X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=ChangeLog;h=dd62b49ded4f58206aa19574ffb9e473ca3283da;hp=f8456a3e61f1e731343c53fbb0aa859751332282;hb=6a0c6f060a60789b48e10a72b1381f6e54599302;hpb=e3b3a0177339fb8c099346986e965e3bd5b85999

diff --git a/ChangeLog b/ChangeLog
index f8456a3..dd62b49 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,151 @@
+------------------------------------------------------------------------
+r844 | lh3lh3 | 2010-11-19 23:16:08 -0500 (Fri, 19 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/prob1.c
+   M /trunk/samtools/bcftools/prob1.h
+
+ * samtools-0.1.10-9 (r844)
+ * added the "folded" or reference-free mode for variant calling
+
+------------------------------------------------------------------------
+r843 | lh3lh3 | 2010-11-19 22:26:36 -0500 (Fri, 19 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/bam_sort.c
+
+In merging, if -R is specified, do not abort if the sequence dictionary is different.
+
+------------------------------------------------------------------------
+r842 | jmarshall | 2010-11-19 21:24:28 -0500 (Fri, 19 Nov 2010) | 5 lines
+Changed paths:
+   M /trunk/samtools/bam_sort.c
+
+When merging BAM headers, compare the list of target reference sequences
+strictly (and fail/abort if there is a mismatch), but allow one list to be a
+prefix of the other.  (i.e., check that the lists are identical up until the
+shorter runs out, and add the excess targets from the longer to the output.)
+
+------------------------------------------------------------------------
+r841 | lh3lh3 | 2010-11-19 14:49:27 -0500 (Fri, 19 Nov 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam_index.c
+   M /trunk/samtools/bam_pileup.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10 (r841)
+ * fixed a bug in pileup when the first CIGAR operation is D
+ * fixed a bug in view with range query
+
+------------------------------------------------------------------------
+r840 | lh3lh3 | 2010-11-19 13:45:51 -0500 (Fri, 19 Nov 2010) | 10 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10-4 (r840)
+
+ * drop the MNP caller. It is slow while does not diliver too much
+   benefit. Possibly I will work on it in future given more time.
+
+ * there is a segfault in pileup 
+
+ * someone has reported segfault from view/index/sort
+
+
+------------------------------------------------------------------------
+r839 | lh3lh3 | 2010-11-18 17:30:11 -0500 (Thu, 18 Nov 2010) | 9 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10-6 (r839)
+
+ * call MNPs without realignment because it seems to me that it is not
+   worthwhile to significantly slow down SNP calling.
+
+ * the result looks quite different from the previous version. I have
+   work to do...
+
+
+------------------------------------------------------------------------
+r838 | lh3lh3 | 2010-11-18 11:26:09 -0500 (Thu, 18 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/knetfile.c
+
+Apply a patch by Rob Davis, which improves fault detection.
+
+------------------------------------------------------------------------
+r836 | lh3lh3 | 2010-11-18 11:09:23 -0500 (Thu, 18 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-r836
+ * initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)
+
+------------------------------------------------------------------------
+r835 | lh3lh3 | 2010-11-18 00:25:13 -0500 (Thu, 18 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+ * modify the filtering rule: also filter SNPs around filtered indels
+ * added MNP filter
+
+------------------------------------------------------------------------
+r834 | lh3lh3 | 2010-11-17 23:13:52 -0500 (Wed, 17 Nov 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10-4 (r834)
+ * fixed a silly bug in printing MNP
+ * restrict to at most 1 alternative allele
+
+------------------------------------------------------------------------
+r833 | lh3lh3 | 2010-11-17 21:58:58 -0500 (Wed, 17 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bamtk.c
+
+fixed a bug in printing MNPs
+
+------------------------------------------------------------------------
+r832 | lh3lh3 | 2010-11-17 21:47:20 -0500 (Wed, 17 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+
+minor change to how seqQ is applied
+
+------------------------------------------------------------------------
+r831 | lh3lh3 | 2010-11-17 21:41:12 -0500 (Wed, 17 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10 (r831)
+ * initial MNP caller
+
+------------------------------------------------------------------------
+r829 | lh3lh3 | 2010-11-16 23:14:15 -0500 (Tue, 16 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/bamtk.c
+
+Release samtools-0.1.10 (r829)
+
 ------------------------------------------------------------------------
 r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines
 Changed paths: