[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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