debian/0000755000000000000000000000000012254267651007200 5ustar debian/gbp.conf0000644000000000000000000000036412254267651010622 0ustar # 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 debian/control0000644000000000000000000000210012254267651010574 0ustar Source: tabix Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science XS-Testsuite: autopkgtest Priority: optional Build-Depends: debhelper (>= 9), zlib1g-dev Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/tabix.git Vcs-Git: git://anonscm.debian.org/debian-med/tabix.git Homepage: http://samtools.sourceforge.net/tabix.shtml 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. debian/install0000644000000000000000000000003412254267651010566 0ustar tabix usr/bin bgzip usr/bin debian/links0000644000000000000000000000007612254267651010246 0ustar /usr/share/man/man1/tabix.1.gz /usr/share/man/man1/bgzip.1.gz debian/rules0000755000000000000000000000012112254267651010252 0ustar #!/usr/bin/make -f %: dh $@ override_dh_compress: dh_compress --exclude=.tbi debian/manpages0000644000000000000000000000001012254267651010705 0ustar tabix.1 debian/examples0000644000000000000000000000004212254267651010735 0ustar example.gtf.gz example.gtf.gz.tbi debian/watch0000644000000000000000000000013312254267651010226 0ustar version=3 http://sf.net/samtools/tabix-(.+)\.(?:zip|tgz|tbz2|txz|tar\.gz|tar\.bz2|tar\.xz) debian/upstream0000644000000000000000000000150312254267651010762 0ustar 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 debian/copyright0000644000000000000000000000301212254267651011127 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://qa.debian.org/watch/sf.php/samtools/tabix-0.2.6.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. © 2011 Attractive Chaos 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. debian/source/0000755000000000000000000000000012254267651010500 5ustar debian/source/format0000644000000000000000000000001412254267651011706 0ustar 3.0 (quilt) debian/README.test0000644000000000000000000000416012254267651011037 0ustar 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 This sequence of tests is also implemented debian/tests/with-example-data in the source package. -- Charles Plessy Fri, 22 Jun 2012 13:11:36 +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"; debian/changelog0000644000000000000000000000462712254267651011063 0ustar tabix (0.2.6-2) unstable; urgency=low [ Charles Plessy ] b8d4e98 Indicate format to avoid stderr comment that makes autopkgtest fail. Closes: #680473, LP: #1021500 [ Andreas Tille ] * debian/control - cme fix dpkg-control - canonical Vcs fields -- Andreas Tille Wed, 18 Dec 2013 10:46:17 +0100 tabix (0.2.6-1) unstable; urgency=low 60eb374 Imported Upstream version 0.2.6 9de2ad5 Removed patches applied or obsoleted upstream. 2836b51 Refreshed hardening patch. 7677e45 Regression tests for autopkgtest. -- Charles Plessy Fri, 22 Jun 2012 13:14:27 +0900 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 ) Closes: #670759 * debian/patches/ld-as-needed.patch: Enable building with --as-needed (Thanks to David Shorten for the patch) Closes: #632150 -- Andreas Tille 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 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 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 Tue, 12 Apr 2011 17:15:33 +0900 tabix (0.2.3-1) unstable; urgency=low * Initial release (Closes: #606446) -- Charles Plessy Wed, 19 Jan 2011 22:16:39 +0900 debian/patches/0000755000000000000000000000000012254267651010627 5ustar debian/patches/use-dpkg-buildflags.patch0000644000000000000000000000310512254267651015500 0ustar Author: Simon Ruderich Date: Sat, 28 Apr 2012 19:09:02 UTC Description: Fix build system to enable hardening flags --- a/Makefile +++ b/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 -DBGZF_CACHE 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) -csru $@ $(LOBJS) tabix:lib $(AOBJS) - $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. -ltabix -lm $(LIBPATH) -lz + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -ltabix -lm $(LIBPATH) -lz bgzip:bgzip.o bgzf.o knetfile.o - $(CC) $(CFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz TabixReader.class:TabixReader.java javac -cp .:sam.jar TabixReader.java debian/patches/series0000644000000000000000000000003212254267651012037 0ustar use-dpkg-buildflags.patch debian/compat0000644000000000000000000000000212254267651010376 0ustar 9 debian/docs0000644000000000000000000000003012254267651010044 0ustar NEWS debian/README.test debian/tests/0000755000000000000000000000000012254267651010342 5ustar debian/tests/control0000644000000000000000000000003112254267651011737 0ustar Tests: with-example-data debian/tests/with-example-data0000755000000000000000000000122212254267651013600 0ustar #!/bin/sh -e # Create a temporary file TABIXDATA=$(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 -p gff $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