[med-svn] [SCM] Processing of sequence alignments in SAM and BAM formats. branch, master, updated. debian/0.1.8-1-7-g349ae4d

[Charles Plessy]

The following commit has been merged in the master branch:
commit 85bb95099e58e20cc03456b7528248f7baed4db4
Author: Charles Plessy <plessy at debian.org>
Date:   Mon Nov 1 20:05:07 2010 +0900

     # Install bcftools, its manpage, bcf-fix.pl, vcfutils.pl, and new examples.

diff --git a/debian/rules b/debian/rules
index f5aaa94..40822dd 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,7 +9,11 @@ DEB_MAKE_BUILD_TARGET = all all-recur razip lib
 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
+	$(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 examples/ex1.bcf
+
+binary-install/samtools::
+	install -m 644 bcftools/README $(CURDIR)/debian/samtools/usr/share/doc/samtools/README.bcftools
+	ln -s samtools.1.gz $(CURDIR)/debian/samtools/usr/share/man/man1/bcftools.1.gz
 
 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.examples b/debian/samtools.examples
index 92114a2..5a25472 100644
--- a/debian/samtools.examples
+++ b/debian/samtools.examples
@@ -2,3 +2,5 @@ examples/ex1.bam
 examples/ex1.fa
 examples/ex1.sam.gz
 examples/00README.txt
+examples/toy.fa
+examples/toy.sam
diff --git a/debian/samtools.install b/debian/samtools.install
index a4bdb28..acf372a 100644
--- a/debian/samtools.install
+++ b/debian/samtools.install
@@ -1,6 +1,9 @@
 #bgzip	usr/bin
+bcftools/bcftools	usr/bin
 razip	usr/bin
 samtools	usr/bin
+bcftools/bcf-fix.pl	usr/share/samtools
+bcftools/vcfutils.pl	usr/share/samtools
 misc/*.pl	usr/share/samtools
 misc/*.py	usr/share/samtools
 misc/wgsim	usr/lib/samtools

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