ at the pileup command line
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-r323 | lh3lh3 | 2009-06-10 10:04:21 +0100 (Wed, 10 Jun 2009) | 3 lines
+r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* indels and SNPs use different mapping quality threshold
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-r322 | lh3lh3 | 2009-06-10 10:03:22 +0100 (Wed, 10 Jun 2009) | 2 lines
+r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/misc/export2sam.pl
fixed a typo
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-r321 | lh3lh3 | 2009-06-09 09:21:48 +0100 (Tue, 09 Jun 2009) | 2 lines
+r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
just typo. no real change
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-r320 | lh3lh3 | 2009-06-08 14:32:51 +0100 (Mon, 08 Jun 2009) | 2 lines
+r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
a little bit code cleanup
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-r319 | lh3lh3 | 2009-06-08 14:22:33 +0100 (Mon, 08 Jun 2009) | 4 lines
+r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* optionally print filtered variants
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-r318 | lh3lh3 | 2009-06-08 14:14:26 +0100 (Mon, 08 Jun 2009) | 3 lines
+r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* combine snpFilter and indelFilter
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-r317 | lh3lh3 | 2009-06-08 11:31:42 +0100 (Mon, 08 Jun 2009) | 3 lines
+r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* change a default parameter
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-r316 | lh3lh3 | 2009-06-08 11:11:06 +0100 (Mon, 08 Jun 2009) | 5 lines
+r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
Changed paths:
M /trunk/samtools/bam_maqcns.c
M /trunk/samtools/bam_maqcns.h
* pileup: allow to output variant sites only
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-r312 | lh3lh3 | 2009-06-04 13:01:10 +0100 (Thu, 04 Jun 2009) | 3 lines
+r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* added pileup2fq
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-r311 | lh3lh3 | 2009-06-03 09:40:40 +0100 (Wed, 03 Jun 2009) | 2 lines
+r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* in snpFilter, suppress non-SNP sites
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-r310 | lh3lh3 | 2009-06-01 14:35:13 +0100 (Mon, 01 Jun 2009) | 3 lines
+r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* fixed a typo
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-r309 | lh3lh3 | 2009-06-01 14:04:39 +0100 (Mon, 01 Jun 2009) | 3 lines
+r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* snpFilter
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-r306 | lh3lh3 | 2009-05-28 11:49:35 +0100 (Thu, 28 May 2009) | 3 lines
+r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/bgzf.c
* suggested by {kdj,jm18}@sanger.ac.uk
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-r305 | lh3lh3 | 2009-05-28 11:16:08 +0100 (Thu, 28 May 2009) | 2 lines
+r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
Changed paths:
A /trunk/samtools/misc/interpolate_sam.pl
Script for paired-end pileup, contributed by Stephen Montgomery.
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-r304 | lh3lh3 | 2009-05-28 11:08:49 +0100 (Thu, 28 May 2009) | 3 lines
+r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/sam.c
* fixed a minor bug in printing headers
------------------------------------------------------------------------
-r297 | lh3lh3 | 2009-05-21 16:06:16 +0100 (Thu, 21 May 2009) | 2 lines
+r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/NEWS
Release samtools-0.1.4
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-r296 | lh3lh3 | 2009-05-21 12:53:14 +0100 (Thu, 21 May 2009) | 3 lines
+r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_maqcns.c
M /trunk/samtools/bamtk.c
* another similar bug in the indel caller
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-r295 | lh3lh3 | 2009-05-21 12:50:28 +0100 (Thu, 21 May 2009) | 3 lines
+r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_maqcns.c
M /trunk/samtools/bamtk.c
* fixed a critical bug in the indel caller
------------------------------------------------------------------------
-r294 | lh3lh3 | 2009-05-20 13:00:20 +0100 (Wed, 20 May 2009) | 2 lines
+r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
Changed paths:
M /trunk/samtools/bam_stat.c
added a missing header file
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-r293 | lh3lh3 | 2009-05-19 23:44:25 +0100 (Tue, 19 May 2009) | 3 lines
+r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_tview.c
M /trunk/samtools/bamtk.c
* open tview in the dot-view mode by default
------------------------------------------------------------------------
-r292 | lh3lh3 | 2009-05-18 21:01:23 +0100 (Mon, 18 May 2009) | 6 lines
+r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
Changed paths:
M /trunk/samtools/samtools.1
------------------------------------------------------------------------
-r286 | lh3lh3 | 2009-05-14 15:23:13 +0100 (Thu, 14 May 2009) | 3 lines
+r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam.h
M /trunk/samtools/bam_aux.c
* declare bam_aux_get_core() in bam.h
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-r276 | lh3lh3 | 2009-05-13 10:07:55 +0100 (Wed, 13 May 2009) | 5 lines
+r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
Changed paths:
M /trunk/samtools/bam.h
M /trunk/samtools/bam_index.c
* As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
------------------------------------------------------------------------
-r275 | lh3lh3 | 2009-05-12 21:14:10 +0100 (Tue, 12 May 2009) | 4 lines
+r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/bam.h
backward compatibility with Bio::DB::Sam
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-r273 | lh3lh3 | 2009-05-12 14:28:39 +0100 (Tue, 12 May 2009) | 3 lines
+r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_rmdupse.c
M /trunk/samtools/bamtk.c
* rmdupse: do not remove unmapped reads
------------------------------------------------------------------------
-r272 | lh3lh3 | 2009-05-12 14:20:00 +0100 (Tue, 12 May 2009) | 2 lines
+r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
Changed paths:
M /trunk/samtools/bam_rmdupse.c
change a parameter. It does nothing
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-r271 | lh3lh3 | 2009-05-12 14:17:58 +0100 (Tue, 12 May 2009) | 3 lines
+r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/Makefile.am
M /trunk/samtools/Makefile.generic
* added 'rmdupse' command
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-r267 | lh3lh3 | 2009-05-05 22:31:41 +0100 (Tue, 05 May 2009) | 3 lines
+r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/sam_view.c
* in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
------------------------------------------------------------------------
-r266 | lh3lh3 | 2009-05-05 22:23:27 +0100 (Tue, 05 May 2009) | 3 lines
+r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_import.c
M /trunk/samtools/bamtk.c
* report an error if a non-* reference is present while @SQ is absent
------------------------------------------------------------------------
-r265 | lh3lh3 | 2009-05-05 22:09:00 +0100 (Tue, 05 May 2009) | 3 lines
+r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam.h
M /trunk/samtools/bam_import.c
* make samopen() recognize @SQ header lines
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-r261 | lh3lh3 | 2009-05-05 15:10:30 +0100 (Tue, 05 May 2009) | 3 lines
+r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* report error for file I/O error
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-r260 | lh3lh3 | 2009-05-05 15:01:16 +0100 (Tue, 05 May 2009) | 2 lines
+r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
Changed paths:
M /trunk/samtools/Makefile.am
update Makefile.am
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-r259 | lh3lh3 | 2009-05-05 14:52:25 +0100 (Tue, 05 May 2009) | 3 lines
+r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam.h
M /trunk/samtools/bam_pileup.c
* use the new I/O interface in pileup
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-r258 | lh3lh3 | 2009-05-05 14:33:22 +0100 (Tue, 05 May 2009) | 3 lines
+r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/Makefile.generic
M /trunk/samtools/Makefile.lite
* unify the interface to BAM and SAM I/O
------------------------------------------------------------------------
-r257 | lh3lh3 | 2009-05-05 09:53:35 +0100 (Tue, 05 May 2009) | 3 lines
+r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/Makefile.lite
M /trunk/samtools/bam_plcmd.c
* allow hex with "pileup -m"
------------------------------------------------------------------------
-r256 | lh3lh3 | 2009-05-04 19:16:50 +0100 (Mon, 04 May 2009) | 4 lines
+r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
Changed paths:
M /trunk/samtools/bam_lpileup.c
M /trunk/samtools/bamtk.c
* I do not know if this also fixes the bug causing assertion failure in the tview
------------------------------------------------------------------------
-r251 | lh3lh3 | 2009-04-28 13:53:23 +0100 (Tue, 28 Apr 2009) | 3 lines
+r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_pileup.c
M /trunk/samtools/bamtk.c
* fixed a bug when there are reads without coordinates
------------------------------------------------------------------------
-r250 | lh3lh3 | 2009-04-28 13:43:33 +0100 (Tue, 28 Apr 2009) | 2 lines
+r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
Changed paths:
A /trunk/samtools/AUTHORS
A /trunk/samtools/README
added missing files
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-r249 | lh3lh3 | 2009-04-28 13:37:16 +0100 (Tue, 28 Apr 2009) | 2 lines
+r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
Changed paths:
M /trunk/samtools/Makefile.generic
M /trunk/samtools/Makefile.lite
improve large file support in compilation
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-r248 | lh3lh3 | 2009-04-28 13:33:24 +0100 (Tue, 28 Apr 2009) | 2 lines
+r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
Changed paths:
M /trunk/samtools/INSTALL
update INSTALL
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-r247 | lh3lh3 | 2009-04-28 13:28:50 +0100 (Tue, 28 Apr 2009) | 2 lines
+r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
Changed paths:
M /trunk/samtools/Makefile.am
M /trunk/samtools/autogen.sh
fixed various issues about the GNU building scripts
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-r246 | lh3lh3 | 2009-04-28 13:10:23 +0100 (Tue, 28 Apr 2009) | 4 lines
+r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
Changed paths:
M /trunk/samtools/ChangeLog
D /trunk/samtools/Makefile
* enhanced support of displaying color-space reads
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-r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
+r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_md.c
M /trunk/samtools/bamtk.c
* fixed segfault for unmapped reads
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-r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines
+r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
Changed paths:
M /trunk/samtools/bam.h
M /trunk/samtools/bam_maqcns.c
* consensus calling now works with "=", but indel calling not
------------------------------------------------------------------------
-r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
+r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_md.c
M /trunk/samtools/bamtk.c
* fixed a memory leak
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-r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines
+r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/Makefile.lite
* the plain pileup now support "=" bases, but consensus calling and glfgen may fail
------------------------------------------------------------------------
-r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
+r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
Changed paths:
M /trunk/samtools/bam.h
M /trunk/samtools/bam_aux.c
* added tagview for testing bam_aux
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-r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
+r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_pileup.c
M /trunk/samtools/bamtk.c
* fixed a bug in pileup: the first read in a chromosome may not be printed
------------------------------------------------------------------------
-r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
+r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
Changed paths:
M /trunk/samtools/Makefile.lite
a missing file in Makefile.lite
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-r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines
+r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
Changed paths:
M /trunk/samtools/NEWS
M /trunk/samtools/bamtk.c
Release samtools-0.1.3
------------------------------------------------------------------------
-r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
+r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* make samtools more robust to weird input such as empty file
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-r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
+r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/NEWS
prepare for release 0.1.3
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-r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
+r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
Changed paths:
A /trunk/samtools/misc/blast2sam.pl
convert NCBI-BLASTN to SAM
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-r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
+r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_lpileup.c
M /trunk/samtools/bamtk.c
* fixed a small memory leak in tview
------------------------------------------------------------------------
-r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines
+r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_rmdup.c
M /trunk/samtools/bamtk.c
* fixed a bug in rmdup when there are unmapped reads
------------------------------------------------------------------------
-r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
+r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/NEWS
proposed NEWS for the new release (have not yet)
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-r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
+r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
on the new pileup indel line implemented in samtools-0.1.2-25
------------------------------------------------------------------------
-r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
+r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
Changed paths:
M /trunk/samtools/bam_maqcns.c
M /trunk/samtools/bam_plcmd.c
containing indels
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-r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
+r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
update ChangeLog from "svn log"
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-r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
+r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
Changed paths:
M /trunk/samtools/bam.c
M /trunk/samtools/bam_import.c
* allow empty header
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-r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
+r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam.c
M /trunk/samtools/bam_import.c
* recognize '*' at the QUAL field
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-r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
+r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_import.c
M /trunk/samtools/bamtk.c
* the field separater is TAB only, now
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-r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
+r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
Changed paths:
M /trunk/samtools/examples/ex1.sam.gz
* fixed the problem in the example alignment due to the bug in fixmate
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-r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
+r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_mate.c
M /trunk/samtools/bamtk.c
* fixed a nasty bug in `fixmate'
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-r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
+r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
Changed paths:
M /trunk/samtools/misc/bowtie2sam.pl
M /trunk/samtools/misc/soap2sam.pl
make the script robust to the bugs in SOAP-2.1.7
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-r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
+r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_stat.c
M /trunk/samtools/bamtk.c
* check if file is truncated in flagstat
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-r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
+r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
* print the header if requested
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-r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
+r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* fixed a minor bug reported by Nils Homer
------------------------------------------------------------------------
-r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
+r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
Changed paths:
A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
D /trunk/samtools/Makefile.std
rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
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-r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
+r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
Changed paths:
D /trunk/samtools/Makefile
A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
* rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
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-r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
+r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/bam_import.c
* added my kstring library for a bit complex parsing of the position list.
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-r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
+r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/soap2sam.pl
* more robust to truncated soap output
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-r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
+r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
Changed paths:
M /trunk/samtools/Makefile.lite
added bam_stat.o to Makefile.lite
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-r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
+r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_maqcns.c
M /trunk/samtools/bamtk.c
* generate RMS of mapQ instead of max mapQ
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-r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
+r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* implemented GLFv3
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-r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
+r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* fixed a minor bug in displaying pileup
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-r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
+r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/bamtk.c
* optionally print SAM header
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-r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
+r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
M /trunk/samtools/glf.c
* use "GLF\3" as the magic for GLFv3 files
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-r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
+r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
Changed paths:
M /trunk/samtools/Makefile
M /trunk/samtools/bam_import.c
* update to GLFv3: pos is changed to offset for better compression
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-r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
+r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/wgsim.c
* fixed a bug in simulating indels
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-r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
+r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
Changed paths:
M /trunk/samtools/misc/wgsim.c
not like long read names.
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-r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
+r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/misc/wgsim.c
* make the script work with color reads
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-r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
+r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
Changed paths:
M /trunk/samtools/misc/Makefile
M /trunk/samtools/misc/wgsim.c
* wgsim: added a note
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-r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
+r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
Changed paths:
M /trunk/samtools/misc/wgsim.c
M /trunk/samtools/misc/wgsim_eval.pl
* change in accordant with wgsim
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-r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
+r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_index.c
M /trunk/samtools/bamtk.c
* fixed a bug in bam_fetch, caused by completely contained adjacent chunks
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-r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
+r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
Changed paths:
M /trunk/samtools/bamtk.c
Fix annoying segv when invalid region specified.
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-r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
+r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
Changed paths:
D /trunk/samtools/misc/indel_filter.pl
A /trunk/samtools/misc/samtools.pl
* move indel_filter.pl to samtools.pl
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-r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
+r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_mate.c
M /trunk/samtools/bamtk.c
* fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
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-r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
+r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_stat.c
M /trunk/samtools/bamtk.c
* fixed a minor bug in flagstat
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-r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
+r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_maqcns.c
M /trunk/samtools/bamtk.c
* improve indel caller by setting maximum window size
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-r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
+r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
Changed paths:
M /trunk/samtools/bam_plcmd.c
M /trunk/samtools/bamtk.c
* output max mapping quality in indel line
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-r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
+r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
Changed paths:
M /trunk/samtools/misc/maq2sam.c
fixed a bug in generating tag AM
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-r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
+r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
Changed paths:
M /trunk/samtools/bam_index.c
M /trunk/samtools/bamtk.c
fixed a potential memory problem in indexing
------------------------------------------------------------------------
-r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
+r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
Changed paths:
M /trunk/samtools/Makefile
Pass LIBS to recursive targets to facilitate building at Broad.
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-r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
+r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/bam_plcmd.c
* improve flagstat report a little bit
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-r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
+r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
Changed paths:
M /trunk/samtools/Makefile
A /trunk/samtools/bam_stat.c
* added flagstat command
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-r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
+r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/NEWS
Release SAMtools-0.1.2
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-r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
+r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
Changed paths:
A /trunk/samtools/misc/indel_filter.pl
Script for filtering indel results
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-r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
+r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
Changed paths:
A /trunk/samtools/misc/zoom2sam.pl
convert ZOOM to SAM
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-r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
+r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
Changed paths:
A /trunk/samtools/misc/novo2sam.pl
add a script to convert novo alignment to SAM
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-r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
+r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
M /trunk/samtools/ChangeLog.old
update documentation and ChangeLog
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-r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
+r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
Changed paths:
M /trunk/samtools/bam_sort.c
M /trunk/samtools/bamtk.c
* fixed a bug in "merge" command line
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-r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
+r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/Makefile
A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
* all future development will happen here
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-r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
+r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
Changed paths:
M /trunk/samtools/COPYING
M /trunk/samtools/ChangeLog
* all future development will happen here at trunk/
------------------------------------------------------------------------
-r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
+r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
Changed paths:
M /trunk/samtools/bam_maqcns.c
M /trunk/samtools/bam_tview.c
Fix problem with compiling without curses.
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-r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
+r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
A /trunk/samtools (from /branches/dev/samtools:62)
Create trunk copy
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-r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
+r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/NEWS
M /branches/dev/samtools/bamtk.c
Release samtools-0.1.1
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-r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
+r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
Changed paths:
M /branches/dev/samtools/bam_aux.c
M /branches/dev/samtools/bam_index.c
* prepare to release 0.1.1
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-r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
+r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/examples
A /branches/dev/samtools/examples/00README.txt
example
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-r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
+r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
update ChangeLog
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-r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
+r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/misc/export2sam.pl
* fixed several bugs
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-r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
+r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/misc/export2sam.pl
convert Export format to SAM; not thoroughly tested
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-r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
+r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_plcmd.c
* tview: fixed a minor bug
------------------------------------------------------------------------
-r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
+r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
Changed paths:
D /branches/dev/samtools/misc/all2sam.pl
remove all2sam.pl
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-r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
+r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/COPYING
M /branches/dev/samtools/bam.h
Added copyright information and a bit more documentation. No code change.
------------------------------------------------------------------------
-r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
+r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam.h
* improved efficiency of the indel caller for spliced alignments
------------------------------------------------------------------------
-r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
+r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam.h
* a bit code cleanup: reduce the dependency between source files
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-r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
+r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_plcmd.c
* fixed a memory leak
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-r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
+r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
M /branches/dev/samtools/bam.h
update documentation, ChangeLog and a comment
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-r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
+r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
* updated documentation
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-r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
+r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c
* fixed another bug in maqcns when there is a nearby deletion
------------------------------------------------------------------------
-r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
+r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_pileup.c
I am not quite sure why the previous version may have problem.
------------------------------------------------------------------------
-r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
+r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bamtk.c
bindings.
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-r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
+r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bgzf.c
Fix bug in tell() after reads that consume to the exact end of a block.
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-r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
+r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/samtools.1
update manual
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-r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
+r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bamtk.c
* made the parser a bit more robust
------------------------------------------------------------------------
-r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
+r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c
* in bam_index.c, check potential bugs in the underlying I/O library
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-r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
+r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/samtools.1
update manual
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-r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
+r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_pileup.c
* made pileup take the reference sequence
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-r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
+r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bamtk.c
* in parser, correctl parse "=" at the MRNM field.
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-r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
+r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/maq2sam.c
fixed a bug in handling maq flag 64 and 192
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-r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
+r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/md5fa.c
also calculate unordered md5sum check
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-r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
+r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/md5fa.c
fixed a minor bug when there are space in the sequence
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-r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
+r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/md5fa.c
fixed a potential memory leak
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-r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
+r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_index.c
* fixed a bug in import: bin is wrongly calculated
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-r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
+r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/all2sam.pl
nothing, really
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-r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
+r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/kseq.h
* added md5sum utilities
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-r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
+r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam_import.c
* also compile stand-alone faidx
------------------------------------------------------------------------
-r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
+r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_sort.c
* sorting by read names is available
------------------------------------------------------------------------
-r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
+r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam.h
* format change to meet the latest specification
------------------------------------------------------------------------
-r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
+r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/misc/maq2sam.c
* change maq2sam to meet the latest specification
------------------------------------------------------------------------
-r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
+r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/razf.c
M /branches/dev/samtools/razf.h
considerable code clean up in razf
------------------------------------------------------------------------
-r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
+r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
M /branches/dev/samtools/Makefile
make RAZF optional in faidx.c
------------------------------------------------------------------------
-r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
+r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
* added routines for retrieving aux data, NOT TESTED YET!
