--- /dev/null
+Notes on how to test tabix
+──────────────────────────
+
+The tabix package contains example data to test the tabix program. It is
+already compressed and indexed. The following instruction decompress,
+recompress, re-index and test the example data.
+
+# Create a temporary file
+TABIXDATA=$(mktemp)
+
+# Uncompress example data
+zcat /usr/share/doc/tabix/examples/example.gtf.gz > $TABIXDATA
+
+# Compress example data with bgzip
+bgzip $TABIXDATA
+
+# Index with tabix
+tabix $TABIXDATA.gz
+
+# Extract with tabix the he features on chromosome 1 whose coordinates overlap
+# the interval 150,309–150,309.
+tabix $TABIXDATA.gz chr1:150309-150309 > $TABIXDATA.out
+
+# Reference result at the bottom of this file
+grep H\AVANA /usr/share/doc/tabix/README.test > $TABIXDATA.ref
+
+# No difference ?
+diff $TABIXDATA.ref $TABIXDATA.out
+
+# Clean
+rm $TABIXDATA.gz $TABIXDATA.gz.tbi $TABIXDATA.out $TABIXDATA.ref
+
+ -- Charles Plessy <plessy@debian.org> Tue, 10 May 2011 19:12:19 +0900
+
+
+
+chr1 HAVANA exon 150309 150553 . + . gene_id "ENSG00000241599"; transcript_id "ENST00000496488"; gene_type "processed_transcript"; gene_status "KNOWN"; gene_name "AL627309.12"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "AL627309.12-201"; level 2; havana_gene "OTTHUMG00000002525"; havana_transcript "OTTHUMT00000007169";
+chr1 HAVANA gene 150309 151388 . + . gene_id "ENSG00000241599"; transcript_id "ENSG00000241599"; gene_type "processed_transcript"; gene_status "KNOWN"; gene_name "AL627309.12"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "AL627309.12"; level 2; havana_gene "OTTHUMG00000002525";
+chr1 HAVANA transcript 150309 151388 . + . gene_id "ENSG00000241599"; transcript_id "ENST00000496488"; gene_type "processed_transcript"; gene_status "KNOWN"; gene_name "AL627309.12"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "AL627309.12-201"; level 2; havana_gene "OTTHUMG00000002525"; havana_transcript "OTTHUMT00000007169";
--- /dev/null
+tabix (0.2.5-3) unstable; urgency=low
+
+ * debian/patches/use-dpkg-buildflags.patch: Really enable hardening
+ build flags (Thanks for the patch to Simon Ruderich <simon@ruderich.org>)
+ Closes: #670759
+ * debian/patches/ld-as-needed.patch: Enable building with --as-needed
+ (Thanks to David Shorten <dpshorten@gmail.com> for the patch)
+ Closes: #632150
+
+ -- Andreas Tille <tille@debian.org> Fri, 11 May 2012 13:32:56 +0200
+
+tabix (0.2.5-2) unstable; urgency=low
+
+ [ Charles Plessy ]
+ 7a09003 Added metadata about Upstream in debian/upstream.
+ 1a85d96 Refreshed Debian copyright file
+ 9c70833 Include 7 digits of the commit ID in the changelog entry.
+
+ [ Andreas Tille ]
+ * debian/patches/count-set-but-not-used.patch: uncomment unused
+ variable
+ Closes: #626267
+ * debian/control:
+ - Standards-Version: 3.9.3 (no changes needed)
+ - removed cdbs from Build-Depends
+ * debian/rules: Switched to dh to easily enable hardening flags
+ * debhelper 9 (control+compat) to enable building with hardening
+ flags
+ * debian/patches/use-dpkg-buildflags.patch: Regard hardening flags
+ * debian/watch: Use sf.net redirector
+
+ -- Andreas Tille <tille@debian.org> Wed, 25 Apr 2012 17:02:10 +0200
+
+tabix (0.2.5-1) unstable; urgency=low
+
+ * New upstream release.
+ * Added debian/README.test to explain how to test tabix and bgzip.
+
+ -- Charles Plessy <plessy@debian.org> Tue, 10 May 2011 19:42:07 +0900
+
+tabix (0.2.4-1) unstable; urgency=low
+
+ * New upstream release.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+ (debian/control).
+
+ -- Charles Plessy <plessy@debian.org> Tue, 12 Apr 2011 17:15:33 +0900
+
+tabix (0.2.3-1) unstable; urgency=low
+
+ * Initial release (Closes: #606446)
+
+ -- Charles Plessy <plessy@debian.org> Wed, 19 Jan 2011 22:16:39 +0900
--- /dev/null
+Source: tabix
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy@debian.org>,
+ Andreas Tille <tille@debian.org>
+Build-Depends: debhelper (>= 9), zlib1g-dev
+Standards-Version: 3.9.3
+Homepage: http://samtools.sourceforge.net/tabix.shtml
+Vcs-Git: git://git.debian.org/debian-med/tabix.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/tabix.git
+
+Package: tabix
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: generic indexer for TAB-delimited genome position files
+ Tabix indexes files where some columns indicate sequence coordinates: name
+ (usually a chromosme), start and stop. The input data file must be position
+ sorted and compressed by bgzip (provided in this package), which has a gzip
+ like interface. After indexing, tabix is able to quickly retrieve data lines by
+ chromosomal coordinates. Fast data retrieval also works over network if an URI
+ is given as a file name.
--- /dev/null
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.5.tar.bz2
+
+Files: *
+Copyright: © 2008 Genome Research Ltd (GRL).
+ © 2008 Broad Institute / Massachusetts Institute of Technology
+ © 2009 Genome Research Ltd (GRL), 2010 Broad Institute
+ © 2010 Broad Institute.
+License: MIT
+
+Files: python/*
+Copyright: © 2011 Seoul National University.
