[Debian-med-packaging] [SCM] Processing of sequence alignments in SAM and BAM formats. branch, master, updated. upstream/0.1.8-20-gcefa180

[Charles Plessy]

The following commit has been merged in the master branch:
commit 4dd37bb88d4feb45d3fcfdc655ea75f72ea2aacb
Author: Charles Plessy <plessy at debian.org>
Date:   Wed Jul 14 14:19:47 2010 +0900

    New upstream release, with among many changes a new python script.

diff --git a/debian/changelog b/debian/changelog
index 96ad453..fbfe520 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,14 @@
+samtools (0.1.8-1) unstable; urgency=low
+
+  * New upstream release.
+  * Updated the VCS fields to the current Git repository (debian/control).
+  * Install python scripts in usr/share/samtools, and suggest python
+    (debian/samtools.install, debian/rules, debian/control).
+  * Incremented Standards-Version to reflect conformance with Policy 3.9.0
+    (debian/control, no changes needed).
+
+ -- Charles Plessy <plessy at debian.org>  Wed, 14 Jul 2010 14:08:59 +0900
+
 samtools (0.1.7a~dfsg-1) unstable; urgency=low
 
   * New upstream release: new script sam2vcf.pl, and many other changes.
diff --git a/debian/control b/debian/control
index e65161b..8bcae5c 100644
--- a/debian/control
+++ b/debian/control
@@ -1,11 +1,11 @@
 Source: samtools
 Section: science
 Priority: optional
-Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy at debian.org>
 Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
-Standards-Version: 3.8.3
+Standards-Version: 3.9.0
 Homepage: http://samtools.sourceforge.net
 Vcs-Browser: http://git.debian.org/?p=debian-med/samtools.git
 Vcs-Git: git://git.debian.org/debian-med/samtools.git
@@ -13,6 +13,7 @@ Vcs-Git: git://git.debian.org/debian-med/samtools.git
 Package: samtools
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: python
 Description: processing sequence alignments in SAM and BAM formats
  Samtools is a set of utilities that manipulate nucleotide sequence alignments
  in the binary BAM format. It imports from and exports to the ascii SAM
diff --git a/debian/rules b/debian/rules
index ac35c57..f5aaa94 100755
--- a/debian/rules
+++ b/debian/rules
@@ -10,3 +10,6 @@ DEB_MAKE_CHECK_TARGET = -C examples all
 
 clean::
 	$(RM) examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg
+
+binary-fixup/samtools::
+	sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' $(CURDIR)/debian/samtools/usr/share/samtools/varfilter.py
diff --git a/debian/samtools.install b/debian/samtools.install
index 17c8a41..a4bdb28 100644
--- a/debian/samtools.install
+++ b/debian/samtools.install
@@ -2,6 +2,7 @@
 razip	usr/bin
 samtools	usr/bin
 misc/*.pl	usr/share/samtools
+misc/*.py	usr/share/samtools
 misc/wgsim	usr/lib/samtools
 misc/maq2sam-long	usr/lib/samtools
 misc/maq2sam-short	usr/lib/samtools

-- 
Processing of sequence alignments in SAM and BAM formats.