------------------------------------------------------------------------
-r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
+r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam_import.c
* supporting hex strings
------------------------------------------------------------------------
-r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
+r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c
* fixed the bug in maqcns
------------------------------------------------------------------------
-r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
+r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
* add MAQ consensus caller, currently BUGGY!
------------------------------------------------------------------------
-r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
+r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bam_tview.c
* better coordinates and reference sequence
------------------------------------------------------------------------
-r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
+r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/ChangeLog
new ChangeLog
------------------------------------------------------------------------
-r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
+r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
D /branches/dev/samtools/ChangeLog
A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
the log of my personal SVN repository.
------------------------------------------------------------------------
-r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
+r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bamtk.c
* use BGZF by default, now
------------------------------------------------------------------------
-r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
+r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c
* give more warnings when the file is truncated (or due to bugs in I/O library)
------------------------------------------------------------------------
-r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
+r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bgzf.c
fixed a bug in bgzf.c at the end of the file
------------------------------------------------------------------------
-r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
+r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bamtk.c
also update the version number anyway to avoid confusion
------------------------------------------------------------------------
-r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
+r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/razf.c
a change from Jue, but I think it should not matter
------------------------------------------------------------------------
-r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
+r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/razf.c
rarely happens, very rarely.
------------------------------------------------------------------------
-r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
+r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/razf.c
fixed a bug in razf, with the help of Jue
------------------------------------------------------------------------
-r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
+r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bam_index.c
remove a comment
------------------------------------------------------------------------
-r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
+r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
* Jue has updated razf to realize Bob's scheme
------------------------------------------------------------------------
-r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
+r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/samtools.1
the manual page
------------------------------------------------------------------------
-r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
+r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
Changed paths:
A /branches/dev/samtools/ChangeLog
A /branches/dev/samtools/Makefile
The current version is: 0.1.0-42. All future development will happen here.
------------------------------------------------------------------------
-r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
+r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
A /branches/dev/samtools
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1
LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o \
- bam_sort.o
+ bam_sort.o sam_header.o
AOBJS= bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o \
bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
- bamtk.o
+ bamtk.o kaln.o
PROG= samtools
INCLUDES=
SUBDIRS= . misc
$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o -lz
razip.o:razf.h
-bam.o:bam.h razf.h bam_endian.h kstring.h
+bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
sam.o:sam.h bam.h
bam_import.o:bam.h kseq.h khash.h razf.h
bam_pileup.o:bam.h razf.h ksort.h
bam_sort.o:bam.h ksort.h razf.h
bam_md.o:bam.h faidx.h
glf.o:glf.h
+sam_header.o:sam_header.h khash.h
faidx.o:faidx.h razf.h khash.h
faidx_main.o:faidx.h razf.h
CC= gcc.exe
AR= ar.exe
CFLAGS= -g -Wall -O2
-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_CURSES_LIB=2 -D_USE_KNETFILE
+DFLAGS= -D_CURSES_LIB=2 -D_USE_KNETFILE
LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bam_sort.o \
knetfile.o
+Beta Release 0.1.7 (10 November, 2009)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Improved the indel caller in complex scenariors, in particular for
+ long reads. The indel caller is now able to make reasonable indel
+ calls from Craig Venter capillary reads.
+
+ * Rewrote single-end duplicate removal with improved
+ performance. Paired-end reads are not touched.
+
+ * Duplicate removal is now library aware. Samtools remove potential
+ PCR/optical dupliates inside a library rather than across libraries.
+
+ * SAM header is now fully parsed, although this functionality is not
+ used in merging and so on.
+
+ * In samtools merge, optionally take the input file name as RG-ID and
+ attach the RG tag to each alignment.
+
+ * Added FTP support in the RAZF library. RAZF-compressed reference
+ sequence can be retrieved remotely.
+
+ * Improved network support for Win32.
+
+ * Samtools sort and merge are now stable.
+
+Changes in other utilities:
+
+ * Implemented sam2vcf.pl that converts the pileup format to the VCF
+ format.
+
+ * This release of samtools is known to work with the latest
+ Bio-Samtools Perl module.
+
+(0.1.7: 10 November 2009, r510)
+
+
+
Beta Release 0.1.6 (2 September, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#include <stdio.h>
#include <ctype.h>
+#include <errno.h>
#include <assert.h>
#include "bam.h"
#include "bam_endian.h"
#include "kstring.h"
+#include "sam_header.h"
int bam_is_be = 0;
char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
* CIGAR related routines *
**************************/
-int bam_segreg(int32_t pos, const bam1_core_t *c, const uint32_t *cigar, bam_segreg_t *reg)
-{
- unsigned k;
- int32_t x = c->pos, y = 0;
- int state = 0;
- for (k = 0; k < c->n_cigar; ++k) {
- int op = cigar[k] & BAM_CIGAR_MASK; // operation
- int l = cigar[k] >> BAM_CIGAR_SHIFT; // length
- if (state == 0 && (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CINS) && x + l > pos) {
- reg->tbeg = x; reg->qbeg = y; reg->cbeg = k;
- state = 1;
- }
- if (op == BAM_CMATCH) { x += l; y += l; }
- else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
- else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
- if (state == 1 && (op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP || op == BAM_CREF_SKIP || k == c->n_cigar - 1)) {
- reg->tend = x; reg->qend = y; reg->cend = k;
- }
- }
- return state? 0 : -1;
-}
-
uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
{
uint32_t k, end;
free(header->target_len);
}
free(header->text);
-#ifndef BAM_NO_HASH
- if (header->rg2lib) bam_strmap_destroy(header->rg2lib);
+ if (header->dict) sam_header_free(header->dict);
+ if (header->rg2lib) sam_tbl_destroy(header->rg2lib);
bam_destroy_header_hash(header);
-#endif
free(header);
}
int32_t i = 1, name_len;
// check EOF
i = bgzf_check_EOF(fp);
- if (i < 0) fprintf(stderr, "[bam_header_read] read from pipe; skip EOF checking.\n");
+ if (i < 0) {
+ // If the file is a pipe, checking the EOF marker will *always* fail
+ // with ESPIPE. Suppress the error message in this case.
+ if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
+ }
else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent.\n");
// read "BAM1"
if (bam_read(fp, buf, 4) != 4) return 0;
printf("%s\n", s);
free(s);
}
+
+// FIXME: we should also check the LB tag associated with each alignment
+const char *bam_get_library(bam_header_t *h, const bam1_t *b)
+{
+ const uint8_t *rg;
+ if (h->dict == 0) h->dict = sam_header_parse2(h->text);
+ if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
+ rg = bam_aux_get(b, "RG");
+ return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
+}
@field n_targets number of reference sequences
@field target_name names of the reference sequences
@field target_len lengths of the referene sequences
+ @field dict header dictionary
@field hash hash table for fast name lookup
@field rg2lib hash table for @RG-ID -> LB lookup
@field l_text length of the plain text in the header
int32_t n_targets;
char **target_name;
uint32_t *target_len;
- void *hash, *rg2lib;
+ void *dict, *hash, *rg2lib;
int l_text;
char *text;
} bam_header_t;
@abstract Free the memory allocated for an alignment.
@param b pointer to an alignment
*/
-#define bam_destroy1(b) do { \
- free((b)->data); free(b); \
+#define bam_destroy1(b) do { \
+ if (b) { free((b)->data); free(b); } \
} while (0)
/*!
char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of);
+ const char *bam_get_library(bam_header_t *header, const bam1_t *b);
+
/*! @typedef
@abstract Structure for one alignment covering the pileup position.
@field b pointer to the alignment
*/
int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar);
- typedef struct {
- int32_t qbeg, qend;
- int32_t tbeg, tend;
- int32_t cbeg, cend;
- } bam_segreg_t;
-
- int bam_segreg(int32_t pos, const bam1_core_t *c, const uint32_t *cigar, bam_segreg_t *reg);
-
#ifdef __cplusplus
}
#endif
if (type == 'Z' || type == 'H') return (char*)s;
else return 0;
}
-
-/******************
- * rg2lib related *
- ******************/
-
-int bam_strmap_put(void *rg2lib, const char *rg, const char *lib)
-{
- int ret;
- khint_t k;
- khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
- char *key;
- if (h == 0) return 1;
- key = strdup(rg);
- k = kh_put(r2l, h, key, &ret);
- if (ret) kh_val(h, k) = strdup(lib);
- else {
- fprintf(stderr, "[bam_rg2lib_put] duplicated @RG ID: %s\n", rg);
- free(key);
- }
- return 0;
-}
-
-const char *bam_strmap_get(const void *rg2lib, const char *rg)
-{
- const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
- khint_t k;
- if (h == 0) return 0;
- k = kh_get(r2l, h, rg);
- if (k != kh_end(h)) return (const char*)kh_val(h, k);
- else return 0;
-}
-
-void *bam_strmap_dup(const void *rg2lib)
-{
- const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
- khash_t(r2l) *g;
- khint_t k, l;
- int ret;
- if (h == 0) return 0;
- g = kh_init(r2l);
- for (k = kh_begin(h); k < kh_end(h); ++k) {
- if (kh_exist(h, k)) {
- char *key = strdup(kh_key(h, k));
- l = kh_put(r2l, g, key, &ret);
- kh_val(g, l) = strdup(kh_val(h, k));
- }
- }
- return g;
-}
-
-void *bam_strmap_init()
-{
- return (void*)kh_init(r2l);
-}
-
-void bam_strmap_destroy(void *rg2lib)
-{
- khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
- khint_t k;
- if (h == 0) return;
- for (k = kh_begin(h); k < kh_end(h); ++k) {
- if (kh_exist(h, k)) {
- free((char*)kh_key(h, k)); free(kh_val(h, k));
- }
- }
- kh_destroy(r2l, h);
-}
#endif
#include "kstring.h"
#include "bam.h"
+#include "sam_header.h"
#include "kseq.h"
#include "khash.h"
header->text[header->l_text] = 0;
}
-int sam_header_parse_rg(bam_header_t *h)
-{
- kstring_t *rgid, *rglib;
- char *p, *q, *s, *r;
- int n = 0;
-
- // free
- if (h == 0) return 0;
- bam_strmap_destroy(h->rg2lib); h->rg2lib = 0;
- if (h->l_text < 3) return 0;
- // parse @RG lines
- h->rg2lib = bam_strmap_init();
- rgid = calloc(1, sizeof(kstring_t));
- rglib = calloc(1, sizeof(kstring_t));
- s = h->text;
- while ((s = strstr(s, "@RG")) != 0) {
- if (rgid->l && rglib->l) {
- bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
- ++n;
- }
- rgid->l = rglib->l = 0;
- s += 3;
- r = s;
- if ((p = strstr(s, "ID:")) != 0) {
- q = p + 3;
- for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
- kputsn(q, p - q, rgid);
- } else {
- fprintf(stderr, "[bam_header_parse] missing ID tag in @RG lines.\n");
- break;
- }
- if (r < p) r = p;
- if ((p = strstr(s, "LB:")) != 0) {
- q = p + 3;
- for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
- kputsn(q, p - q, rglib);
- } else {
- fprintf(stderr, "[bam_header_parse] missing LB tag in @RG lines.\n");
- break;
- }
- if (r < p) r = p;
- s = r + 3;
- }
- if (rgid->l && rglib->l) {
- bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
- ++n;
- }
- free(rgid->s); free(rgid);
- free(rglib->s); free(rglib);
- if (n == 0) {
- bam_strmap_destroy(h->rg2lib);
- h->rg2lib = 0;
- }
- return n;
-}
-
int sam_header_parse(bam_header_t *h)
{
+ char **tmp;
int i;
- char *s, *p, *q, *r;
-
- // free
free(h->target_len); free(h->target_name);
h->n_targets = 0; h->target_len = 0; h->target_name = 0;
if (h->l_text < 3) return 0;
- // count number of @SQ
- s = h->text;
- while ((s = strstr(s, "@SQ")) != 0) {
- ++h->n_targets;
- s += 3;
- }
+ if (h->dict == 0) h->dict = sam_header_parse2(h->text);
+ tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
if (h->n_targets == 0) return 0;
- h->target_len = (uint32_t*)calloc(h->n_targets, 4);
- h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
- // parse @SQ lines
- i = 0;
- s = h->text;
- while ((s = strstr(s, "@SQ")) != 0) {
- s += 3;
- r = s;
- if ((p = strstr(s, "SN:")) != 0) {
- q = p + 3;
- for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
- h->target_name[i] = (char*)calloc(p - q + 1, 1);
- strncpy(h->target_name[i], q, p - q);
- } else goto header_err_ret;
- if (r < p) r = p;
- if ((p = strstr(s, "LN:")) != 0) h->target_len[i] = strtol(p + 3, 0, 10);
- else goto header_err_ret;
- if (r < p) r = p;
- s = r + 3;
- ++i;
- }
- sam_header_parse_rg(h);
+ h->target_name = calloc(h->n_targets, sizeof(void*));
+ for (i = 0; i < h->n_targets; ++i)
+ h->target_name[i] = strdup(tmp[i]);
+ free(tmp);
+ tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
+ h->target_len = calloc(h->n_targets, 4);
+ for (i = 0; i < h->n_targets; ++i)
+ h->target_len[i] = atoi(tmp[i]);
+ free(tmp);
return h->n_targets;
-
-header_err_ret:
- fprintf(stderr, "[bam_header_parse] missing SN or LN tag in @SQ lines.\n");
- free(h->target_len); free(h->target_name);
- h->n_targets = 0; h->target_len = 0; h->target_name = 0;
- return 0;
}
bam_header_t *sam_header_read(tamFile fp)
return (rend > beg && rbeg < end);
}
-int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
+// bam_fetch helper function retrieves
+pair64_t * get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int* cnt_off)
{
uint16_t *bins;
int i, n_bins, n_off;
}
free(bins);
{
- bam1_t *b;
- int l, ret, n_seeks;
- uint64_t curr_off;
- b = (bam1_t*)calloc(1, sizeof(bam1_t));
+ bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
+ int l;
ks_introsort(off, n_off, off);
// resolve completely contained adjacent blocks
for (i = 1, l = 0; i < n_off; ++i)
n_off = l + 1;
#endif
}
+ bam_destroy1(b);
+ }
+ *cnt_off = n_off;
+ return off;
+}
+
+int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
+{
+ int n_off;
+ pair64_t *off = get_chunk_coordinates(idx, tid, beg, end, &n_off);
+ if (off == 0) return 0;
+ {
// retrive alignments
+ uint64_t curr_off;
+ int i, ret, n_seeks;
n_seeks = 0; i = -1; curr_off = 0;
+ bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
for (;;) {
if (curr_off == 0 || curr_off >= off[i].v) { // then jump to the next chunk
if (i == n_off - 1) break; // no more chunks
#include <math.h>
+#include <assert.h>
#include "bam.h"
#include "bam_maqcns.h"
#include "ksort.h"
+#include "kaln.h"
KSORT_INIT_GENERIC(uint32_t)
-#define MAX_WINDOW 33
+#define INDEL_WINDOW_SIZE 50
+#define INDEL_EXT_DEP 0.9
typedef struct __bmc_aux_t {
int max;
/*
P(<b1,b2>) = \theta \sum_{i=1}^{N-1} 1/i
P(D|<b1,b2>) = \sum_{k=1}^{N-1} p_k 1/2 [(k/N)^n_2(1-k/N)^n_1 + (k/N)^n1(1-k/N)^n_2]
- p_k = i/k / \sum_{i=1}^{N-1} 1/i
+ p_k = 1/k / \sum_{i=1}^{N-1} 1/i
*/
static void cal_het(bam_maqcns_t *aa)
{
int k, n1, n2;
double sum_harmo; // harmonic sum
double poly_rate;
- double p1 = 0.0, p3 = 0.0; // just for testing
free(aa->lhet);
aa->lhet = (double*)calloc(256 * 256, sizeof(double));
for (n1 = 0; n1 < 256; ++n1) {
for (n2 = 0; n2 < 256; ++n2) {
long double sum = 0.0;
- double lC = lgamma(n1+n2+1) - lgamma(n1+1) - lgamma(n2+1); // \binom{n1+n2}{n1}
+ double lC = aa->is_soap? 0 : lgamma(n1+n2+1) - lgamma(n1+1) - lgamma(n2+1); // \binom{n1+n2}{n1}
for (k = 1; k <= aa->n_hap - 1; ++k) {
double pk = 1.0 / k / sum_harmo;
double log1 = log((double)k/aa->n_hap);
sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2));
}
aa->lhet[n1<<8|n2] = lC + logl(sum);
- if (n1 == 17 && n2 == 3) p3 = lC + logl(expl(logl(0.5) * 20));
