Author: plessy Date: 2009-08-08 05:42:41 +0000 (Sat, 08 Aug 2009) New Revision: 3746
Added: trunk/packages/samtools/trunk/debian/samtools.examples trunk/packages/samtools/trunk/debian/upstream-metadata.yaml Removed: trunk/packages/samtools/trunk/debian/samtools-examples.examples Modified: trunk/packages/samtools/trunk/debian/changelog trunk/packages/samtools/trunk/debian/control trunk/packages/samtools/trunk/debian/copyright trunk/packages/samtools/trunk/debian/samtools.docs trunk/packages/samtools/trunk/debian/samtools.install Log: Package almost ready, but giving a bit of time for feedback on long descriptions in the ITP?\226?\128?\166 Modified: trunk/packages/samtools/trunk/debian/changelog =================================================================== --- trunk/packages/samtools/trunk/debian/changelog 2009-08-07 13:29:41 UTC (rev 3745) +++ trunk/packages/samtools/trunk/debian/changelog 2009-08-08 05:42:41 UTC (rev 3746) @@ -1,7 +1,7 @@ samtools (0.1.5c-1) UNRELEASED; urgency=low - Non-free files found; sort out before upload. + Giving a bit of time for feedback on long descriptions in the ITP… - * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP> + * Initial release (Closes: #540453) - -- Charles Plessy <[email protected]> Tue, 03 Feb 2009 13:46:43 +0900 + -- Charles Plessy <[email protected]> Sat, 08 Aug 2009 11:50:09 +0900 Modified: trunk/packages/samtools/trunk/debian/control =================================================================== --- trunk/packages/samtools/trunk/debian/control 2009-08-07 13:29:41 UTC (rev 3745) +++ trunk/packages/samtools/trunk/debian/control 2009-08-08 05:42:41 UTC (rev 3746) @@ -13,20 +13,19 @@ Package: samtools Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} -Description: Processing sequence alignments in SAM format. - Samtools is a set of utilities that manipulate alignments in the BAM format. - It imports from and exports to the SAM (Sequence Alignment/Map) format, does - sorting, merging and indexing, and allows to retrieve reads in any regions - swiftly. +Description: processing sequence alignments in SAM and BAM formats + Samtools is a set of utilities that manipulate nucleotide sequence alignments + in the BAM format. It imports from and exports to the SAM (Sequence + Alignment/Map) format, does sorting, merging and indexing, and allows to + retrieve reads in any regions swiftly. It is designed to work on a stream, and + is able to open a BAM (not SAM) file on a remote FTP server. Package: libbam-dev Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} -Description: libbam - ............ - -Package: samtools-examples -Architecture: all -Depends: ${misc:Depends} -Description: examples - ............. +Description: manipulates nucleotide sequence alignments in BAM or SAM format + The BAM library provides I/O and various operations on manipulating nucleotide + sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence + Alignment/Map) format. It now supports importing from or exporting to TAM, + sorting, merging, generating pileup, and quickly retrieval of reads overlapped + with a specified region. Modified: trunk/packages/samtools/trunk/debian/copyright =================================================================== --- trunk/packages/samtools/trunk/debian/copyright 2009-08-07 13:29:41 UTC (rev 3745) +++ trunk/packages/samtools/trunk/debian/copyright 2009-08-08 05:42:41 UTC (rev 3746) @@ -6,7 +6,7 @@ Copyright : © 2008–2009, Genome Research Ltd. 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 @@ -83,3 +83,6 @@ These notices must be retained in any copies of any part of this documentation and/or software. + +The above source files for MD5 support will be replaced in the next SAMtools +release by the public domain implementation of ‘http://www.fourmilab.ch/md5/’. Deleted: trunk/packages/samtools/trunk/debian/samtools-examples.examples =================================================================== --- trunk/packages/samtools/trunk/debian/samtools-examples.examples 2009-08-07 13:29:41 UTC (rev 3745) +++ trunk/packages/samtools/trunk/debian/samtools-examples.examples 2009-08-08 05:42:41 UTC (rev 3746) @@ -1,3 +0,0 @@ -examples/ex1.bam -examples/ex1.fa -examples/00README.txt Modified: trunk/packages/samtools/trunk/debian/samtools.docs =================================================================== --- trunk/packages/samtools/trunk/debian/samtools.docs 2009-08-07 13:29:41 UTC (rev 3745) +++ trunk/packages/samtools/trunk/debian/samtools.docs 2009-08-08 05:42:41 UTC (rev 3746) @@ -1,2 +1,3 @@ +AUTHORS debian/reference NEWS Copied: trunk/packages/samtools/trunk/debian/samtools.examples (from rev 3745, trunk/packages/samtools/trunk/debian/samtools-examples.examples) =================================================================== --- trunk/packages/samtools/trunk/debian/samtools.examples (rev 0) +++ trunk/packages/samtools/trunk/debian/samtools.examples 2009-08-08 05:42:41 UTC (rev 3746) @@ -0,0 +1,3 @@ +examples/ex1.bam +examples/ex1.fa +examples/00README.txt Property changes on: trunk/packages/samtools/trunk/debian/samtools.examples ___________________________________________________________________ Added: svn:mergeinfo + Modified: trunk/packages/samtools/trunk/debian/samtools.install =================================================================== --- trunk/packages/samtools/trunk/debian/samtools.install 2009-08-07 13:29:41 UTC (rev 3745) +++ trunk/packages/samtools/trunk/debian/samtools.install 2009-08-08 05:42:41 UTC (rev 3746) @@ -1,3 +1,5 @@ #bgzip usr/bin razip usr/bin samtools usr/bin +misc/*.pl usr/share/samtools +misc/wgsim usr/bin Added: trunk/packages/samtools/trunk/debian/upstream-metadata.yaml =================================================================== --- trunk/packages/samtools/trunk/debian/upstream-metadata.yaml (rev 0) +++ trunk/packages/samtools/trunk/debian/upstream-metadata.yaml 2009-08-08 05:42:41 UTC (rev 3746) @@ -0,0 +1,17 @@ +DOI: 10.1093/bioinformatics/btp352 +Homepage: http://samtools.sourceforge.net +PMID: 19505943 +Reference: | + @article{HengLi06082009, + author = {Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard and 1000 Genome Project Data Processing Subgroup, }, + title = {{The Sequence Alignment/Map (SAM) Format and SAMtools}}, + journal = {Bioinformatics}, + volume = {}, + number = {}, + pages = {btp352}, + doi = {10.1093/bioinformatics/btp352}, + year = {2009}, + URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp352v1}, + eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/btp352v1.pdf} + } +Repository: https://samtools.svn.sourceforge.net/svnroot/samtools _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