+License: MIT
+
+License: MIT
+ 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.
+
--- /dev/null
+NEWS
+debian/README.test
--- /dev/null
+example.gtf.gz
+example.gtf.gz.tbi
--- /dev/null
+# Configuration file for git-buildpackage and friends
+
+[DEFAULT]
+# use pristine-tar:
+pristine-tar = True
+# Configuration file for git-buildpackage and friends
+
+[git-dch]
+# Include 7 digits of the commit ID in the changelog entry.
+id-length = 7
--- /dev/null
+tabix usr/bin
+bgzip usr/bin
--- /dev/null
+/usr/share/man/man1/tabix.1.gz /usr/share/man/man1/bgzip.1.gz
--- /dev/null
+Author: Andreas Tille <tille@debian.org>
+Date: Wed, 25 Apr 2012 17:01:06 +0200
+Bug-Closed: http://bugs.debian.org/626267
+Description: Do not set unused variables
+
+--- tabix.orig/bgzf.c
++++ tabix/bgzf.c
+@@ -627,11 +627,11 @@
+ if (fp->open_mode == 'w') {
+ if (bgzf_flush(fp) != 0) return -1;
+ { // add an empty block
+- int count, block_length = deflate_block(fp, 0);
++ int /* count, */ block_length = deflate_block(fp, 0);
+ #ifdef _USE_KNETFILE
+- count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
++ /* count = */ fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
+ #else
+- count = fwrite(fp->compressed_block, 1, block_length, fp->file);
++ /* count = */ fwrite(fp->compressed_block, 1, block_length, fp->file);
+ #endif
+ }
+ #ifdef _USE_KNETFILE
--- /dev/null
+Description: Reorder libraries to build with ld --as-needed
+Author: David Shorten <dpshorten@gmail.com>
+Bug-Ubuntu: http://bugs.launchpad.net/ubuntu/+source/tabix/+bug/803202
+Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=632150
+Last-Update: 2011-06-30
+--- tabix.orig/Makefile
++++ tabix/Makefile
+@@ -41,7 +41,7 @@
+ $(AR) -cru $@ $(LOBJS)
+
+ tabix:lib $(AOBJS)
+- $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -ltabix
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -ltabix -lm $(LIBPATH) -lz
+
+ bgzip:bgzip.o bgzf.o knetfile.o
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
--- /dev/null
+count-set-but-not-used.patch
+use-dpkg-buildflags.patch
+ld-as-needed.patch
--- /dev/null
+Author: Simon Ruderich <simon@ruderich.org>
+Date: Sat, 28 Apr 2012 19:09:02 UTC
+Description: Fix build system to enable hardening flags
+
+--- tabix.orig/Makefile
++++ tabix/Makefile
+@@ -1,5 +1,8 @@
+ CC= gcc
+-CFLAGS= -g -Wall -O2 -fPIC #-m64 #-arch ppc
++# Use flags when CFLAGS is not already defined in the environment.
++CFLAGS?= -g -Wall -O2
++# But always append special flags we need.
++CFLAGS+= -fPIC #-m64 #-arch ppc
+ DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+ LOBJS= bgzf.o kstring.o knetfile.o index.o bedidx.o
+ AOBJS= main.o
+@@ -12,7 +15,7 @@
+ .SUFFIXES:.c .o
+
+ .c.o:
+- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+ all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+ @target=`echo $@ | sed s/-recur//`; \
+@@ -29,19 +32,19 @@
+ lib:libtabix.a
+
+ libtabix.so.1:$(LOBJS)
+- $(CC) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
++ $(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
+
+ libtabix.1.dylib:$(LOBJS)
+- libtool -dynamic $(LOBJS) -o $@ -lc -lz
++ libtool $(CFLAGS) $(LDFLAGS) -dynamic $(LOBJS) -o $@ -lc -lz
+
+ libtabix.a:$(LOBJS)
+ $(AR) -cru $@ $(LOBJS)
+
+ tabix:lib $(AOBJS)
+- $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -ltabix
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -ltabix
+
+ bgzip:bgzip.o bgzf.o knetfile.o
+- $(CC) $(CFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
+
+ TabixReader.class:TabixReader.java
+ javac -cp .:sam.jar TabixReader.java
--- /dev/null
+#!/usr/bin/make -f
+
+%:
+ dh $@
+
+override_dh_compress:
+ dh_compress --exclude=.tbi
--- /dev/null
+3.0 (quilt)
--- /dev/null
+Archive: SourceForge
+Name: Tabix
+Homepage: http://samtools.sourceforge.net/tabix.shtml
+Reference:
+ author: Li, Heng
+ title: >
+ Tabix: Fast retrieval of sequence features from generic TAB-delimited files
+ journal: Bioinformatics
+ year: 2011
+ volume: 27
+ number: 5
+ pages: 718-9
+ pmid: 21208982
+ doi: 10.1093/bioinformatics/btq671
+ URL: http://bioinformatics.oxfordjournals.org/content/early/2011/01/05/bioinformatics.btq671.abstract
+ eprint: http://bioinformatics.oxfordjournals.org/content/early/2011/01/05/bioinformatics.btq671.full.pdf+html
+watch: |
+ version=3
+ opts=downloadurlmangle=s/\/download//,filenamemangle=s/http...sourceforge.net.projects.samtools.files.tabix.//;s/.download// \
+ http://sourceforge.net/projects/samtools/files/tabix/ \
+ http://sourceforge.net/projects/samtools/files/tabix/tabix-(.*).tar.bz2/download
--- /dev/null
+version=3
+http://sf.net/samtools/tabix-(.+)\.(?:zip|tgz|tbz2|txz|tar\.gz|tar\.bz2|tar\.xz)
projects / tabix.git / commitdiff