- if (n1 == 19 && n2 == 1) p1 = lC + logl(expl(logl(0.5) * 20));
}
}
poly_rate = aa->het_rate * sum_harmo;
long double sum_a[257], b[256], q_c[256], tmp[256], fk2[256];
double *lC;
- lC = (double*)calloc(256 * 256, sizeof(double));
// aa->lhet will be allocated and initialized
free(aa->fk); free(aa->coef);
+ aa->coef = 0;
aa->fk = (double*)calloc(256, sizeof(double));
- aa->coef = (double*)calloc(256*256*64, sizeof(double));
aa->fk[0] = fk2[0] = 1.0;
for (n = 1; n != 256; ++n) {
aa->fk[n] = pow(aa->theta, n) * (1.0 - aa->eta) + aa->eta;
fk2[n] = aa->fk[n>>1]; // this is an approximation, assuming reads equally likely come from both strands
}
+ if (aa->is_soap) return;
+ aa->coef = (double*)calloc(256*256*64, sizeof(double));
+ lC = (double*)calloc(256 * 256, sizeof(double));
for (n = 1; n != 256; ++n)
for (k = 1; k <= n; ++k)
lC[n<<8|k] = lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1);
if (w[k] < 0xff) ++w[k];
++b->c[k&3];
}
- tmp = (int)(info&0x7f) < bm->cap_mapQ? (int)(info&0x7f) : bm->cap_mapQ;
+ tmp = (int)(info&0xff) < bm->cap_mapQ? (int)(info&0xff) : bm->cap_mapQ;
rms += tmp * tmp;
}
b->rms_mapQ = (uint8_t)(sqrt((double)rms / n) + .499);
for (j = 0; j != 4; ++j) b->c[j] = (int)(254.0 * b->c[j] / c + 0.5);
for (j = c = 0; j != 4; ++j) c += b->c[j];
}
- // generate likelihood
- for (j = 0; j != 4; ++j) {
- // homozygous
- float tmp1, tmp3;
- int tmp2, bar_e;
- for (k = 0, tmp1 = tmp3 = 0.0, tmp2 = 0; k != 4; ++k) {
- if (j == k) continue;
- tmp1 += b->esum[k]; tmp2 += b->c[k]; tmp3 += b->fsum[k];
- }
- if (tmp2) {
- bar_e = (int)(tmp1 / tmp3 + 0.5);
- if (bar_e < 4) bar_e = 4; // should not happen
- if (bar_e > 63) bar_e = 63;
- p[j<<2|j] = tmp1 + bm->coef[bar_e<<16|c<<8|tmp2];
- } else p[j<<2|j] = 0.0; // all the bases are j
- // heterozygous
- for (k = j + 1; k < 4; ++k) {
- for (i = 0, tmp2 = 0, tmp1 = tmp3 = 0.0; i != 4; ++i) {
- if (i == j || i == k) continue;
- tmp1 += b->esum[i]; tmp2 += b->c[i]; tmp3 += b->fsum[i];
+ if (!bm->is_soap) {
+ // generate likelihood
+ for (j = 0; j != 4; ++j) {
+ // homozygous
+ float tmp1, tmp3;
+ int tmp2, bar_e;
+ for (k = 0, tmp1 = tmp3 = 0.0, tmp2 = 0; k != 4; ++k) {
+ if (j == k) continue;
+ tmp1 += b->esum[k]; tmp2 += b->c[k]; tmp3 += b->fsum[k];
}
if (tmp2) {
bar_e = (int)(tmp1 / tmp3 + 0.5);
- if (bar_e < 4) bar_e = 4;
+ if (bar_e < 4) bar_e = 4; // should not happen
if (bar_e > 63) bar_e = 63;
- p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]] + tmp1 + bm->coef[bar_e<<16|c<<8|tmp2];
- } else p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]]; // all the bases are either j or k
+ p[j<<2|j] = tmp1 + bm->coef[bar_e<<16|c<<8|tmp2];
+ } else p[j<<2|j] = 0.0; // all the bases are j
+ // heterozygous
+ for (k = j + 1; k < 4; ++k) {
+ for (i = 0, tmp2 = 0, tmp1 = tmp3 = 0.0; i != 4; ++i) {
+ if (i == j || i == k) continue;
+ tmp1 += b->esum[i]; tmp2 += b->c[i]; tmp3 += b->fsum[i];
+ }
+ if (tmp2) {
+ bar_e = (int)(tmp1 / tmp3 + 0.5);
+ if (bar_e < 4) bar_e = 4;
+ if (bar_e > 63) bar_e = 63;
+ p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]] + tmp1 + bm->coef[bar_e<<16|c<<8|tmp2];
+ } else p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]]; // all the bases are either j or k
+ }
+ //
+ for (k = 0; k != 4; ++k)
+ if (p[j<<2|k] < 0.0) p[j<<2|k] = 0.0;
}
- //
- for (k = 0; k != 4; ++k)
- if (p[j<<2|k] < 0.0) p[j<<2|k] = 0.0;
- }
- { // fix p[k<<2|k]
- float max1, max2, min1, min2;
- int max_k, min_k;
- max_k = min_k = -1;
- max1 = max2 = -1.0; min1 = min2 = 1e30;
- for (k = 0; k < 4; ++k) {
- if (b->esum[k] > max1) {
- max2 = max1; max1 = b->esum[k]; max_k = k;
- } else if (b->esum[k] > max2) max2 = b->esum[k];
+ { // fix p[k<<2|k]
+ float max1, max2, min1, min2;
+ int max_k, min_k;
+ max_k = min_k = -1;
+ max1 = max2 = -1.0; min1 = min2 = 1e30;
+ for (k = 0; k < 4; ++k) {
+ if (b->esum[k] > max1) {
+ max2 = max1; max1 = b->esum[k]; max_k = k;
+ } else if (b->esum[k] > max2) max2 = b->esum[k];
+ }
+ for (k = 0; k < 4; ++k) {
+ if (p[k<<2|k] < min1) {
+ min2 = min1; min1 = p[k<<2|k]; min_k = k;
+ } else if (p[k<<2|k] < min2) min2 = p[k<<2|k];
+ }
+ if (max1 > max2 && (min_k != max_k || min1 + 1.0 > min2))
+ p[max_k<<2|max_k] = min1 > 1.0? min1 - 1.0 : 0.0;
}
- for (k = 0; k < 4; ++k) {
- if (p[k<<2|k] < min1) {
- min2 = min1; min1 = p[k<<2|k]; min_k = k;
- } else if (p[k<<2|k] < min2) min2 = p[k<<2|k];
+ } else { // apply the SOAP model
+ // generate likelihood
+ for (j = 0; j != 4; ++j) {
+ float tmp;
+ // homozygous
+ for (k = 0, tmp = 0.0; k != 4; ++k)
+ if (j != k) tmp += b->esum[k];
+ p[j<<2|j] = tmp;
+ // heterozygous
+ for (k = j + 1; k < 4; ++k) {
+ for (i = 0, tmp = 0.0; i != 4; ++i)
+ if (i != j && i != k) tmp += b->esum[i];
+ p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]] + tmp;
+ }
}
- if (max1 > max2 && (min_k != max_k || min1 + 1.0 > min2))
- p[max_k<<2|max_k] = min1 > 1.0? min1 - 1.0 : 0.0;
}
// convert necessary information to glf1_t
free(mir->s[0]); free(mir->s[1]); free(mir);
}
+int bam_tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos)
+{
+ int k, x = c->pos, y = 0, last_y = 0;
+ *_tpos = c->pos;
+ for (k = 0; k < c->n_cigar; ++k) {
+ int op = cigar[k] & BAM_CIGAR_MASK;
+ int l = cigar[k] >> BAM_CIGAR_SHIFT;
+ if (op == BAM_CMATCH) {
+ if (c->pos > tpos) return y;
+ if (x + l > tpos) {
+ *_tpos = tpos;
+ return y + (tpos - x);
+ }
+ x += l; y += l;
+ last_y = y;
+ } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+ else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
+ if (x + l > tpos) {
+ *_tpos = is_left? x : x + l;
+ return y;
+ }
+ x += l;
+ }
+ }
+ *_tpos = x;
+ return last_y;
+}
+
#define MINUS_CONST 0x10000000
bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref,
int _n_types, int *_types)
{
- int i, j, n_types, *types, left, right;
+ int i, j, n_types, *types, left, right, max_rd_len = 0;
bam_maqindel_ret_t *ret = 0;
// if there is no proposed indel, check if there is an indel from the alignment
if (_n_types == 0) {
const bam_pileup1_t *p = pl + i;
if (!(p->b->core.flag&BAM_FUNMAP) && p->indel != 0)
aux[m++] = MINUS_CONST + p->indel;
+ j = bam_cigar2qlen(&p->b->core, bam1_cigar(p->b));
+ if (j > max_rd_len) max_rd_len = j;
}
if (_n_types) // then also add this to aux[]
for (i = 0; i < _n_types; ++i)
free(aux);
}
{ // calculate left and right boundary
- bam_segreg_t seg;
- left = 0x7fffffff; right = 0;
- for (i = 0; i < n; ++i) {
- const bam_pileup1_t *p = pl + i;
- if (!(p->b->core.flag&BAM_FUNMAP)) {
- bam_segreg(pos, &p->b->core, bam1_cigar(p->b), &seg);
- if (seg.tbeg < left) left = seg.tbeg;
- if (seg.tend > right) right = seg.tend;
- }
- }
- if (pos - left > MAX_WINDOW) left = pos - MAX_WINDOW;
- if (right - pos> MAX_WINDOW) right = pos + MAX_WINDOW;
+ left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0;
+ right = pos + INDEL_WINDOW_SIZE;
+ if (types[0] < 0) right -= types[0];
+ // in case the alignments stand out the reference
+ for (i = pos; i < right; ++i)
+ if (ref[i] == 0) break;
+ right = i;
}
{ // the core part
- char *ref2, *inscns = 0;
+ char *ref2, *rs, *inscns = 0;
int k, l, *score, *pscore, max_ins = types[n_types-1];
- ref2 = (char*)calloc(right - left + types[n_types-1] + 2, 1);
if (max_ins > 0) { // get the consensus of inserted sequences
int *inscns_aux = (int*)calloc(4 * n_types * max_ins, sizeof(int));
// count occurrences
free(inscns_aux);
}
// calculate score
+ ref2 = (char*)calloc(right - left + types[n_types-1] + 2, 1);
+ rs = (char*)calloc(right - left + max_rd_len + types[n_types-1] + 2, 1);
score = (int*)calloc(n_types * n, sizeof(int));
pscore = (int*)calloc(n_types * n, sizeof(int));
for (i = 0; i < n_types; ++i) {
+ ka_param_t ap = ka_param_blast;
+ ap.band_width = 2 * types[n_types - 1] + 2;
// write ref2
for (k = 0, j = left; j <= pos; ++j)
- ref2[k++] = bam_nt16_table[(int)ref[j]];
+ ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
if (types[i] <= 0) j += -types[i];
else for (l = 0; l < types[i]; ++l)
- ref2[k++] = inscns[i*max_ins + l];
+ ref2[k++] = bam_nt16_nt4_table[(int)inscns[i*max_ins + l]];
for (; j < right && ref[j]; ++j)
- ref2[k++] = bam_nt16_table[(int)ref[j]];
+ ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
+ if (j < right) right = j;
// calculate score for each read
for (j = 0; j < n; ++j) {
const bam_pileup1_t *p = pl + j;
- uint32_t *cigar;
- bam1_core_t *c = &p->b->core;
- int s, ps;
- bam_segreg_t seg;
- if (c->flag&BAM_FUNMAP) continue;
- cigar = bam1_cigar(p->b);
- bam_segreg(pos, c, cigar, &seg);
- for (ps = s = 0, l = seg.qbeg; c->pos + l < right && l < seg.qend; ++l) {
- int cq = bam1_seqi(bam1_seq(p->b), l), ct;
- // in the following line, "<" will happen if reads are too long
- ct = c->pos + l - seg.qbeg >= left? ref2[c->pos + l - seg.qbeg - left] : 15;
- if (cq < 15 && ct < 15) {
- s += cq == ct? 1 : -mi->mm_penalty;
- if (cq != ct) ps += bam1_qual(p->b)[l];
+ int qbeg, qend, tbeg, tend;
+ if (p->b->core.flag & BAM_FUNMAP) continue;
+ qbeg = bam_tpos2qpos(&p->b->core, bam1_cigar(p->b), left, 0, &tbeg);
+ qend = bam_tpos2qpos(&p->b->core, bam1_cigar(p->b), right, 1, &tend);
+ assert(tbeg >= left);
+ for (l = qbeg; l < qend; ++l)
+ rs[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), l)];
+ {
+ int x, y, n_acigar, ps;
+ uint32_t *acigar;
+ ps = 0;
+ if (tend - tbeg + types[i] <= 0) {
+ score[i*n+j] = -(1<<20);
+ pscore[i*n+j] = 1<<20;
+ continue;
}
- }
- score[i*n + j] = s; pscore[i*n + j] = ps;
- if (types[i] != 0) { // then try the other way to calculate the score
- for (ps = s = 0, l = seg.qbeg; c->pos + l + types[i] < right && l < seg.qend; ++l) {
- int cq = bam1_seqi(bam1_seq(p->b), l), ct;
- ct = c->pos + l - seg.qbeg + types[i] >= left? ref2[c->pos + l - seg.qbeg + types[i] - left] : 15;
- if (cq < 15 && ct < 15) {
- s += cq == ct? 1 : -mi->mm_penalty;
- if (cq != ct) ps += bam1_qual(p->b)[l];
+ acigar = ka_global_core((uint8_t*)ref2 + tbeg - left, tend - tbeg + types[i], (uint8_t*)rs, qend - qbeg, &ap, &score[i*n+j], &n_acigar);
+ x = tbeg - left; y = 0;
+ for (l = 0; l < n_acigar; ++l) {
+ int op = acigar[l]&0xf;
+ int len = acigar[l]>>4;
+ if (op == BAM_CMATCH) {
+ int k;
+ for (k = 0; k < len; ++k)
+ if (ref2[x+k] != rs[y+k]) ps += bam1_qual(p->b)[y+k];
+ x += len; y += len;
+ } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) {
+ if (op == BAM_CINS) ps += mi->q_indel * len;
+ y += len;
+ } else if (op == BAM_CDEL) {
+ ps += mi->q_indel * len;
+ x += len;
}
}
+ pscore[i*n+j] = ps;
+ /*if (pos == 2618517) { // for debugging only
+ fprintf(stderr, "pos=%d, type=%d, j=%d, score=%d, psore=%d, %d, %d, %d, %d, ", pos+1, types[i], j, score[i*n+j], pscore[i*n+j], tbeg, tend, qbeg, qend);
+ for (l = 0; l < n_acigar; ++l) fprintf(stderr, "%d%c", acigar[l]>>4, "MIDS"[acigar[l]&0xf]); fprintf(stderr, "\n");
+ for (l = 0; l < tend - tbeg + types[i]; ++l) fputc("ACGTN"[ref2[l]], stderr); fputc('\n', stderr);
+ for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[rs[l]], stderr); fputc('\n', stderr);
+ }*/
+ free(acigar);
}
- if (score[i*n+j] < s) score[i*n+j] = s; // choose the higher of the two scores
- if (pscore[i*n+j] > ps) pscore[i*n+j] = ps;
- //if (types[i] != 0) score[i*n+j] -= mi->indel_err;
- //printf("%d, %d, %d, %d, %d, %d, %d\n", p->b->core.pos + 1, seg.qbeg, i, types[i], j,
- // score[i*n+j], pscore[i*n+j]);
}
}
{ // get final result
else if (p->indel == ret->indel2) ++ret->cnt2;
else ++ret->cnt_anti;
}
- // write gl[]
- ret->gl[0] = ret->gl[1] = 0;
- for (j = 0; j < n; ++j) {
- int s1 = pscore[max1_i*n + j], s2 = pscore[max2_i*n + j];
- //printf("%d, %d, %d, %d, %d\n", pl[j].b->core.pos+1, max1_i, max2_i, s1, s2);
- if (s1 > s2) ret->gl[0] += s1 - s2 < mi->q_indel? s1 - s2 : mi->q_indel;
- else ret->gl[1] += s2 - s1 < mi->q_indel? s2 - s1 : mi->q_indel;
+ { // write gl[]
+ int tmp, seq_err = 0;
+ double x = 1.0;
+ tmp = max1_i - max2_i;
+ if (tmp < 0) tmp = -tmp;
+ for (j = 0; j < tmp + 1; ++j) x *= INDEL_EXT_DEP;
+ seq_err = mi->q_indel * (1.0 - x) / (1.0 - INDEL_EXT_DEP);
+ ret->gl[0] = ret->gl[1] = 0;
+ for (j = 0; j < n; ++j) {
+ int s1 = pscore[max1_i*n + j], s2 = pscore[max2_i*n + j];
+ //printf("%d, %d, %d, %d, %d\n", pl[j].b->core.pos+1, max1_i, max2_i, s1, s2);
+ if (s1 > s2) ret->gl[0] += s1 - s2 < seq_err? s1 - s2 : seq_err;
+ else ret->gl[1] += s2 - s1 < seq_err? s2 - s1 : seq_err;
+ }
}
// write cnt_ref and cnt_ambi
if (max1_i != 0 && max2_i != 0) {
}
}
}
- free(score); free(pscore); free(ref2); free(inscns);
+ free(score); free(pscore); free(ref2); free(rs); free(inscns);
}
{ // call genotype
int q[3], qr_indel = (int)(-4.343 * log(mi->r_indel) + 0.5);
typedef struct {
float het_rate, theta;
- int n_hap, cap_mapQ;
+ int n_hap, cap_mapQ, is_soap;
float eta, q_r;
double *fk, *coef;
free(ref);
ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len);
tid = b->core.tid;
+ if (ref == 0)
+ fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
+ fp->header->target_name[tid]);
}
- bam_fillmd1(b, ref, is_equal);
+ if (ref) bam_fillmd1(b, ref, is_equal);
}
samwrite(fpout, b);
}
g3->offset = pos - d->last_pos;
d->last_pos = pos;
glf3_write1(d->fp_glf, g3);
- if (proposed_indels)
- r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
- else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0);
+ if (pos < d->len) {
+ if (proposed_indels)
+ r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
+ else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0);
+ }
if (r) { // then write indel line
int het = 3 * n, min;
min = het;
// call the consensus and indel
if (d->format & BAM_PLF_CNS) // call consensus
cns = bam_maqcns_call(n, pu, d->c);
- if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref) { // call indels
+ if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // call indels
if (proposed_indels) // the first element gives the size of the array
r = bam_maqindel(n, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
else r = bam_maqindel(n, pos, d->ido, pu, d->ref, 0, 0);
d->tid = -1; d->mask = BAM_DEF_MASK;
d->c = bam_maqcns_init();
d->ido = bam_maqindel_opt_init();
- while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:S2")) >= 0) {
+ while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:S2a")) >= 0) {
switch (c) {
+ case 'a': d->c->is_soap = 1; break;
case 's': d->format |= BAM_PLF_SIMPLE; break;
case 't': fn_list = strdup(optarg); break;
case 'l': fn_pos = strdup(optarg); break;
fprintf(stderr, "Usage: samtools pileup [options] <in.bam>|<in.sam>\n\n");
fprintf(stderr, "Option: -s simple (yet incomplete) pileup format\n");
fprintf(stderr, " -S the input is in SAM\n");
+ fprintf(stderr, " -a use the SOAPsnp model for SNP calling\n");
fprintf(stderr, " -2 output the 2nd best call and quality\n");
fprintf(stderr, " -i only show lines/consensus with indels\n");
fprintf(stderr, " -m INT filtering reads with bits in INT [%d]\n", d->mask);
#include <string.h>
#include <stdio.h>
#include <zlib.h>
-#include "bam.h"
+#include <unistd.h>
+#include "sam.h"
typedef bam1_t *bam1_p;
+
#include "khash.h"
KHASH_SET_INIT_STR(name)
KHASH_MAP_INIT_INT64(pos, bam1_p)
#define BUFFER_SIZE 0x40000
+typedef struct {
+ uint64_t n_checked, n_removed;
+ khash_t(pos) *best_hash;
+} lib_aux_t;
+KHASH_MAP_INIT_STR(lib, lib_aux_t)
+
typedef struct {
int n, max;
bam1_t **a;
stack->a[stack->n++] = b;
}
-static inline void dump_best(tmp_stack_t *stack, khash_t(pos) *best_hash, bamFile out)
+static inline void dump_best(tmp_stack_t *stack, samfile_t *out)
{
int i;
for (i = 0; i != stack->n; ++i) {
- bam_write1(out, stack->a[i]);
+ samwrite(out, stack->a[i]);
bam_destroy1(stack->a[i]);
}
stack->n = 0;
- if (kh_size(best_hash) > BUFFER_SIZE) kh_clear(pos, best_hash);
}
static void clear_del_set(khash_t(name) *del_set)
kh_clear(name, del_set);
}
-void bam_rmdup_core(bamFile in, bamFile out)
+static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
+{
+ khint_t k = kh_get(lib, aux, lib);
+ if (k == kh_end(aux)) {
+ int ret;
+ char *p = strdup(lib);
+ lib_aux_t *q;
+ k = kh_put(lib, aux, p, &ret);
+ q = &kh_val(aux, k);
+ q->n_checked = q->n_removed = 0;
+ q->best_hash = kh_init(pos);
+ return q;
+ } else return &kh_val(aux, k);
+}
+
+static void clear_best(khash_t(lib) *aux, int max)
+{
+ khint_t k;
+ for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+ if (kh_exist(aux, k)) {
+ lib_aux_t *q = &kh_val(aux, k);
+ if (kh_size(q->best_hash) >= max)
+ kh_clear(pos, q->best_hash);
+ }
+ }
+}
+
+static inline int sum_qual(const bam1_t *b)
+{
+ int i, q;
+ uint8_t *qual = bam1_qual(b);
+ for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
+ return q;
+}
+
+void bam_rmdup_core(samfile_t *in, samfile_t *out)
{
- bam_header_t *header;
bam1_t *b;
int last_tid = -1, last_pos = -1;
- uint64_t n_checked = 0, n_removed = 0;
tmp_stack_t stack;
khint_t k;
- khash_t(pos) *best_hash;
+ khash_t(lib) *aux;
khash_t(name) *del_set;
-
- best_hash = kh_init(pos);
+
+ aux = kh_init(lib);
del_set = kh_init(name);
b = bam_init1();
memset(&stack, 0, sizeof(tmp_stack_t));
- header = bam_header_read(in);
- bam_header_write(out, header);
kh_resize(name, del_set, 4 * BUFFER_SIZE);
- kh_resize(pos, best_hash, 3 * BUFFER_SIZE);
- while (bam_read1(in, b) >= 0) {
+ while (samread(in, b) >= 0) {
bam1_core_t *c = &b->core;
if (c->tid != last_tid || last_pos != c->pos) {
- dump_best(&stack, best_hash, out); // write the result
