[med-svn] r3746 - trunk/packages/samtools/trunk/debian
Charles Plessy
plessy at alioth.debian.org
Sat Aug 8 05:42:41 UTC 2009
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 <plessy at debian.org> Tue, 03 Feb 2009 13:46:43 +0900
+ -- Charles Plessy <plessy at debian.org> 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
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