+ dump_best(&stack, out); // write the result
+ clear_best(aux, BUFFER_SIZE);
if (c->tid != last_tid) {
- kh_clear(pos, best_hash);
+ clear_best(aux, 0);
if (kh_size(del_set)) { // check
fprintf(stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set));
clear_del_set(del_set);
}
if ((int)c->tid == -1) { // append unmapped reads
- bam_write1(out, b);
- while (bam_read1(in, b) >= 0) bam_write1(out, b);
+ samwrite(out, b);
+ while (samread(in, b) >= 0) samwrite(out, b);
break;
}
last_tid = c->tid;
- fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", header->target_name[c->tid]);
+ fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", in->header->target_name[c->tid]);
}
}
if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) {
- bam_write1(out, b);
+ samwrite(out, b);
} else if (c->isize > 0) { // paired, head
uint64_t key = (uint64_t)c->pos<<32 | c->isize;
+ const char *lib;
+ lib_aux_t *q;
int ret;
- ++n_checked;
- k = kh_put(pos, best_hash, key, &ret);
+ lib = bam_get_library(in->header, b);
+ q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
+ ++q->n_checked;
+ k = kh_put(pos, q->best_hash, key, &ret);
if (ret == 0) { // found in best_hash
- bam1_t *p = kh_val(best_hash, k);
- ++n_removed;
- if (p->core.qual < c->qual) { // the current alignment is better
+ bam1_t *p = kh_val(q->best_hash, k);
+ ++q->n_removed;
+ if (sum_qual(p) < sum_qual(b)) { // the current alignment is better; this can be accelerated in principle
kh_put(name, del_set, strdup(bam1_qname(p)), &ret); // p will be removed
bam_copy1(p, b); // replaced as b
} else kh_put(name, del_set, strdup(bam1_qname(b)), &ret); // b will be removed
if (ret == 0)
fprintf(stderr, "[bam_rmdup_core] inconsistent BAM file for pair '%s'. Continue anyway.\n", bam1_qname(b));
} else { // not found in best_hash
- kh_val(best_hash, k) = bam_dup1(b);
- stack_insert(&stack, kh_val(best_hash, k));
+ kh_val(q->best_hash, k) = bam_dup1(b);
+ stack_insert(&stack, kh_val(q->best_hash, k));
}
} else { // paired, tail
k = kh_get(name, del_set, bam1_qname(b));
if (k != kh_end(del_set)) {
free((char*)kh_key(del_set, k));
kh_del(name, del_set, k);
- } else bam_write1(out, b);
+ } else samwrite(out, b);
}
last_pos = c->pos;
}
- dump_best(&stack, best_hash, out);
- bam_header_destroy(header);
+ for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+ if (kh_exist(aux, k)) {
+ lib_aux_t *q = &kh_val(aux, k);
+ dump_best(&stack, out);
+ fprintf(stderr, "[bam_rmdup_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
+ (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
+ kh_destroy(pos, q->best_hash);
+ free((char*)kh_key(aux, k));
+ }
+ }
+ kh_destroy(lib, aux);
+
clear_del_set(del_set);
kh_destroy(name, del_set);
- kh_destroy(pos, best_hash);
free(stack.a);
bam_destroy1(b);
- fprintf(stderr, "[bam_rmdup_core] %lld / %lld = %.4lf\n", (long long)n_removed, (long long)n_checked,
- (double)n_removed/n_checked);
}
+
+void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se);
+
int bam_rmdup(int argc, char *argv[])
{
- bamFile in, out;
- if (argc < 3) {
- fprintf(stderr, "Usage: samtools rmdup <input.srt.bam> <output.bam>\n\n");
- fprintf(stderr, "Note: Picard is recommended for this task.\n");
+ int c, is_se = 0, force_se = 0;
+ samfile_t *in, *out;
+ while ((c = getopt(argc, argv, "sS")) >= 0) {
+ switch (c) {
+ case 's': is_se = 1; break;
+ case 'S': force_se = is_se = 1; break;
+ }
+ }
+ if (optind + 2 > argc) {
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools rmdup [-sS] <input.srt.bam> <output.bam>\n\n");
+ fprintf(stderr, "Option: -s rmdup for SE reads\n");
+ fprintf(stderr, " -S treat PE reads as SE in rmdup (force -s)\n\n");
return 1;
}
- in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
- out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
+ in = samopen(argv[optind], "rb", 0);
+ out = samopen(argv[optind+1], "wb", in->header);
if (in == 0 || out == 0) {
fprintf(stderr, "[bam_rmdup] fail to read/write input files\n");
return 1;
}
- bam_rmdup_core(in, out);
- bam_close(in);
- bam_close(out);
+ if (is_se) bam_rmdupse_core(in, out, force_se);
+ else bam_rmdup_core(in, out);
+ samclose(in); samclose(out);
return 0;
}
#include <math.h>
#include "sam.h"
#include "khash.h"
+#include "klist.h"
-typedef struct {
- int n, m;
- int *a;
-} listelem_t;
-
-KHASH_MAP_INIT_INT(32, listelem_t)
-
-#define BLOCK_SIZE 65536
+#define QUEUE_CLEAR_SIZE 0x100000
+#define MAX_POS 0x7fffffff
typedef struct {
+ int endpos;
+ uint32_t score:31, discarded:1;
bam1_t *b;
- int rpos, score;
-} elem_t;
+} elem_t, *elem_p;
+#define __free_elem(p) bam_destroy1((p)->data.b)
+KLIST_INIT(q, elem_t, __free_elem)
+typedef klist_t(q) queue_t;
+
+KHASH_MAP_INIT_INT(best, elem_p)
+typedef khash_t(best) besthash_t;
typedef struct {
- int n, max, x;
- elem_t *buf;
-} buffer_t;
+ uint64_t n_checked, n_removed;
+ besthash_t *left, *rght;
+} lib_aux_t;
+KHASH_MAP_INIT_STR(lib, lib_aux_t)
-static int fill_buf(samfile_t *in, buffer_t *buf)
+static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
{
- int i, ret, last_tid, min_rpos = 0x7fffffff, capacity;
- bam1_t *b = bam_init1();
- bam1_core_t *c = &b->core;
- // squeeze out the empty cells at the beginning
- for (i = 0; i < buf->n; ++i)
- if (buf->buf[i].b) break;
- if (i < buf->n) { // squeeze
- if (i > 0) {
- memmove(buf->buf, buf->buf + i, sizeof(elem_t) * (buf->n - i));
- buf->n = buf->n - i;
- }
- } else buf->n = 0;
- // calculate min_rpos
- for (i = 0; i < buf->n; ++i) {
- elem_t *e = buf->buf + i;
- if (e->b && e->rpos >= 0 && e->rpos < min_rpos)
- min_rpos = buf->buf[i].rpos;
- }
- // fill the buffer
- buf->x = -1;
- last_tid = buf->n? buf->buf[0].b->core.tid : -1;
- capacity = buf->n + BLOCK_SIZE;
- while ((ret = samread(in, b)) >= 0) {
- elem_t *e;
- uint8_t *qual = bam1_qual(b);
- int is_mapped;
- if (last_tid < 0) last_tid = c->tid;
- if (c->tid != last_tid) {
- if (buf->x < 0) buf->x = buf->n;
- }
- if (buf->n >= buf->max) { // enlarge
- buf->max = buf->max? buf->max<<1 : 8;
- buf->buf = (elem_t*)realloc(buf->buf, sizeof(elem_t) * buf->max);
- }
- e = &buf->buf[buf->n++];
- e->b = bam_dup1(b);
- e->rpos = -1; e->score = 0;
- for (i = 0; i < c->l_qseq; ++i) e->score += qual[i] + 1;
- e->score = (double)e->score / sqrt(c->l_qseq + 1);
- is_mapped = (c->tid < 0 || c->tid >= in->header->n_targets || (c->flag&BAM_FUNMAP))? 0 : 1;
- if (!is_mapped) e->score = -1;
- if (is_mapped && (c->flag & BAM_FREVERSE)) {
- e->rpos = b->core.pos + bam_calend(&b->core, bam1_cigar(b));
- if (min_rpos > e->rpos) min_rpos = e->rpos;
- }
- if (buf->n >= capacity) {
- if (is_mapped && c->pos <= min_rpos) capacity += BLOCK_SIZE;
- else break;
- }
- }
- if (ret >= 0 && buf->x < 0) buf->x = buf->n;
- bam_destroy1(b);
- return buf->n;
+ khint_t k = kh_get(lib, aux, lib);
+ if (k == kh_end(aux)) {
+ int ret;
+ char *p = strdup(lib);
+ lib_aux_t *q;
+ k = kh_put(lib, aux, p, &ret);
+ q = &kh_val(aux, k);
+ q->left = kh_init(best);
+ q->rght = kh_init(best);
+ q->n_checked = q->n_removed = 0;
+ return q;
+ } else return &kh_val(aux, k);
+}
+
+static inline int sum_qual(const bam1_t *b)
+{
+ int i, q;
+ uint8_t *qual = bam1_qual(b);
+ for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
+ return q;
+}
+
+static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score)
+{
+ elem_t *p = kl_pushp(q, queue);
+ p->discarded = 0;
+ p->endpos = endpos; p->score = score;
+ if (p->b == 0) p->b = bam_init1();
+ bam_copy1(p->b, b);
+ return p;
}
-static void rmdupse_buf(buffer_t *buf)
+static void clear_besthash(besthash_t *h, int32_t pos)
{
- khash_t(32) *h;
- uint32_t key;
khint_t k;
- int mpos, i, upper;
- listelem_t *p;
- mpos = 0x7fffffff;
- mpos = (buf->x == buf->n)? buf->buf[buf->x-1].b->core.pos : 0x7fffffff;
- upper = (buf->x < 0)? buf->n : buf->x;
- // fill the hash table
- h = kh_init(32);
- for (i = 0; i < upper; ++i) {
- elem_t *e = buf->buf + i;
- int ret;
- if (e->score < 0) continue;
- if (e->rpos >= 0) {
- if (e->rpos <= mpos) key = (uint32_t)e->rpos<<1 | 1;
- else continue;
- } else {
- if (e->b->core.pos < mpos) key = (uint32_t)e->b->core.pos<<1;
- else continue;
- }
- k = kh_put(32, h, key, &ret);
- p = &kh_val(h, k);
- if (ret == 0) { // present in the hash table
- if (p->n == p->m) {
- p->m <<= 1;
- p->a = (int*)realloc(p->a, p->m * sizeof(int));
+ for (k = kh_begin(h); k != kh_end(h); ++k)
+ if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos)
+ kh_del(best, h, k);
+}
+
+static void dump_alignment(samfile_t *out, queue_t *queue, int32_t pos, khash_t(lib) *h)
+{
+ if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) {
+ khint_t k;
+ while (1) {
+ elem_t *q;
+ if (queue->head == queue->tail) break;
+ q = &kl_val(queue->head);
+ if (q->discarded) {
+ q->b->data_len = 0;
+ kl_shift(q, queue, 0);
+ continue;
}
- p->a[p->n++] = i;
- } else {
- p->m = p->n = 1;
- p->a = (int*)calloc(p->m, sizeof(int));
- p->a[0] = i;
+ if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break;
+ samwrite(out, q->b);
+ q->b->data_len = 0;
+ kl_shift(q, queue, 0);
}
- }
- // rmdup
- for (k = kh_begin(h); k < kh_end(h); ++k) {
- if (kh_exist(h, k)) {
- int max, maxi;
- p = &kh_val(h, k);
- // get the max
- for (i = max = 0, maxi = -1; i < p->n; ++i) {
- if (buf->buf[p->a[i]].score > max) {
- max = buf->buf[p->a[i]].score;
- maxi = i;
- }
- }
- // mark the elements
- for (i = 0; i < p->n; ++i) {
- buf->buf[p->a[i]].score = -1;
- if (i != maxi) {
- bam_destroy1(buf->buf[p->a[i]].b);
- buf->buf[p->a[i]].b = 0;
- }
+ for (k = kh_begin(h); k != kh_end(h); ++k) {
+ if (kh_exist(h, k)) {
+ clear_besthash(kh_val(h, k).left, pos);
+ clear_besthash(kh_val(h, k).rght, pos);
}
- // free
- free(p->a);
}
}
- kh_destroy(32, h);
}
-static void dump_buf(buffer_t *buf, samfile_t *out)
+void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se)
{
- int i;
- for (i = 0; i < buf->n; ++i) {
- elem_t *e = buf->buf + i;
- if (e->score != -1) break;
- if (e->b) {
- samwrite(out, e->b);
- bam_destroy1(e->b);
- e->b = 0;
+ bam1_t *b;
+ queue_t *queue;
+ khint_t k;
+ int last_tid = -2;
+ khash_t(lib) *aux;
+
+ aux = kh_init(lib);
+ b = bam_init1();
+ queue = kl_init(q);
+ while (samread(in, b) >= 0) {
+ bam1_core_t *c = &b->core;
+ int endpos = bam_calend(c, bam1_cigar(b));
+ int score = sum_qual(b);
+
+ if (last_tid != c->tid) {
+ if (last_tid >= 0) dump_alignment(out, queue, MAX_POS, aux);
+ last_tid = c->tid;
+ } else dump_alignment(out, queue, c->pos, aux);
+ if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) {
+ push_queue(queue, b, endpos, score);
+ } else {
+ const char *lib;
+ lib_aux_t *q;
+ besthash_t *h;
+ uint32_t key;
+ int ret;
+ lib = bam_get_library(in->header, b);
+ q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
+ ++q->n_checked;
+ h = (c->flag&BAM_FREVERSE)? q->rght : q->left;
+ key = (c->flag&BAM_FREVERSE)? endpos : c->pos;
+ k = kh_put(best, h, key, &ret);
+ if (ret == 0) { // in the hash table
+ elem_t *p = kh_val(h, k);
+ ++q->n_removed;
+ if (p->score < score) {
+ if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue
+ p->discarded = 1;
+ kh_val(h, k) = push_queue(queue, b, endpos, score);
+ } else { // replace
+ p->score = score; p->endpos = endpos;
+ bam_copy1(p->b, b);
+ }
+ } // otherwise, discard the alignment
+ } else kh_val(h, k) = push_queue(queue, b, endpos, score);
}
}
-}
+ dump_alignment(out, queue, MAX_POS, aux);
-int bam_rmdupse(int argc, char *argv[])
-{
- samfile_t *in, *out;
- buffer_t *buf;
- if (argc < 3) {
- fprintf(stderr, "Usage: samtools rmdupse <in.bam> <out.bam>\n\n");
- fprintf(stderr, "Note: Picard is recommended for this task.\n");
- return 1;
- }
- buf = calloc(1, sizeof(buffer_t));
- in = samopen(argv[1], "rb", 0);
- out = samopen(argv[2], "wb", in->header);
- while (fill_buf(in, buf)) {
- rmdupse_buf(buf);
- dump_buf(buf, out);
+ for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+ if (kh_exist(aux, k)) {
+ lib_aux_t *q = &kh_val(aux, k);
+ fprintf(stderr, "[bam_rmdupse_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
+ (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
+ kh_destroy(best, q->left); kh_destroy(best, q->rght);
+ free((char*)kh_key(aux, k));
+ }
}
- samclose(in); samclose(out);
- free(buf->buf); free(buf);
- return 0;
+ kh_destroy(lib, aux);
+ bam_destroy1(b);
+ kl_destroy(q, queue);
}
typedef struct {
int i;
- uint64_t pos;
+ uint64_t pos, idx;
bam1_t *b;
} heap1_t;
+#define __pos_cmp(a, b) ((a).pos > (b).pos || ((a).pos == (b).pos && ((a).i > (b).i || ((a).i == (b).i && (a).idx > (b).idx))))
+
static inline int heap_lt(const heap1_t a, const heap1_t b)
{
if (g_is_by_qname) {
int t;
if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0;
t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b));
- return (t > 0 || (t == 0 && a.pos > b.pos));
- } else return (a.pos > b.pos);
+ return (t > 0 || (t == 0 && __pos_cmp(a, b)));
+ } else return __pos_cmp(a, b);
}
KSORT_INIT(heap, heap1_t, heap_lt)
@discussion Padding information may NOT correctly maintained. This
function is NOT thread safe.
*/
-void bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn)
+void bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int add_RG)
{
bamFile fpout, *fp;
heap1_t *heap;
bam_header_t *hout = 0;
bam_header_t *hheaders = NULL;
- int i, j;
+ int i, j, *RG_len = 0;
+ uint64_t idx = 0;
+ char **RG = 0;
if (headers) {
tamFile fpheaders = sam_open(headers);
g_is_by_qname = by_qname;
fp = (bamFile*)calloc(n, sizeof(bamFile));
heap = (heap1_t*)calloc(n, sizeof(heap1_t));
+ // prepare RG tag
+ if (add_RG) {
+ RG = (char**)calloc(n, sizeof(void*));
+ RG_len = (int*)calloc(n, sizeof(int));
+ for (i = 0; i != n; ++i) {
+ int l = strlen(fn[i]);
+ const char *s = fn[i];
+ if (l > 4 && strcmp(s + l - 4, ".bam") == 0) l -= 4;
+ for (j = l - 1; j >= 0; --j) if (s[j] == '/') break;
+ ++j; l -= j;
+ RG[i] = calloc(l + 1, 1);
+ RG_len[i] = l;
+ strncpy(RG[i], s + j, l);
+ }
+ }
+ // read the first
for (i = 0; i != n; ++i) {
heap1_t *h;
bam_header_t *hin;
- assert(fp[i] = bam_open(fn[i], "r"));
+ fp[i] = bam_open(fn[i], "r");
+ if (fp[i] == 0) {
+ int j;
+ fprintf(stderr, "[bam_merge_core] fail to open file %s\n", fn[i]);
+ for (j = 0; j < i; ++j) bam_close(fp[j]);
+ free(fp); free(heap);
+ // FIXME: possible memory leak
+ return;
+ }
hin = bam_header_read(fp[i]);
if (i == 0) { // the first SAM
hout = hin;
h = heap + i;
h->i = i;
h->b = (bam1_t*)calloc(1, sizeof(bam1_t));
- if (bam_read1(fp[i], h->b) >= 0)
+ if (bam_read1(fp[i], h->b) >= 0) {
h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)h->b->core.pos<<1 | bam1_strand(h->b);
+ h->idx = idx++;
+ }
else h->pos = HEAP_EMPTY;
}
fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w");
ks_heapmake(heap, n, heap);
while (heap->pos != HEAP_EMPTY) {
bam1_t *b = heap->b;
+ if (add_RG && bam_aux_get(b, "RG") == 0)
+ bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
bam_write1_core(fpout, &b->core, b->data_len, b->data);
if ((j = bam_read1(fp[heap->i], b)) >= 0) {
heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)b->core.pos<<1 | bam1_strand(b);
+ heap->idx = idx++;
} else if (j == -1) {
heap->pos = HEAP_EMPTY;
free(heap->b->data); free(heap->b);
ks_heapadjust(heap, 0, n, heap);
}
+ if (add_RG) {
+ for (i = 0; i != n; ++i) free(RG[i]);
+ free(RG); free(RG_len);
+ }
for (i = 0; i != n; ++i) bam_close(fp[i]);
bam_close(fpout);
free(fp); free(heap);
}
int bam_merge(int argc, char *argv[])
{
- int c, is_by_qname = 0;
+ int c, is_by_qname = 0, add_RG = 0;
char *fn_headers = NULL;
- while ((c = getopt(argc, argv, "h:n")) >= 0) {
+ while ((c = getopt(argc, argv, "h:nr")) >= 0) {
switch (c) {
+ case 'r': add_RG = 1; break;
case 'h': fn_headers = strdup(optarg); break;
case 'n': is_by_qname = 1; break;
}
}
if (optind + 2 >= argc) {
fprintf(stderr, "\n");
- fprintf(stderr, "Usage: samtools merge [-n] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]\n\n");
+ fprintf(stderr, "Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]\n\n");
fprintf(stderr, "Options: -n sort by read names\n");
+ fprintf(stderr, " -r attach RG tag (inferred from file names)\n");
fprintf(stderr, " -h FILE copy the header in FILE to <out.bam> [in1.bam]\n\n");
fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
fprintf(stderr, " must provide the correct header with -h, or uses Picard which properly maintains\n");
fprintf(stderr, " the header dictionary in merging.\n\n");
return 1;
}
- bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1);
+ bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, add_RG);
free(fn_headers);
return 0;
}
}
KSORT_INIT(sort, bam1_p, bam1_lt)
-static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam_header_t *h)
+static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam_header_t *h, int is_stdout)
{
char *name;
int i;
name = (char*)calloc(strlen(prefix) + 20, 1);
if (n >= 0) sprintf(name, "%s.%.4d.bam", prefix, n);
else sprintf(name, "%s.bam", prefix);
- assert(fp = bam_open(name, "w"));
+ fp = is_stdout? bam_dopen(fileno(stdout), "w") : bam_open(name, "w");
+ if (fp == 0) {
+ fprintf(stderr, "[sort_blocks] fail to create file %s.\n", name);
+ free(name);
+ // FIXME: possible memory leak
+ return;
+ }
free(name);
bam_header_write(fp, h);
for (i = 0; i < k; ++i)
and then merge them by calling bam_merge_core(). This function is
NOT thread safe.
*/
-void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
+void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t max_mem, int is_stdout)
{
int n, ret, k, i;
size_t mem;
g_is_by_qname = is_by_qname;
n = k = 0; mem = 0;
fp = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
- assert(fp);
+ if (fp == 0) {
+ fprintf(stderr, "[bam_sort_core] fail to open file %s\n", fn);
+ return;
+ }
header = bam_header_read(fp);
buf = (bam1_t**)calloc(max_mem / BAM_CORE_SIZE, sizeof(bam1_t*));
// write sub files
mem += ret;
++k;
if (mem >= max_mem) {
- sort_blocks(n++, k, buf, prefix, header);
+ sort_blocks(n++, k, buf, prefix, header, is_stdout);
mem = 0; k = 0;
}
}
if (ret != -1)
fprintf(stderr, "[bam_sort_core] truncated file. Continue anyway.\n");
- if (n == 0) sort_blocks(-1, k, buf, prefix, header);
+ if (n == 0) sort_blocks(-1, k, buf, prefix, header, is_stdout);
else { // then merge
char **fns, *fnout;
fprintf(stderr, "[bam_sort_core] merging from %d files...\n", n+1);
- sort_blocks(n++, k, buf, prefix, header);
+ sort_blocks(n++, k, buf, prefix, header, is_stdout);
fnout = (char*)calloc(strlen(prefix) + 20, 1);
- sprintf(fnout, "%s.bam", prefix);
+ if (is_stdout) sprintf(fnout, "-");
+ else sprintf(fnout, "%s.bam", prefix);
fns = (char**)calloc(n, sizeof(char*));
for (i = 0; i < n; ++i) {
fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
sprintf(fns[i], "%s.%.4d.bam", prefix, i);
}
- bam_merge_core(is_by_qname, fnout, 0, n, fns);
+ bam_merge_core(is_by_qname, fnout, 0, n, fns, 0);
free(fnout);
for (i = 0; i < n; ++i) {
unlink(fns[i]);
bam_close(fp);
}
+void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
+{
+ bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0);
+}
+
int bam_sort(int argc, char *argv[])
{
size_t max_mem = 500000000;
- int c, is_by_qname = 0;
- while ((c = getopt(argc, argv, "nm:")) >= 0) {
+ int c, is_by_qname = 0, is_stdout = 0;
+ while ((c = getopt(argc, argv, "nom:")) >= 0) {
switch (c) {
+ case 'o': is_stdout = 1; break;
case 'n': is_by_qname = 1; break;
case 'm': max_mem = atol(optarg); break;
}
}
if (optind + 2 > argc) {
- fprintf(stderr, "Usage: samtools sort [-n] [-m <maxMem>] <in.bam> <out.prefix>\n");
+ fprintf(stderr, "Usage: samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>\n");
return 1;
}
- bam_sort_core(is_by_qname, argv[optind], argv[optind+1], max_mem);
+ bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout);
return 0;
}
#endif
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.6 (r453)"
+#define PACKAGE_VERSION "0.1.7 (r510)"
#endif
int bam_taf2baf(int argc, char *argv[]);
int bam_tview_main(int argc, char *argv[]);
int bam_mating(int argc, char *argv[]);
int bam_rmdup(int argc, char *argv[]);
-int bam_rmdupse(int argc, char *argv[]);
int bam_flagstat(int argc, char *argv[]);
int bam_fillmd(int argc, char *argv[]);
fprintf(stderr, " glfview print GLFv3 file\n");
fprintf(stderr, " flagstat simple stats\n");
fprintf(stderr, " calmd recalculate MD/NM tags and '=' bases\n");
- fprintf(stderr, " merge merge sorted alignments (Picard recommended)\n");
- fprintf(stderr, " rmdup remove PCR duplicates (Picard recommended)\n");
+ fprintf(stderr, " merge merge sorted alignments\n");
+ fprintf(stderr, " rmdup remove PCR duplicates\n");
fprintf(stderr, "\n");
return 1;
}
else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
- else if (strcmp(argv[1], "rmdupse") == 0) return bam_rmdupse(argc-1, argv+1);
else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
else if (strcmp(argv[1], "tagview") == 0) return bam_tagview(argc-1, argv+1);
#ifdef _WIN32
oflag |= O_BINARY;
#endif
- fd = open(path, oflag, 0644);
+ fd = open(path, oflag, 0666);
if (fd == -1) return 0;
fp = open_write(fd, strstr(mode, "u")? 1 : 0);
}
int fd = -1;
char c;
if (!is_forced) {
- if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0644)) < 0 && errno == EEXIST) {
+ if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
printf("bgzip: %s already exists; do you wish to overwrite (y or n)? ", fn);
scanf("%c", &c);
if (c != 'Y' && c != 'y') {
}
}
if (fd < 0) {
- if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0644)) < 0) {
+ if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) {
fprintf(stderr, "bgzip: %s: Fail to write\n", fn);
exit(1);
}
-all:../libbam.a ../samtools ex1.glf ex1.pileup.gz ex1.bam.bai ex1.glfview.gz calDepth
+all:../libbam.a ../samtools ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.glfview.gz calDepth
@echo; echo \# You can now launch the viewer with: \'samtools tview ex1.bam ex1.fa\'; echo;
ex1.fa.fai:ex1.fa
../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
ex1.glfview.gz:ex1.glf
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
+ex1a.bam:ex1.bam
+ ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"a";print}}' | ../samtools view -bS - > $@
+ex1b.bam:ex1.bam
+ ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"b";print}}' | ../samtools view -bS - > $@
+ex1f.rg:
+ (echo "@RG ID:ex1 LB:ex1"; echo "@RG ID:ex1a LB:ex1"; echo "@RG ID:ex1b LB:ex1b") > $@
+ex1f.bam:ex1.bam ex1a.bam ex1b.bam ex1f.rg
+ ../samtools merge -rh ex1f.rg $@ ex1.bam ex1a.bam ex1b.bam
+ex1f-rmduppe.bam:ex1f.bam
+ ../samtools rmdup ex1f.bam $@
+ex1f-rmdupse.bam:ex1f.bam
+ ../samtools rmdup -S ex1f.bam $@
../samtools:
(cd ..; make samtools)
gcc -g -Wall -O2 -I.. calDepth.c -o $@ -lm -lz -L.. -lbam
clean:
- rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM
\ No newline at end of file
+ rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg
\ No newline at end of file
#define razf_seek(fp, offset, whence) fseeko(fp, offset, whence)
#define razf_tell(fp) ftello(fp)
#endif
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
struct __faidx_t {
RAZF *rz;
sprintf(str, "%s.fai", fn);
rz = razf_open(fn, "r");
if (rz == 0) {
- fprintf(stderr, "[fai_build] fail to open the FASTA file.\n");
+ fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",str);
free(str);
return -1;
}
razf_close(rz);
fp = fopen(str, "wb");
if (fp == 0) {
- fprintf(stderr, "[fai_build] fail to write FASTA index.\n");
+ fprintf(stderr, "[fai_build] fail to write FASTA index %s\n",str);
fai_destroy(fai); free(str);
return -1;
}
return 0;
}
+#ifdef _USE_KNETFILE
+FILE *download_and_open(const char *fn)
+{
+ const int buf_size = 1 * 1024 * 1024;
+ uint8_t *buf;
+ FILE *fp;
+ knetFile *fp_remote;
+ const char *url = fn;
+ const char *p;
+ int l = strlen(fn);
+ for (p = fn + l - 1; p >= fn; --p)
+ if (*p == '/') break;
+ fn = p + 1;
+
+ // First try to open a local copy
+ fp = fopen(fn, "r");
+ if (fp)
+ return fp;
+
+ // If failed, download from remote and open
+ fp_remote = knet_open(url, "rb");
+ if (fp_remote == 0) {
+ fprintf(stderr, "[download_from_remote] fail to open remote file %s\n",url);
+ return NULL;
+ }
+ if ((fp = fopen(fn, "wb")) == 0) {
+ fprintf(stderr, "[download_from_remote] fail to create file in the working directory %s\n",fn);
+ knet_close(fp_remote);
+ return NULL;
+ }
+ buf = (uint8_t*)calloc(buf_size, 1);
+ while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
+ fwrite(buf, 1, l, fp);
+ free(buf);
+ fclose(fp);
+ knet_close(fp_remote);
+
+ return fopen(fn, "r");
+}
+#endif
+
faidx_t *fai_load(const char *fn)
{
char *str;
faidx_t *fai;
str = (char*)calloc(strlen(fn) + 5, 1);
sprintf(str, "%s.fai", fn);
- fp = fopen(str, "rb");
+
+#ifdef _USE_KNETFILE
+ if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)
+ {
+ fp = download_and_open(str);
+ if ( !fp )
+ {
+ fprintf(stderr, "[fai_load] failed to open remote FASTA index %s\n", str);
+ free(str);
+ return 0;
+ }
+ }
+ else
+#endif
+ fp = fopen(str, "rb");
if (fp == 0) {
fprintf(stderr, "[fai_load] build FASTA index.\n");
fai_build(fn);
- fp = fopen(str, "r");
+ fp = fopen(str, "rb");
if (fp == 0) {
fprintf(stderr, "[fai_load] fail to open FASTA index.\n");
free(str);
return 0;
}
}
+
fai = fai_read(fp);
fclose(fp);
+
fai->rz = razf_open(fn, "rb");
free(str);
if (fai->rz == 0) {
l = 0;
s = (char*)malloc(end - beg + 2);
razf_seek(fai->rz, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET);
- while (razf_read(fai->rz, &c, 1) == 1 && l < end - beg)
+ while (razf_read(fai->rz, &c, 1) == 1 && l < end - beg && !fai->rz->z_err)
if (isgraph(c)) s[l++] = c;
s[l] = '\0';
*len = l;
return 0;
}
+int faidx_fetch_nseq(const faidx_t *fai)
+{
+ return fai->n;
+}
+
+char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len)
+{
+ int l;
+ char c;
+ khiter_t iter;
+ faidx1_t val;
+ char *seq=NULL;
+
+ // Adjust position
+ iter = kh_get(s, fai->hash, c_name);
+ if(iter == kh_end(fai->hash)) return 0;
+ val = kh_value(fai->hash, iter);
+ if(p_end_i < p_beg_i) p_beg_i = p_end_i;
+ if(p_beg_i < 0) p_beg_i = 0;
+ else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
+ if(p_end_i < 0) p_end_i = 0;
+ else if(val.len <= p_end_i) p_end_i = val.len - 1;
+
+ // Now retrieve the sequence
+ l = 0;
+ seq = (char*)malloc(p_end_i - p_beg_i + 2);
+ razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
+ while (razf_read(fai->rz, &c, 1) == 1 && l < p_end_i - p_beg_i + 1)
+ if (isgraph(c)) seq[l++] = c;
+ seq[l] = '\0';
+ *len = l;
+ return seq;
+}
+
#ifdef FAIDX_MAIN
int main(int argc, char *argv[]) { return faidx_main(argc, argv); }
#endif
*/
char *fai_fetch(const faidx_t *fai, const char *reg, int *len);
+ /*!
+ @abstract Fetch the number of sequences.
+ @param fai Pointer to the faidx_t struct
+ @return The number of sequences
+ */
+ int faidx_fetch_nseq(const faidx_t *fai);
+
+ /*!
+ @abstract Fetch the sequence in a region.
+ @param fai Pointer to the faidx_t struct
+ @param c_name Region name
+ @param p_beg_i Beginning position number (zero-based)
+ @param p_end_i End position number (zero-based)
+ @param len Length of the region
+ @return Pointer to the sequence; null on failure
+
+ @discussion The returned sequence is allocated by malloc family
+ and should be destroyed by end users by calling free() on it.
+ */
+ char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len);
+
#ifdef __cplusplus
}
#endif
--- /dev/null
+/* The MIT License
+
+ Copyright (c) 2003-2006, 2008, 2009, by Heng Li <lh3lh3@gmail.com>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdint.h>
+#include "kaln.h"
+
+#define FROM_M 0
+#define FROM_I 1
+#define FROM_D 2
+
+typedef struct {
+ int i, j;
+ unsigned char ctype;
+} path_t;
+
+int aln_sm_blosum62[] = {
+/* A R N D C Q E G H I L K M F P S T W Y V * X */
+ 4,-1,-2,-2, 0,-1,-1, 0,-2,-1,-1,-1,-1,-2,-1, 1, 0,-3,-2, 0,-4, 0,
+ -1, 5, 0,-2,-3, 1, 0,-2, 0,-3,-2, 2,-1,-3,-2,-1,-1,-3,-2,-3,-4,-1,
+ -2, 0, 6, 1,-3, 0, 0, 0, 1,-3,-3, 0,-2,-3,-2, 1, 0,-4,-2,-3,-4,-1,
+ -2,-2, 1, 6,-3, 0, 2,-1,-1,-3,-4,-1,-3,-3,-1, 0,-1,-4,-3,-3,-4,-1,
+ 0,-3,-3,-3, 9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-4,-2,
+ -1, 1, 0, 0,-3, 5, 2,-2, 0,-3,-2, 1, 0,-3,-1, 0,-1,-2,-1,-2,-4,-1,
+ -1, 0, 0, 2,-4, 2, 5,-2, 0,-3,-3, 1,-2,-3,-1, 0,-1,-3,-2,-2,-4,-1,
+ 0,-2, 0,-1,-3,-2,-2, 6,-2,-4,-4,-2,-3,-3,-2, 0,-2,-2,-3,-3,-4,-1,
+ -2, 0, 1,-1,-3, 0, 0,-2, 8,-3,-3,-1,-2,-1,-2,-1,-2,-2, 2,-3,-4,-1,
+ -1,-3,-3,-3,-1,-3,-3,-4,-3, 4, 2,-3, 1, 0,-3,-2,-1,-3,-1, 3,-4,-1,
+ -1,-2,-3,-4,-1,-2,-3,-4,-3, 2, 4,-2, 2, 0,-3,-2,-1,-2,-1, 1,-4,-1,
+ -1, 2, 0,-1,-3, 1, 1,-2,-1,-3,-2, 5,-1,-3,-1, 0,-1,-3,-2,-2,-4,-1,
+ -1,-1,-2,-3,-1, 0,-2,-3,-2, 1, 2,-1, 5, 0,-2,-1,-1,-1,-1, 1,-4,-1,
+ -2,-3,-3,-3,-2,-3,-3,-3,-1, 0, 0,-3, 0, 6,-4,-2,-2, 1, 3,-1,-4,-1,
+ -1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4, 7,-1,-1,-4,-3,-2,-4,-2,
+ 1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-2, 0,-1,-2,-1, 4, 1,-3,-2,-2,-4, 0,
+ 0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 1, 5,-2,-2, 0,-4, 0,
+ -3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, 1,-4,-3,-2,11, 2,-3,-4,-2,
+ -2,-2,-2,-3,-2,-1,-2,-3, 2,-1,-1,-2,-1, 3,-3,-2,-2, 2, 7,-1,-4,-1,
+ 0,-3,-3,-3,-1,-2,-2,-3,-3, 3, 1,-2, 1,-1,-2,-2, 0,-3,-1, 4,-4,-1,
+ -4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4, 1,-4,
+ 0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2, 0, 0,-2,-1,-1,-4,-1
+};
+
+int aln_sm_blast[] = {
+ 1, -3, -3, -3, -2,
+ -3, 1, -3, -3, -2,
+ -3, -3, 1, -3, -2,
+ -3, -3, -3, 1, -2,
+ -2, -2, -2, -2, -2
+};
+
+ka_param_t ka_param_blast = { 5, 2, 2, aln_sm_blast, 5, 50 };
+ka_param_t ka_param_aa2aa = { 10, 2, 2, aln_sm_blosum62, 22, 50 };
+
+static uint32_t *ka_path2cigar32(const path_t *path, int path_len, int *n_cigar)
+{
+ int i, n;
+ uint32_t *cigar;
+ unsigned char last_type;
+
+ if (path_len == 0 || path == 0) {
+ *n_cigar = 0;
+ return 0;
+ }
+
+ last_type = path->ctype;
+ for (i = n = 1; i < path_len; ++i) {
+ if (last_type != path[i].ctype) ++n;
+ last_type = path[i].ctype;
+ }
+ *n_cigar = n;
+ cigar = (uint32_t*)calloc(*n_cigar, 4);
+
+ cigar[0] = 1u << 4 | path[path_len-1].ctype;
+ last_type = path[path_len-1].ctype;
+ for (i = path_len - 2, n = 0; i >= 0; --i) {
+ if (path[i].ctype == last_type) cigar[n] += 1u << 4;
+ else {
+ cigar[++n] = 1u << 4 | path[i].ctype;
+ last_type = path[i].ctype;
+ }
+ }
+
+ return cigar;
+}
+
+/***************************/
+/* START OF common_align.c */
+/***************************/
+
+#define SET_INF(s) (s).M = (s).I = (s).D = MINOR_INF;
+
+#define set_M(MM, cur, p, sc) \
+{ \
+ if ((p)->M >= (p)->I) { \
+ if ((p)->M >= (p)->D) { \
+ (MM) = (p)->M + (sc); (cur)->Mt = FROM_M; \
+ } else { \
+ (MM) = (p)->D + (sc); (cur)->Mt = FROM_D; \
+ } \
+ } else { \
+ if ((p)->I > (p)->D) { \
+ (MM) = (p)->I + (sc); (cur)->Mt = FROM_I; \
+ } else { \
+ (MM) = (p)->D + (sc); (cur)->Mt = FROM_D; \
+ } \
+ } \
+}
+#define set_I(II, cur, p) \
+{ \
+ if ((p)->M - gap_open > (p)->I) { \
+ (cur)->It = FROM_M; \
+ (II) = (p)->M - gap_open - gap_ext; \
+ } else { \
+ (cur)->It = FROM_I; \
+ (II) = (p)->I - gap_ext; \
+ } \
+}
+#define set_end_I(II, cur, p) \
+{ \
+ if (gap_end >= 0) { \
+ if ((p)->M - gap_open > (p)->I) { \
+ (cur)->It = FROM_M; \
+ (II) = (p)->M - gap_open - gap_end; \
+ } else { \
+ (cur)->It = FROM_I; \
+ (II) = (p)->I - gap_end; \
+ } \
+ } else set_I(II, cur, p); \
+}
+#define set_D(DD, cur, p) \
+{ \
+ if ((p)->M - gap_open > (p)->D) { \
+ (cur)->Dt = FROM_M; \
+ (DD) = (p)->M - gap_open - gap_ext; \
+ } else { \
+ (cur)->Dt = FROM_D; \
+ (DD) = (p)->D - gap_ext; \
+ } \
+}
+#define set_end_D(DD, cur, p) \
+{ \
+ if (gap_end >= 0) { \
+ if ((p)->M - gap_open > (p)->D) { \
+ (cur)->Dt = FROM_M; \
+ (DD) = (p)->M - gap_open - gap_end; \
+ } else { \
+ (cur)->Dt = FROM_D; \
+ (DD) = (p)->D - gap_end; \
+ } \
+ } else set_D(DD, cur, p); \
+}
+
+typedef struct {
+ uint8_t Mt:3, It:2, Dt:2;
+} dpcell_t;
+
+typedef struct {
+ int M, I, D;
+} dpscore_t;
+
+/***************************
+ * banded global alignment *
+ ***************************/
+uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap, int *_score, int *n_cigar)
+{
+ int i, j;
+ dpcell_t **dpcell, *q;
+ dpscore_t *curr, *last, *s;
+ int b1, b2, tmp_end;
+ int *mat, end, max = 0;
+ uint8_t type, ctype;
+ uint32_t *cigar = 0;
+
+ int gap_open, gap_ext, gap_end, b;
+ int *score_matrix, N_MATRIX_ROW;
+
+ /* initialize some align-related parameters. just for compatibility */
+ gap_open = ap->gap_open;
+ gap_ext = ap->gap_ext;
+ gap_end = ap->gap_end;
+ b = ap->band_width;
+ score_matrix = ap->matrix;
+ N_MATRIX_ROW = ap->row;
+
+ *n_cigar = 0;
+ if (len1 == 0 || len2 == 0) return 0;
+
+ /* calculate b1 and b2 */
+ if (len1 > len2) {
+ b1 = len1 - len2 + b;
+ b2 = b;
+ } else {
+ b1 = b;
+ b2 = len2 - len1 + b;
+ }
+ if (b1 > len1) b1 = len1;
+ if (b2 > len2) b2 = len2;
+ --seq1; --seq2;
+
+ /* allocate memory */
+ end = (b1 + b2 <= len1)? (b1 + b2 + 1) : (len1 + 1);
+ dpcell = (dpcell_t**)malloc(sizeof(dpcell_t*) * (len2 + 1));
+ for (j = 0; j <= len2; ++j)
+ dpcell[j] = (dpcell_t*)malloc(sizeof(dpcell_t) * end);
+ for (j = b2 + 1; j <= len2; ++j)
+ dpcell[j] -= j - b2;
+ curr = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1));
+ last = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1));
+
+ /* set first row */
+ SET_INF(*curr); curr->M = 0;
+ for (i = 1, s = curr + 1; i < b1; ++i, ++s) {
+ SET_INF(*s);
+ set_end_D(s->D, dpcell[0] + i, s - 1);
+ }
+ s = curr; curr = last; last = s;
+
+ /* core dynamic programming, part 1 */
+ tmp_end = (b2 < len2)? b2 : len2 - 1;
+ for (j = 1; j <= tmp_end; ++j) {
+ q = dpcell[j]; s = curr; SET_INF(*s);
+ set_end_I(s->I, q, last);
+ end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1;
+ mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+ ++s; ++q;
+ for (i = 1; i != end; ++i, ++s, ++q) {
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */
+ set_I(s->I, q, last + i);
+ set_D(s->D, q, s - 1);
+ }
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+ set_D(s->D, q, s - 1);
+ if (j + b1 - 1 > len1) { /* bug fixed, 040227 */
+ set_end_I(s->I, q, last + i);
+ } else s->I = MINOR_INF;
+ s = curr; curr = last; last = s;
+ }
+ /* last row for part 1, use set_end_D() instead of set_D() */
+ if (j == len2 && b2 != len2 - 1) {
+ q = dpcell[j]; s = curr; SET_INF(*s);
+ set_end_I(s->I, q, last);
+ end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1;
+ mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+ ++s; ++q;
+ for (i = 1; i != end; ++i, ++s, ++q) {
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */
+ set_I(s->I, q, last + i);
+ set_end_D(s->D, q, s - 1);
+ }
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+ set_end_D(s->D, q, s - 1);
+ if (j + b1 - 1 > len1) { /* bug fixed, 040227 */
+ set_end_I(s->I, q, last + i);
+ } else s->I = MINOR_INF;
+ s = curr; curr = last; last = s;
+ ++j;
+ }
+
+ /* core dynamic programming, part 2 */
+ for (; j <= len2 - b2 + 1; ++j) {
+ SET_INF(curr[j - b2]);
+ mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+ end = j + b1 - 1;
+ for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i != end; ++i, ++s, ++q) {
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+ set_I(s->I, q, last + i);
+ set_D(s->D, q, s - 1);
+ }
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+ set_D(s->D, q, s - 1);
+ s->I = MINOR_INF;
+ s = curr; curr = last; last = s;
+ }
+
+ /* core dynamic programming, part 3 */
+ for (; j < len2; ++j) {
+ SET_INF(curr[j - b2]);
+ mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+ for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) {
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+ set_I(s->I, q, last + i);
+ set_D(s->D, q, s - 1);
+ }
+ set_M(s->M, q, last + len1 - 1, mat[seq1[i]]);
+ set_end_I(s->I, q, last + i);
+ set_D(s->D, q, s - 1);
+ s = curr; curr = last; last = s;
+ }
+ /* last row */
+ if (j == len2) {
+ SET_INF(curr[j - b2]);
+ mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+ for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) {
+ set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+ set_I(s->I, q, last + i);
+ set_end_D(s->D, q, s - 1);
+ }
+ set_M(s->M, q, last + len1 - 1, mat[seq1[i]]);
+ set_end_I(s->I, q, last + i);
+ set_end_D(s->D, q, s - 1);
+ s = curr; curr = last; last = s;
+ }
+
+ *_score = last[len1].M;
+ if (n_cigar) { /* backtrace */
+ path_t *p, *path = (path_t*)malloc(sizeof(path_t) * (len1 + len2 + 2));
+ i = len1; j = len2;
+ q = dpcell[j] + i;
+ s = last + len1;
+ max = s->M; type = q->Mt; ctype = FROM_M;
+ if (s->I > max) { max = s->I; type = q->It; ctype = FROM_I; }
+ if (s->D > max) { max = s->D; type = q->Dt; ctype = FROM_D; }
+
+ p = path;
+ p->ctype = ctype; p->i = i; p->j = j; /* bug fixed 040408 */
+ ++p;
+ do {
+ switch (ctype) {
+ case FROM_M: --i; --j; break;
+ case FROM_I: --j; break;
+ case FROM_D: --i; break;
+ }
+ q = dpcell[j] + i;
+ ctype = type;
+ switch (type) {
+ case FROM_M: type = q->Mt; break;
+ case FROM_I: type = q->It; break;
+ case FROM_D: type = q->Dt; break;
+ }
+ p->ctype = ctype; p->i = i; p->j = j;
+ ++p;
+ } while (i || j);
+ cigar = ka_path2cigar32(path, p - path - 1, n_cigar);
+ free(path);
+ }
+
+ /* free memory */
+ for (j = b2 + 1; j <= len2; ++j)
+ dpcell[j] += j - b2;
+ for (j = 0; j <= len2; ++j)
+ free(dpcell[j]);
+ free(dpcell);
+ free(curr); free(last);
+
+ return cigar;
+}
--- /dev/null
+/* The MIT License
+
+ Copyright (c) 2003-2006, 2008, 2009 by Heng Li <lh3@live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+#ifndef LH3_KALN_H_
+#define LH3_KALN_H_
+
+#include <stdint.h>
+
+#define MINOR_INF -1073741823
+
+typedef struct {
+ int gap_open;
+ int gap_ext;
+ int gap_end;
+
+ int *matrix;
+ int row;
+ int band_width;
+} ka_param_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap, int *_score, int *n_cigar);
+
+#ifdef __cplusplus
+}
+#endif
+
+extern ka_param_t ka_param_blast; /* = { 5, 2, 2, aln_sm_blast, 5, 50 }; */
+
+#endif
--- /dev/null
+#ifndef _LH3_KLIST_H
+#define _LH3_KLIST_H
+
+#include <stdlib.h>
+
+#define KMEMPOOL_INIT(name, kmptype_t, kmpfree_f) \
+ typedef struct { \
+ size_t cnt, n, max; \
+ kmptype_t **buf; \
+ } kmp_##name##_t; \
+ static inline kmp_##name##_t *kmp_init_##name() { \
+ return calloc(1, sizeof(kmp_##name##_t)); \
+ } \
+ static inline void kmp_destroy_##name(kmp_##name##_t *mp) { \
+ size_t k; \
+ for (k = 0; k < mp->n; ++k) { \
+ kmpfree_f(mp->buf[k]); free(mp->buf[k]); \
+ } \
+ free(mp->buf); free(mp); \
+ } \
+ static inline kmptype_t *kmp_alloc_##name(kmp_##name##_t *mp) { \
+ ++mp->cnt; \
+ if (mp->n == 0) return calloc(1, sizeof(kmptype_t)); \
+ return mp->buf[--mp->n]; \
+ } \
+ static inline void kmp_free_##name(kmp_##name##_t *mp, kmptype_t *p) { \
+ --mp->cnt; \
+ if (mp->n == mp->max) { \
+ mp->max = mp->max? mp->max<<1 : 16; \
+ mp->buf = realloc(mp->buf, sizeof(void*) * mp->max); \
+ } \
+ mp->buf[mp->n++] = p; \
+ }
+
+#define kmempool_t(name) kmp_##name##_t
+#define kmp_init(name) kmp_init_##name()
+#define kmp_destroy(name, mp) kmp_destroy_##name(mp)
+#define kmp_alloc(name, mp) kmp_alloc_##name(mp)
+#define kmp_free(name, mp, p) kmp_free_##name(mp, p)
+
+#define KLIST_INIT(name, kltype_t, kmpfree_t) \
+ struct __kl1_##name { \
+ kltype_t data; \
+ struct __kl1_##name *next; \
+ }; \
+ typedef struct __kl1_##name kl1_##name; \
+ KMEMPOOL_INIT(name, kl1_##name, kmpfree_t) \
+ typedef struct { \
+ kl1_##name *head, *tail; \
+ kmp_##name##_t *mp; \
+ size_t size; \
+ } kl_##name##_t; \
+ static inline kl_##name##_t *kl_init_##name() { \
+ kl_##name##_t *kl = calloc(1, sizeof(kl_##name##_t)); \
+ kl->mp = kmp_init(name); \
+ kl->head = kl->tail = kmp_alloc(name, kl->mp); \
+ kl->head->next = 0; \
+ return kl; \
+ } \
+ static inline void kl_destroy_##name(kl_##name##_t *kl) { \
+ kl1_##name *p; \
+ for (p = kl->head; p != kl->tail; p = p->next) \
+ kmp_free(name, kl->mp, p); \
+ kmp_free(name, kl->mp, p); \
+ kmp_destroy(name, kl->mp); \
+ free(kl); \
+ } \
+ static inline kltype_t *kl_pushp_##name(kl_##name##_t *kl) { \
+ kl1_##name *q, *p = kmp_alloc(name, kl->mp); \
+ q = kl->tail; p->next = 0; kl->tail->next = p; kl->tail = p; \
+ ++kl->size; \
+ return &q->data; \
+ } \
+ static inline int kl_shift_##name(kl_##name##_t *kl, kltype_t *d) { \
+ kl1_##name *p; \
+ if (kl->head->next == 0) return -1; \
+ --kl->size; \
+ p = kl->head; kl->head = kl->head->next; \
+ if (d) *d = p->data; \
+ kmp_free(name, kl->mp, p); \
+ return 0; \
+ }
+
+#define kliter_t(name) kl1_##name
+#define klist_t(name) kl_##name##_t
+#define kl_val(iter) ((iter)->data)
+#define kl_next(iter) ((iter)->next)
+#define kl_begin(kl) ((kl)->head)
+#define kl_end(kl) ((kl)->tail)
+
+#define kl_init(name) kl_init_##name()
+#define kl_destroy(name, kl) kl_destroy_##name(kl)
+#define kl_pushp(name, kl) kl_pushp_##name(kl)
+#define kl_shift(name, kl, d) kl_shift_##name(kl, d)
+
+#endif
#include <ctype.h>
#include <stdlib.h>
#include <string.h>
+#include <errno.h>
#include <unistd.h>
#include <sys/types.h>
if (is_read) fdr = &fds;
else fdw = &fds;
ret = select(fd+1, fdr, fdw, 0, &tv);
+#ifndef _WIN32
if (ret == -1) perror("select");
+#else
+ if (ret == 0)
+ fprintf(stderr, "select time-out\n");
+ else if (ret == SOCKET_ERROR)
+ fprintf(stderr, "select: %d\n", WSAGetLastError());
+#endif
return ret;
}
}
#else
/* MinGW's printf has problem with "%lld" */
-char *uint64tostr(char *buf, uint64_t x)
+char *int64tostr(char *buf, int64_t x)
{
- int i, cnt;
- for (i = 0; x; x /= 10) buf[i++] = '0' + x%10;
+ int cnt;
+ int i = 0;
+ do {
+ buf[i++] = '0' + x % 10;
+ x /= 10;
+ } while (x);
buf[i] = 0;
for (cnt = i, i = 0; i < cnt/2; ++i) {
int c = buf[i]; buf[i] = buf[cnt-i-1]; buf[cnt-i-1] = c;
}
return buf;
}
+
+int64_t strtoint64(const char *buf)
+{
+ int64_t x;
+ for (x = 0; *buf != '\0'; ++buf)
+ x = x * 10 + ((int64_t) *buf - 48);
+ return x;
+}
/* In windows, the first thing is to establish the TCP connection. */
int knet_win32_init()
{
* non-Windows OS, I do not use this one. */
static SOCKET socket_connect(const char *host, const char *port)
{
-#define __err_connect(func) do { perror(func); return -1; } while (0)
+#define __err_connect(func) \
+ do { \
+ fprintf(stderr, "%s: %d\n", func, WSAGetLastError()); \
+ return -1; \
+ } while (0)
int on = 1;
SOCKET fd;
static int kftp_get_response(knetFile *ftp)
{
+#ifndef _WIN32
unsigned char c;
+#else
+ char c;
+#endif
int n = 0;
char *p;
if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0;
ftp->ctrl_fd = -1;
}
netclose(ftp->fd);
+ ftp->fd = -1;
return kftp_connect(ftp);
}
-// initialize ->type, ->host and ->retr
+// initialize ->type, ->host, ->retr and ->size
knetFile *kftp_parse_url(const char *fn, const char *mode)
{
knetFile *fp;
strncpy(fp->host, fn + 6, l);
fp->retr = calloc(strlen(p) + 8, 1);
sprintf(fp->retr, "RETR %s\r\n", p);
- fp->seek_offset = -1;
+ fp->size_cmd = calloc(strlen(p) + 8, 1);
+ sprintf(fp->size_cmd, "SIZE %s\r\n", p);
+ fp->seek_offset = 0;
return fp;
}
// place ->fd at offset off
int kftp_connect_file(knetFile *fp)
{
int ret;
+ long long file_size;
if (fp->fd != -1) {
netclose(fp->fd);
if (fp->no_reconnect) kftp_get_response(fp);
}
kftp_pasv_prep(fp);
- if (fp->offset) {
+ kftp_send_cmd(fp, fp->size_cmd, 1);
+#ifndef _WIN32
+ if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 )
+ {
+ fprintf(stderr,"[kftp_connect_file] %s\n", fp->response);
+ return -1;
+ }
+#else
+ const char *p = fp->response;
+ while (*p != ' ') ++p;
+ while (*p < '0' || *p > '9') ++p;
+ file_size = strtoint64(p);
+#endif
+ fp->file_size = file_size;
+ if (fp->offset>=0) {
char tmp[32];
#ifndef _WIN32
sprintf(tmp, "REST %lld\r\n", (long long)fp->offset);
#else
strcpy(tmp, "REST ");
- uint64tostr(tmp + 5, fp->offset);
+ int64tostr(tmp + 5, fp->offset);
strcat(tmp, "\r\n");
#endif
kftp_send_cmd(fp, tmp, 1);
return 0;
}
+
/**************************
* HTTP specific routines *
**************************/
}
fp->type = KNF_TYPE_HTTP;
fp->ctrl_fd = fp->fd = -1;
- fp->seek_offset = -1;
+ fp->seek_offset = 0;
return fp;
}
fp->fd = socket_connect(fp->host, fp->port);
buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host);
- if (fp->offset)
- l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
+ l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
l += sprintf(buf + l, "\r\n");
netwrite(fp->fd, buf, l);
l = 0;
return -1;
}
ret = strtol(buf + 8, &p, 0); // HTTP return code
- if (ret == 200 && fp->offset) { // 200 (complete result); then skip beginning of the file
+ if (ret == 200 && fp->offset>0) { // 200 (complete result); then skip beginning of the file
off_t rest = fp->offset;
while (rest) {
off_t l = rest < 0x10000? rest : 0x10000;
return l;
}
-int knet_seek(knetFile *fp, off_t off, int whence)
+off_t knet_seek(knetFile *fp, int64_t off, int whence)
{
if (whence == SEEK_SET && off == fp->offset) return 0;
if (fp->type == KNF_TYPE_LOCAL) {
* while fseek() returns zero on success. */
off_t offset = lseek(fp->fd, off, whence);
if (offset == -1) {
- perror("lseek");
+ // Be silent, it is OK for knet_seek to fail when the file is streamed
+ // fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
return -1;
}
fp->offset = offset;
return 0;
- } else if (fp->type == KNF_TYPE_FTP || fp->type == KNF_TYPE_HTTP) {
- if (whence != SEEK_SET) { // FIXME: we can surely allow SEEK_CUR and SEEK_END in future
- fprintf(stderr, "[knet_seek] only SEEK_SET is supported for FTP/HTTP. Offset is unchanged.\n");
+ }
+ else if (fp->type == KNF_TYPE_FTP)
+ {
+ if (whence==SEEK_CUR)
+ fp->offset += off;
+ else if (whence==SEEK_SET)
+ fp->offset = off;
+ else if ( whence==SEEK_END)
+ fp->offset = fp->file_size+off;
+ fp->is_ready = 0;
+ return 0;
+ }
+ else if (fp->type == KNF_TYPE_HTTP)
+ {
+ if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future?
+ fprintf(stderr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n");
+ errno = ESPIPE;
return -1;
}
- fp->offset = off;
+ if (whence==SEEK_CUR)
+ fp->offset += off;
+ else if (whence==SEEK_SET)
+ fp->offset = off;
fp->is_ready = 0;
- return 0;
+ return fp->offset;
}
+ errno = EINVAL;
+ fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
return -1;
}
#define netwrite(fd, ptr, len) write(fd, ptr, len)
#define netclose(fd) close(fd)
#else
-#include <winsock.h>
+#include <winsock2.h>
#define netread(fd, ptr, len) recv(fd, ptr, len, 0)
#define netwrite(fd, ptr, len) send(fd, ptr, len, 0)
#define netclose(fd) closesocket(fd)
// the following are for FTP only
int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready;
- char *response, *retr;
+ char *response, *retr, *size_cmd;
int64_t seek_offset; // for lazy seek
+ int64_t file_size;
// the following are for HTTP only
char *path, *http_host;
This routine only sets ->offset and ->is_ready=0. It does not
communicate with the FTP server.
*/
- int knet_seek(knetFile *fp, off_t off, int whence);
+ off_t knet_seek(knetFile *fp, int64_t off, int whence);
int knet_close(knetFile *fp);
#ifdef __cplusplus
$q+=1;
}
if ($indeltype eq "-") {
- my $deletedbase = $2 if $string =~ /(\d+)\-([A-Z]+)/;
+ my $deletedbase = $2 if $string =~ /(\d+)\-([A-Za-z]+)/;
if ($deleteflag == 0 ) {
$mdtag.="^";
}
my $string = shift;
my $insert="";
my $indeltype;
- if ($string =~ /([A-Z]+)\>/) {
+ if ($string =~ /([A-Za-z]+)\>/) {
$indeltype=">";
$insert=$1;
} elsif ($string =~ /\-/) {
$indeltype="-";
- } elsif ($string =~ /\+([A-Z]+)/) {
+ } elsif ($string =~ /\+([A-Za-z]+)/) {
$indeltype="+";
$insert=$1;
}
next if $string =~ />/;
my $pos = $1 if $string =~ /^(\d+)/;
- if ($string =~ /\+([A-Z]+)/) {
+ if ($string =~ /\+([A-Za-z]+)/) {
$indeltype="+";
$insert = $1;
- }elsif ($string =~ /\-([A-Z]+)/) {
+ }elsif ($string =~ /\-([A-Za-z]+)/) {
$indeltype="-";
$insert = $1;
}
--- /dev/null
+#!/usr/bin/perl -w
+#
+# VCF specs: http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcfv3.2
+
+# Contact: pd3@sanger
+# Version: 2009-10-08
+
+use strict;
+use warnings;
+use Carp;
+
+my $opts = parse_params();
+do_pileup_to_vcf($opts);
+
+exit;
+
+#---------------
+
+sub error
+{
+ my (@msg) = @_;
+ if ( scalar @msg ) { croak(@msg); }
+ die
+ "Usage: sam2vcf.pl [OPTIONS] < in.pileup > out.vcf\n",
+ "Options:\n",
+ " -r, -refseq <file.fa> The reference sequence, required when indels are present.\n",
+ " -h, -?, --help This help message.\n",
+ "\n";
+}
+
+
+sub parse_params
+{
+ my %opts = ();
+
+ $opts{fh_in} = *STDIN;
+ $opts{fh_out} = *STDOUT;
+
+ while (my $arg=shift(@ARGV))
+ {
+ if ( $arg eq '-r' || $arg eq '--refseq' ) { $opts{refseq}=shift(@ARGV); next; }
+ if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
+
+ error("Unknown parameter \"$arg\". Run -h for help.\n");
+ }
+ return \%opts;
+}
+
+sub iupac_to_gtype
+{
+ my ($ref,$base) = @_;
+ my %iupac = (
+ 'K' => ['G','T'],
+ 'M' => ['A','C'],
+ 'S' => ['C','G'],
+ 'R' => ['A','G'],
+ 'W' => ['A','T'],
+ 'Y' => ['C','T'],
+ );
+ if ( !exists($iupac{$base}) )
+ {
+ if ( $ref eq $base ) { return ('.','0|0'); }
+ return ($base,'1|1');
+ }
+ my $gt = $iupac{$base};
+ if ( $$gt[0] eq $ref ) { return ($$gt[1],'0|1'); }
+ elsif ( $$gt[1] eq $ref ) { return ($$gt[0],'0|1'); }
+ return ("$$gt[0],$$gt[1]",'1|2');
+}
+
+
+sub parse_indel
+{
+ my ($cons) = @_;
+ if ( $cons=~/^-/ )
+ {
+ my $len = length($');
+ return "D$len";
+ }
+ elsif ( $cons=~/^\+/ ) { return "I$'"; }
+ elsif ( $cons eq '*' ) { return undef; }
+ error("FIXME: could not parse [$cons]\n");
+}
+
+
+# An example of the pileup format:
+# 1 3000011 C C 32 0 98 1 ^~, A
+# 1 3002155 * +T/+T 53 119 52 5 +T * 4 1 0
+# 1 3003094 * -TT/-TT 31 164 60 11 -TT * 5 6 0
+# 1 3073986 * */-AAAAAAAAAAAAAA 3 3 45 9 * -AAAAAAAAAAAAAA 7 2 0
+#
+sub do_pileup_to_vcf
+{
+ my ($opts) = @_;
+
+ my $fh_in = $$opts{fh_in};
+ my $fh_out = $$opts{fh_out};
+ my ($prev_chr,$prev_pos,$prev_ref);
+ my $refseq;
+
+ while (my $line=<$fh_in>)
+ {
+ chomp($line);
+ my ($chr,$pos,$ref,$cons,$cons_qual,$snp_qual,$rms_qual,$depth,@items) = split(/\t/,$line);
+
+ my ($alt,$gt);
+ if ( $ref eq '*' )
+ {
+ # An indel is involved.
+ if ($chr ne $prev_chr || $pos ne $prev_pos)
+ {
+ if ( !$$opts{refseq} ) { error("Cannot do indels without the reference.\n"); }
+ if ( !$refseq ) { $refseq = Fasta->new(file=>$$opts{refseq}); }
+ $ref = $refseq->get_base($chr,$pos);
+ }
+ else { $ref = $prev_ref; }
+
+ # One of the alleles can be a reference and it can come in arbitrary order
+ my ($al1,$al2) = split(m{/},$cons);
+ my $alt1 = parse_indel($al1);
+ my $alt2 = parse_indel($al2);
+ if ( !$alt1 && !$alt2 ) { error("FIXME: could not parse indel:\n", $line); }
+ if ( $alt1 && $alt2 && $alt1 eq $alt2 ) { $alt2=''; }
+ if ( !$alt1 )
+ {
+ $alt=$alt2;
+ $gt='0|1';
+ }
+ elsif ( !$alt2 )
+ {
+ $alt=$alt1;
+ $gt='0|1';
+ }
+ else
+ {
+ $alt="$alt1,$alt2";
+ $gt='1|2';
+ }
+ }
+ else
+ {
+ # SNP
+ ($alt,$gt) = iupac_to_gtype($ref,$cons);
+ }
+
+ print $fh_out "$chr\t$pos\t.\t$ref\t$alt\t$snp_qual\t0\t\tGT:GQ:DP\t$gt:$cons_qual:$depth\n";
+
+ $prev_ref = $ref;
+ $prev_pos = $pos;
+ $prev_chr = $chr;
+ }
+}
+
+
+#------------- Fasta --------------------
+#
+# Uses samtools to get a requested base from a fasta file. For efficiency, preloads
+# a chunk to memory. The size of the cached sequence can be controlled by the 'size'
+# parameter.
+#
+package Fasta;
+
+use strict;
+use warnings;
+use Carp;
+
+sub Fasta::new
+{
+ my ($class,@args) = @_;
+ my $self = @args ? {@args} : {};
+ if ( !$$self{file} ) { $self->throw(qq[Missing the parameter "file"\n]); }
+ $$self{chr} = undef;
+ $$self{from} = undef;
+ $$self{to} = undef;
+ if ( !$$self{size} ) { $$self{size}=10_000_000; }
+ bless $self, ref($class) || $class;
+ return $self;
+}
+
+sub read_chunk
+{
+ my ($self,$chr,$pos) = @_;
+ my $to = $pos + $$self{size};
+ my $cmd = "samtools faidx $$self{file} $chr:$pos-$to";
+ my @out = `$cmd`;
+ if ( $? ) { $self->throw("$cmd: $!"); }
+ my $line = shift(@out);
+ if ( !($line=~/^>$chr:(\d+)-(\d+)/) ) { $self->throw("Could not parse: $line"); }
+ $$self{chr} = $chr;
+ $$self{from} = $1;
+ $$self{to} = $2;
+ my $chunk = '';
+ while ($line=shift(@out))
+ {
+ chomp($line);
+ $chunk .= $line;
+ }
+ $$self{chunk} = $chunk;
+ return;
+}
+
+sub get_base
+{
+ my ($self,$chr,$pos) = @_;
+ if ( !$$self{chr} || $chr ne $$self{chr} || $pos<$$self{from} || $pos>$$self{to} )
+ {
+ $self->read_chunk($chr,$pos);
+ }
+ my $idx = $pos - $$self{from};
+ return substr($$self{chunk},$idx,1);
+}
+
+sub throw
+{
+ my ($self,@msg) = @_;
+ croak(@msg);
+}
my $command = shift(@ARGV);
my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter,
- unique=>\&unique, uniqcmp=>\&uniqcmp);
+ unique=>\&unique, uniqcmp=>\&uniqcmp, sra2hdr=>\&sra2hdr);
die("Unknown command \"$command\".\n") if (!defined($func{$command}));
&{$func{$command}};
# varFilter
#
+#
+# Filtration code:
+#
+# d low depth
+# D high depth
+# W too many SNPs in a window (SNP only)
+# G close to a high-quality indel (SNP only)
+# Q low RMS mapping quality (SNP only)
+# g close to another indel with higher quality (indel only)
+
sub varFilter {
my %opts = (d=>3, D=>100, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef);
getopts('pq:d:D:l:Q:w:W:N:G:', \%opts);
}
}
+#
+# sra2hdr
+#
+
+# This subroutine does not use an XML parser. It requires that the SRA
+# XML files are properly formated.
+sub sra2hdr {
+ my %opts = ();
+ getopts('', \%opts);
+ die("Usage: samtools.pl sra2hdr <SRA.prefix>\n") if (@ARGV == 0);
+ my $pre = $ARGV[0];
+ my $fh;
+ # read sample
+ my $sample = 'UNKNOWN';
+ open($fh, "$pre.sample.xml") || die;
+ while (<$fh>) {
+ $sample = $1 if (/<SAMPLE.*alias="([^"]+)"/i);
+ }
+ close($fh);
+ # read experiment
+ my (%exp2lib, $exp);
+ open($fh, "$pre.experiment.xml") || die;
+ while (<$fh>) {
+ if (/<EXPERIMENT.*accession="([^\s"]+)"/i) {
+ $exp = $1;
+ } elsif (/<LIBRARY_NAME>\s*(\S+)\s*<\/LIBRARY_NAME>/i) {
+ $exp2lib{$exp} = $1;
+ }
+ }
+ close($fh);
+ # read run
+ my ($run, @fn);
+ open($fh, "$pre.run.xml") || die;
+ while (<$fh>) {
+ if (/<RUN.*accession="([^\s"]+)"/i) {
+ $run = $1; @fn = ();
+ } elsif (/<EXPERIMENT_REF.*accession="([^\s"]+)"/i) {
+ print "\@RG\tID:$run\tSM:$sample\tLB:$exp2lib{$1}\n";
+ } elsif (/<FILE.*filename="([^\s"]+)"/i) {
+ push(@fn, $1);
+ } elsif (/<\/RUN>/i) {
+ if (@fn == 1) {
+ print STDERR "$fn[0]\t$run\n";
+ } else {
+ for (0 .. $#fn) {
+ print STDERR "$fn[$_]\t$run", "_", $_+1, "\n";
+ }
+ }
+ }
+ }
+ close($fh);
+}
+
#
# unique
#
#include <unistd.h>
#include "razf.h"
+
#if ZLIB_VERNUM < 0x1221
struct _gz_header_s {
int text;
}
#endif
+#ifdef _USE_KNETFILE
+static void load_zindex(RAZF *rz, knetFile *fp){
+#else
static void load_zindex(RAZF *rz, int fd){
+#endif
int32_t i, v32;
int is_be;
if(!rz->load_index) return;
if(rz->index == NULL) rz->index = malloc(sizeof(ZBlockIndex));
is_be = is_big_endian();
+#ifdef _USE_KNETFILE
+ knet_read(fp, &rz->index->size, sizeof(int));
+#else
read(fd, &rz->index->size, sizeof(int));
+#endif
if(!is_be) rz->index->size = byte_swap_4((uint32_t)rz->index->size);
rz->index->cap = rz->index->size;
v32 = rz->index->size / RZ_BIN_SIZE + 1;
rz->index->bin_offsets = malloc(sizeof(int64_t) * v32);
+#ifdef _USE_KNETFILE
+ knet_read(fp, rz->index->bin_offsets, sizeof(int64_t) * v32);
+#else
read(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
+#endif
rz->index->cell_offsets = malloc(sizeof(int) * rz->index->size);
+#ifdef _USE_KNETFILE
+ knet_read(fp, rz->index->cell_offsets, sizeof(int) * rz->index->size);
+#else
read(fd, rz->index->cell_offsets, sizeof(int) * rz->index->size);
+#endif
if(!is_be){
for(i=0;i<v32;i++) rz->index->bin_offsets[i] = byte_swap_8((uint64_t)rz->index->bin_offsets[i]);
for(i=0;i<rz->index->size;i++) rz->index->cell_offsets[i] = byte_swap_4((uint32_t)rz->index->cell_offsets[i]);
#endif
rz = calloc(1, sizeof(RAZF));
rz->mode = 'w';
+#ifdef _USE_KNETFILE
+ rz->x.fpw = fd;
+#else
rz->filedes = fd;
+#endif
rz->stream = calloc(sizeof(z_stream), 1);
rz->inbuf = malloc(RZ_BUFFER_SIZE);
rz->outbuf = malloc(RZ_BUFFER_SIZE);
deflate(rz->stream, Z_NO_FLUSH);
rz->out += tout - rz->stream->avail_out;
if(rz->stream->avail_out) break;
+#ifdef _USE_KNETFILE
+ write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#else
write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#endif
rz->stream->avail_out = RZ_BUFFER_SIZE;
rz->stream->next_out = rz->outbuf;
if(rz->stream->avail_in == 0) break;
rz->buf_off = rz->buf_len = 0;
}
if(rz->stream->avail_out){
+#ifdef _USE_KNETFILE
+ write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#else
write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#endif
rz->stream->avail_out = RZ_BUFFER_SIZE;
rz->stream->next_out = rz->outbuf;
}
deflate(rz->stream, Z_FULL_FLUSH);
rz->out += tout - rz->stream->avail_out;
if(rz->stream->avail_out == 0){
+#ifdef _USE_KNETFILE
+ write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#else
write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#endif
rz->stream->avail_out = RZ_BUFFER_SIZE;
rz->stream->next_out = rz->outbuf;
} else break;
deflate(rz->stream, Z_FINISH);
rz->out += tout - rz->stream->avail_out;
if(rz->stream->avail_out < RZ_BUFFER_SIZE){
+#ifdef _USE_KNETFILE
+ write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#else
write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
+#endif
rz->stream->avail_out = RZ_BUFFER_SIZE;
rz->stream->next_out = rz->outbuf;
} else break;
return n;
}
+#ifdef _USE_KNETFILE
+static RAZF* razf_open_r(knetFile *fp, int _load_index){
+#else
static RAZF* razf_open_r(int fd, int _load_index){
+#endif
RAZF *rz;
int ext_off, ext_len;
int n, is_be, ret;
int64_t end;
unsigned char c[] = "RAZF";
+ rz = calloc(1, sizeof(RAZF));
+ rz->mode = 'r';
+#ifdef _USE_KNETFILE
+ rz->x.fpr = fp;
+#else
#ifdef _WIN32
setmode(fd, O_BINARY);
#endif
- rz = calloc(1, sizeof(RAZF));
- rz->mode = 'r';
rz->filedes = fd;
+#endif
rz->stream = calloc(sizeof(z_stream), 1);
rz->inbuf = malloc(RZ_BUFFER_SIZE);
rz->outbuf = malloc(RZ_BUFFER_SIZE);
rz->end = rz->src_end = 0x7FFFFFFFFFFFFFFFLL;
+#ifdef _USE_KNETFILE
+ n = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
+#else
n = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE);
+#endif
ret = _read_gz_header(rz->inbuf, n, &ext_off, &ext_len);
if(ret == 0){
PLAIN_FILE:
}
rz->load_index = _load_index;
rz->file_type = FILE_TYPE_RZ;
+#ifdef _USE_KNETFILE
+ if(knet_seek(fp, -16, SEEK_END) == -1){
+#else
if(lseek(fd, -16, SEEK_END) == -1){
+#endif
UNSEEKABLE:
rz->seekable = 0;
rz->index = NULL;
} else {
is_be = is_big_endian();
rz->seekable = 1;
+#ifdef _USE_KNETFILE
+ knet_read(fp, &end, sizeof(int64_t));
+#else
read(fd, &end, sizeof(int64_t));
+#endif
if(!is_be) rz->src_end = (int64_t)byte_swap_8((uint64_t)end);
else rz->src_end = end;
+
+#ifdef _USE_KNETFILE
+ knet_read(fp, &end, sizeof(int64_t));
+#else
read(fd, &end, sizeof(int64_t));
+#endif
if(!is_be) rz->end = (int64_t)byte_swap_8((uint64_t)end);
else rz->end = end;
if(n > rz->end){
n = rz->end;
}
if(rz->end > rz->src_end){
+#ifdef _USE_KNETFILE
+ knet_seek(fp, rz->in, SEEK_SET);
+#else
lseek(fd, rz->in, SEEK_SET);
+#endif
goto UNSEEKABLE;
}
+#ifdef _USE_KNETFILE
+ knet_seek(fp, rz->end, SEEK_SET);
+ if(knet_tell(fp) != rz->end){
+ knet_seek(fp, rz->in, SEEK_SET);
+#else
if(lseek(fd, rz->end, SEEK_SET) != rz->end){
lseek(fd, rz->in, SEEK_SET);
+#endif
goto UNSEEKABLE;
}
+#ifdef _USE_KNETFILE
+ load_zindex(rz, fp);
+ knet_seek(fp, n, SEEK_SET);
+#else
load_zindex(rz, fd);
lseek(fd, n, SEEK_SET);
+#endif
}
return rz;
}
+#ifdef _USE_KNETFILE
+RAZF* razf_dopen(int fd, const char *mode){
+ if (strstr(mode, "r")) fprintf(stderr,"[razf_dopen] implement me\n");
+ else if(strstr(mode, "w")) return razf_open_w(fd);
+ return NULL;
+}
+
+RAZF* razf_dopen2(int fd, const char *mode)
+{
+ fprintf(stderr,"[razf_dopen2] implement me\n");
+ return NULL;
+}
+#else
RAZF* razf_dopen(int fd, const char *mode){
if(strstr(mode, "r")) return razf_open_r(fd, 1);
else if(strstr(mode, "w")) return razf_open_w(fd);
else if(strstr(mode, "w")) return razf_open_w(fd);
else return NULL;
}
+#endif
static inline RAZF* _razf_open(const char *filename, const char *mode, int _load_index){
int fd;
RAZF *rz;
if(strstr(mode, "r")){
+#ifdef _USE_KNETFILE
+ knetFile *fd = knet_open(filename, "r");
+ if (fd == 0) {
+ fprintf(stderr, "[_razf_open] fail to open %s\n", filename);
+ return NULL;
+ }
+#else
#ifdef _WIN32
fd = open(filename, O_RDONLY | O_BINARY);
#else
fd = open(filename, O_RDONLY);
#endif
+#endif
+ if(fd < 0) return NULL;
rz = razf_open_r(fd, _load_index);
} else if(strstr(mode, "w")){
#ifdef _WIN32
- fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC | O_BINARY, 0644);
+ fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC | O_BINARY, 0666);
#else
- fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC, 0644);
+ fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC, 0666);
#endif
+ if(fd < 0) return NULL;
rz = razf_open_w(fd);
} else return NULL;
return rz;
switch(rz->file_type){
case FILE_TYPE_PLAIN:
if(rz->end == 0x7fffffffffffffffLL){
+#ifdef _USE_KNETFILE
+ if(knet_seek(rz->x.fpr, 0, SEEK_CUR) == -1) return 0;
+ n = knet_tell(rz->x.fpr);
+ knet_seek(rz->x.fpr, 0, SEEK_END);
+ rz->end = knet_tell(rz->x.fpr);
+ knet_seek(rz->x.fpr, n, SEEK_SET);
+#else
if((n = lseek(rz->filedes, 0, SEEK_CUR)) == -1) return 0;
rz->end = lseek(rz->filedes, 0, SEEK_END);
lseek(rz->filedes, n, SEEK_SET);
+#endif
}
*u_size = *c_size = rz->end;
return 1;
int ret, tin;
if(rz->z_eof || rz->z_err) return 0;
if (rz->file_type == FILE_TYPE_PLAIN) {
+#ifdef _USE_KNETFILE
+ ret = knet_read(rz->x.fpr, data, size);
+#else
ret = read(rz->filedes, data, size);
+#endif
if (ret == 0) rz->z_eof = 1;
return ret;
}
if(rz->stream->avail_in == 0){
if(rz->in >= rz->end){ rz->z_eof = 1; break; }
if(rz->end - rz->in < RZ_BUFFER_SIZE){
+#ifdef _USE_KNETFILE
+ rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, rz->end -rz->in);
+#else
rz->stream->avail_in = read(rz->filedes, rz->inbuf, rz->end -rz->in);
+#endif
} else {
+#ifdef _USE_KNETFILE
+ rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
+#else
rz->stream->avail_in = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE);
+#endif
}
if(rz->stream->avail_in == 0){
rz->z_eof = 1;
ret = inflate(rz->stream, Z_BLOCK);
rz->in += tin - rz->stream->avail_in;
if(ret == Z_NEED_DICT || ret == Z_MEM_ERROR || ret == Z_DATA_ERROR){
- fprintf(stderr, "[_razf_read] inflate error: %d (at %s:%d)\n", ret, __FILE__, __LINE__);
+ fprintf(stderr, "[_razf_read] inflate error: %d %s (at %s:%d)\n", ret, rz->stream->msg ? rz->stream->msg : "", __FILE__, __LINE__);
rz->z_err = 1;
break;
}
}
if(rz->buf_flush) continue;
rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE);
- if(rz->z_eof) break;
+ if(rz->z_eof || rz->z_err) break;
}
rz->out += ori_size - size;
return ori_size - size;
}
static void _razf_reset_read(RAZF *rz, int64_t in, int64_t out){
+#ifdef _USE_KNETFILE
+ knet_seek(rz->x.fpr, in, SEEK_SET);
+#else
lseek(rz->filedes, in, SEEK_SET);
+#endif
rz->in = in;
rz->out = out;
rz->block_pos = in;
if(rz->file_type == FILE_TYPE_PLAIN){
rz->buf_off = rz->buf_len = 0;
pos = block_start + block_offset;
+#ifdef _USE_KNETFILE
+ knet_seek(rz->x.fpr, pos, SEEK_SET);
+ pos = knet_tell(rz->x.fpr);
+#else
pos = lseek(rz->filedes, pos, SEEK_SET);
+#endif
rz->out = rz->in = pos;
return pos;
}
if (where == SEEK_CUR) pos += rz->out;
else if (where == SEEK_END) pos += rz->src_end;
if(rz->file_type == FILE_TYPE_PLAIN){
+#ifdef _USE_KNETFILE
+ knet_seek(rz->x.fpr, pos, SEEK_SET);
+ seek_pos = knet_tell(rz->x.fpr);
+#else
seek_pos = lseek(rz->filedes, pos, SEEK_SET);
+#endif
rz->buf_off = rz->buf_len = 0;
rz->out = rz->in = seek_pos;
return seek_pos;
#ifndef _RZ_READONLY
razf_end_flush(rz);
deflateEnd(rz->stream);
+#ifdef _USE_KNETFILE
+ save_zindex(rz, rz->x.fpw);
+ if(is_big_endian()){
+ write(rz->x.fpw, &rz->in, sizeof(int64_t));
+ write(rz->x.fpw, &rz->out, sizeof(int64_t));
+ } else {
+ uint64_t v64 = byte_swap_8((uint64_t)rz->in);
+ write(rz->x.fpw, &v64, sizeof(int64_t));
+ v64 = byte_swap_8((uint64_t)rz->out);
+ write(rz->x.fpw, &v64, sizeof(int64_t));
+ }
+#else
save_zindex(rz, rz->filedes);
if(is_big_endian()){
write(rz->filedes, &rz->in, sizeof(int64_t));
v64 = byte_swap_8((uint64_t)rz->out);
write(rz->filedes, &v64, sizeof(int64_t));
}
+#endif
#endif
} else if(rz->mode == 'r'){
if(rz->stream) inflateEnd(rz->stream);
free(rz->index);
}
free(rz->stream);
+#ifdef _USE_KNETFILE
+ if (rz->mode == 'r')
+ knet_close(rz->x.fpr);
+ if (rz->mode == 'w')
+ close(rz->x.fpw);
+#else
close(rz->filedes);
+#endif
free(rz);
}
#include <stdio.h>
#include "zlib.h"
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
#if ZLIB_VERNUM < 0x1221
#define _RZ_READONLY
struct _gz_header_s;
char mode; /* 'w' : write mode; 'r' : read mode */
int file_type;
/* plain file or rz file, razf_read support plain file as input too, in this case, razf_read work as buffered fread */
+#ifdef _USE_KNETFILE
+ union {
+ knetFile *fpr;
+ int fpw;
+ } x;
+#else
int filedes; /* the file descriptor */
+#endif
z_stream *stream;
ZBlockIndex *index;
int64_t in, out, end, src_end;
int fd = -1;
char c;
if (!is_forced) {
- if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0644)) < 0 && errno == EEXIST) {
+ if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
printf("razip: %s already exists; do you wish to overwrite (y or n)? ", fn);
scanf("%c", &c);
if (c != 'Y' && c != 'y') {
}
}
if (fd < 0) {
- if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0644)) < 0) {
+ if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) {
fprintf(stderr, "razip: %s: Fail to write\n", fn);
exit(1);
}
int i;
h = bam_header_init();
*h = *h0;
- h->hash = 0;
+ h->hash = h->dict = h->rg2lib = 0;
h->text = (char*)calloc(h->l_text + 1, 1);
memcpy(h->text, h0->text, h->l_text);
h->target_len = (uint32_t*)calloc(h->n_targets, 4);
h->target_len[i] = h0->target_len[i];
h->target_name[i] = strdup(h0->target_name[i]);
}
- if (h0->rg2lib) h->rg2lib = bam_strmap_dup(h0->rg2lib);
return h;
}
static void append_header_text(bam_header_t *header, char* text, int len)
fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
} else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
}
- sam_header_parse_rg(fp->header);
} else if (mode[0] == 'w') { // write
fp->header = bam_header_dup((const bam_header_t*)aux);
if (mode[1] == 'b') { // binary
--- /dev/null
+#include "sam_header.h"
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <stdarg.h>
+
+#include "khash.h"
+KHASH_MAP_INIT_STR(str, const char *)
+
+struct _HeaderList
+{
+ struct _HeaderList *next;
+ void *data;
+};
+typedef struct _HeaderList list_t;
+typedef list_t HeaderDict;
+
+typedef struct
+{
+ char key[2];
+ char *value;
+}
+HeaderTag;
+
+typedef struct
+{
+ char type[2];
+ list_t *tags;
+}
+HeaderLine;
+
+const char *o_hd_tags[] = {"SO","GO",NULL};
+const char *r_hd_tags[] = {"VN",NULL};
+
+const char *o_sq_tags[] = {"AS","M5","UR","SP",NULL};
+const char *r_sq_tags[] = {"SN","LN",NULL};
+const char *u_sq_tags[] = {"SN",NULL};
+
+const char *o_rg_tags[] = {"LB","DS","PU","PI","CN","DT","PL",NULL};
+const char *r_rg_tags[] = {"ID",NULL};
+const char *u_rg_tags[] = {"ID",NULL};
+
+const char *o_pg_tags[] = {"VN","CL",NULL};
+const char *r_pg_tags[] = {"ID",NULL};
+
+const char *types[] = {"HD","SQ","RG","PG","CO",NULL};
+const char **optional_tags[] = {o_hd_tags,o_sq_tags,o_rg_tags,o_pg_tags,NULL,NULL};
+const char **required_tags[] = {r_hd_tags,r_sq_tags,r_rg_tags,r_pg_tags,NULL,NULL};
+const char **unique_tags[] = {NULL, u_sq_tags,u_rg_tags,NULL,NULL,NULL};
+
+
+static void debug(const char *format, ...)
+{
+ va_list ap;
+ va_start(ap, format);
+ vfprintf(stderr, format, ap);
+ va_end(ap);
+}
+
+static list_t *list_append(list_t *root, void *data)
+{
+ list_t *l = root;
+ while (l && l->next)
+ l = l->next;
+ if ( l )
+ {
+ l->next = malloc(sizeof(list_t));
+ l = l->next;
+ }
+ else
+ {
+ l = malloc(sizeof(list_t));
+ root = l;
+ }
+ l->data = data;
+ l->next = NULL;
+ return root;
+}
+
+static void list_free(list_t *root)
+{
+ list_t *l = root;
+ while (root)
+ {
+ l = root;
+ root = root->next;
+ free(l);
+ }
+}
+
+
+
+// Look for a tag "XY" in a predefined const char *[] array.
+static int tag_exists(const char *tag, const char **tags)
+{
+ int itag=0;
+ if ( !tags ) return -1;
+ while ( tags[itag] )
+ {
+ if ( tags[itag][0]==tag[0] && tags[itag][1]==tag[1] ) return itag;
+ itag++;
+ }
+ return -1;
+}
+
+
+
+// Mimics the behaviour of getline, except it returns pointer to the next chunk of the text
+// or NULL if everything has been read. The lineptr should be freed by the caller. The
+// newline character is stripped.
+static const char *nextline(char **lineptr, size_t *n, const char *text)
+{
+ int len;
+ const char *to = text;
+
+ if ( !*to ) return NULL;
+
+ while ( *to && *to!='\n' && *to!='\r' ) to++;
+ len = to - text + 1;
+
+ if ( *to )
+ {
+ // Advance the pointer for the next call
+ if ( *to=='\n' ) to++;
+ else if ( *to=='\r' && *(to+1)=='\n' ) to+=2;
+ }
+ if ( !len )
+ return to;
+
+ if ( !*lineptr )
+ {
+ *lineptr = malloc(len);
+ *n = len;
+ }
+ else if ( *n<len )
+ {
+ *lineptr = realloc(*lineptr, len);
+ *n = len;
+ }
+ if ( !*lineptr ) {
+ debug("[nextline] Insufficient memory!\n");
+ return 0;
+ }
+
+ memcpy(*lineptr,text,len);
+ (*lineptr)[len-1] = 0;
+
+ return to;
+}
+
+// name points to "XY", value_from points to the first character of the value string and
+// value_to points to the last character of the value string.
+static HeaderTag *new_tag(const char *name, const char *value_from, const char *value_to)
+{
+ HeaderTag *tag = malloc(sizeof(HeaderTag));
+ int len = value_to-value_from+1;
+
+ tag->key[0] = name[0];
+ tag->key[1] = name[1];
+ tag->value = malloc(len+1);
+ memcpy(tag->value,value_from,len+1);
+ tag->value[len] = 0;
+ return tag;
+}
+
+static HeaderTag *header_line_has_tag(HeaderLine *hline, const char *key)
+{
+ list_t *tags = hline->tags;
+ while (tags)
+ {
+ HeaderTag *tag = tags->data;
+ if ( tag->key[0]==key[0] && tag->key[1]==key[1] ) return tag;
+ tags = tags->next;
+ }
+ return NULL;
+}
+
+
+// Return codes:
+// 0 .. different types or unique tags differ or conflicting tags, cannot be merged
+// 1 .. all tags identical -> no need to merge, drop one
+// 2 .. the unique tags match and there are some conflicting tags (same tag, different value) -> error, cannot be merged nor duplicated
+// 3 .. there are some missing complementary tags and no unique conflict -> can be merged into a single line
+static int sam_header_compare_lines(HeaderLine *hline1, HeaderLine *hline2)
+{
+ HeaderTag *t1, *t2;
+
+ if ( hline1->type[0]!=hline2->type[0] || hline1->type[1]!=hline2->type[1] )
+ return 0;
+
+ int itype = tag_exists(hline1->type,types);
+ if ( itype==-1 ) {
+ debug("[sam_header_compare_lines] Unknown type [%c%c]\n", hline1->type[0],hline1->type[1]);
+ return -1; // FIXME (lh3): error; I do not know how this will be handled in Petr's code
+ }
+
+ if ( unique_tags[itype] )
+ {
+ t1 = header_line_has_tag(hline1,unique_tags[itype][0]);
+ t2 = header_line_has_tag(hline2,unique_tags[itype][0]);
+ if ( !t1 || !t2 ) // this should never happen, the unique tags are required
+ return 2;
+
+ if ( strcmp(t1->value,t2->value) )
+ return 0; // the unique tags differ, cannot be merged
+ }
+ if ( !required_tags[itype] && !optional_tags[itype] )
+ {
+ t1 = hline1->tags->data;
+ t2 = hline2->tags->data;
+ if ( !strcmp(t1->value,t2->value) ) return 1; // identical comments
+ return 0;
+ }
+
+ int missing=0, itag=0;
+ while ( required_tags[itype] && required_tags[itype][itag] )
+ {
+ t1 = header_line_has_tag(hline1,required_tags[itype][itag]);
+ t2 = header_line_has_tag(hline2,required_tags[itype][itag]);
+ if ( !t1 && !t2 )
+ return 2; // this should never happen
+ else if ( !t1 || !t2 )
+ missing = 1; // there is some tag missing in one of the hlines
+ else if ( strcmp(t1->value,t2->value) )
+ {
+ if ( unique_tags[itype] )
+ return 2; // the lines have a matching unique tag but have a conflicting tag
+
+ return 0; // the lines contain conflicting tags, cannot be merged
+ }
+ itag++;
+ }
+ itag = 0;
+ while ( optional_tags[itype] && optional_tags[itype][itag] )
+ {
+ t1 = header_line_has_tag(hline1,optional_tags[itype][itag]);
+ t2 = header_line_has_tag(hline2,optional_tags[itype][itag]);
+ if ( !t1 && !t2 )
+ {
+ itag++;
+ continue;
+ }
+ if ( !t1 || !t2 )
+ missing = 1; // there is some tag missing in one of the hlines
+ else if ( strcmp(t1->value,t2->value) )
+ {
+ if ( unique_tags[itype] )
+ return 2; // the lines have a matching unique tag but have a conflicting tag
+
+ return 0; // the lines contain conflicting tags, cannot be merged
+ }
+ itag++;
+ }
+ if ( missing ) return 3; // there are some missing complementary tags with no conflicts, can be merged
+ return 1;
+}
+
+
+static HeaderLine *sam_header_line_clone(const HeaderLine *hline)
+{
+ list_t *tags;
+ HeaderLine *out = malloc(sizeof(HeaderLine));
+ out->type[0] = hline->type[0];
+ out->type[1] = hline->type[1];
+ out->tags = NULL;
+
+ tags = hline->tags;
+ while (tags)
+ {
+ HeaderTag *old = tags->data;
+
+ HeaderTag *new = malloc(sizeof(HeaderTag));
+ new->key[0] = old->key[0];
+ new->key[1] = old->key[1];
+ new->value = strdup(old->value);
+ out->tags = list_append(out->tags, new);
+
+ tags = tags->next;
+ }
+ return out;
+}
+
+static int sam_header_line_merge_with(HeaderLine *out_hline, const HeaderLine *tmpl_hline)
+{
+ list_t *tmpl_tags;
+
+ if ( out_hline->type[0]!=tmpl_hline->type[0] || out_hline->type[1]!=tmpl_hline->type[1] )
+ return 0;
+
+ tmpl_tags = tmpl_hline->tags;
+ while (tmpl_tags)
+ {
+ HeaderTag *tmpl_tag = tmpl_tags->data;
+ HeaderTag *out_tag = header_line_has_tag(out_hline, tmpl_tag->key);
+ if ( !out_tag )
+ {
+ HeaderTag *tag = malloc(sizeof(HeaderTag));
+ tag->key[0] = tmpl_tag->key[0];
+ tag->key[1] = tmpl_tag->key[1];
+ tag->value = strdup(tmpl_tag->value);
+ out_hline->tags = list_append(out_hline->tags,tag);
+ }
+ tmpl_tags = tmpl_tags->next;
+ }
+ return 1;
+}
+
+
+static HeaderLine *sam_header_line_parse(const char *headerLine)
+{
+ HeaderLine *hline;
+ HeaderTag *tag;
+ const char *from, *to;
+ from = headerLine;
+
+ if ( *from != '@' ) {
+ debug("[sam_header_line_parse] expected '@', got [%s]\n", headerLine);
+ return 0;
+ }
+ to = ++from;
+
+ while (*to && *to!='\t') to++;
+ if ( to-from != 2 ) {
+ debug("[sam_header_line_parse] expected '@XY', got [%s]\n", headerLine);
+ return 0;
+ }
+
+ hline = malloc(sizeof(HeaderLine));
+ hline->type[0] = from[0];
+ hline->type[1] = from[1];
+ hline->tags = NULL;
+
+ int itype = tag_exists(hline->type, types);
+
+ from = to;
+ while (*to && *to=='\t') to++;
+ if ( to-from != 1 ) {
+ debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
+ return 0;
+ }
+ from = to;
+ while (*from)
+ {
+ while (*to && *to!='\t') to++;
+
+ if ( !required_tags[itype] && !optional_tags[itype] )
+ tag = new_tag(" ",from,to-1);
+ else
+ tag = new_tag(from,from+3,to-1);
+
+ if ( header_line_has_tag(hline,tag->key) )
+ debug("The tag '%c%c' present (at least) twice on line [%s]\n", tag->key[0],tag->key[1], headerLine);
+ hline->tags = list_append(hline->tags, tag);
+
+ from = to;
+ while (*to && *to=='\t') to++;
+ if ( *to && to-from != 1 ) {
+ debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
+ return 0;
+ }
+
+ from = to;
+ }
+ return hline;
+}
+
+
+// Must be of an existing type, all tags must be recognised and all required tags must be present
+static int sam_header_line_validate(HeaderLine *hline)
+{
+ list_t *tags;
+ HeaderTag *tag;
+ int itype, itag;
+
+ // Is the type correct?
+ itype = tag_exists(hline->type, types);
+ if ( itype==-1 )
+ {
+ debug("The type [%c%c] not recognised.\n", hline->type[0],hline->type[1]);
+ return 0;
+ }
+
+ // Has all required tags?
+ itag = 0;
+ while ( required_tags[itype] && required_tags[itype][itag] )
+ {
+ if ( !header_line_has_tag(hline,required_tags[itype][itag]) )
+ {
+ debug("The tag [%c%c] required for [%c%c] not present.\n", required_tags[itype][itag][0],required_tags[itype][itag][1],
+ hline->type[0],hline->type[1]);
+ return 0;
+ }
+ itag++;
+ }
+
+ // Are all tags recognised?
+ tags = hline->tags;
+ while ( tags )
+ {
+ tag = tags->data;
+ if ( !tag_exists(tag->key,required_tags[itype]) && !tag_exists(tag->key,optional_tags[itype]) )
+ {
+ debug("Unknown tag [%c%c] for [%c%c].\n", tag->key[0],tag->key[1], hline->type[0],hline->type[1]);
+ return 0;
+ }
+ tags = tags->next;
+ }
+
+ return 1;
+}
+
+
+static void print_header_line(FILE *fp, HeaderLine *hline)
+{
+ list_t *tags = hline->tags;
+ HeaderTag *tag;
+
+ fprintf(fp, "@%c%c", hline->type[0],hline->type[1]);
+ while (tags)
+ {
+ tag = tags->data;
+
+ fprintf(fp, "\t");
+ if ( tag->key[0]!=' ' || tag->key[1]!=' ' )
+ fprintf(fp, "%c%c:", tag->key[0],tag->key[1]);
+ fprintf(fp, "%s", tag->value);
+
+ tags = tags->next;
+ }
+ fprintf(fp,"\n");
+}
+
+
+static void sam_header_line_free(HeaderLine *hline)
+{
+ list_t *tags = hline->tags;
+ while (tags)
+ {
+ HeaderTag *tag = tags->data;
+ free(tag->value);
+ free(tag);
+ tags = tags->next;
+ }
+ list_free(hline->tags);
+ free(hline);
+}
+
+void sam_header_free(void *_header)
+{
+ HeaderDict *header = (HeaderDict*)_header;
+ list_t *hlines = header;
+ while (hlines)
+ {
+ sam_header_line_free(hlines->data);
+ hlines = hlines->next;
+ }
+ list_free(header);
+}
+
+HeaderDict *sam_header_clone(const HeaderDict *dict)
+{
+ HeaderDict *out = NULL;
+ while (dict)
+ {
+ HeaderLine *hline = dict->data;
+ out = list_append(out, sam_header_line_clone(hline));
+ dict = dict->next;
+ }
+ return out;
+}
+
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