[med-svn] [SCM] samtools branch, master, updated. debian/0.1.18-1-10-g8220f2b

[Charles Plessy]

The following commit has been merged in the master branch:
commit 336698895224c8c299881f3eab27c8b303634997
Author: Charles Plessy <plessy at debian.org>
Date:   Fri May 18 15:33:20 2012 +0900

    Bash completion, see https://github.com/arq5x/bash_completion.

diff --git a/debian/control b/debian/control
index 62a270f..91eb536 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Priority: optional
 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 (>= 9), cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
 Standards-Version: 3.9.2
 Homepage: http://samtools.sourceforge.net
 Vcs-Browser: http://git.debian.org/?p=debian-med/samtools.git
diff --git a/debian/rules b/debian/rules
index 904bfbd..3736d28 100755
--- a/debian/rules
+++ b/debian/rules
@@ -18,6 +18,7 @@ clean::
 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
+	dh_bash-completion
 
 binary-fixup/samtools::
 	sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' $(CURDIR)/debian/samtools/usr/share/samtools/varfilter.py
diff --git a/debian/samtools.bash-completion b/debian/samtools.bash-completion
new file mode 100644
index 0000000..cae64e6
--- /dev/null
+++ b/debian/samtools.bash-completion
@@ -0,0 +1,21 @@
+# From https://raw.github.com/arq5x/bash_completion/master/samtools revision e931a8b46d9582672cc506e45ad9b4f4d6fbd743
+_samtools()
+{
+  local cur prev opts
+  COMPREPLY=()
+  cur="${COMP_WORDS[COMP_CWORD]}"
+  prev="${COMP_WORDS[COMP_CWORD-1]}"
+  opts="view sort mpileup depth 
+        faidx tview index idxstats 
+        fixmate flagstat calmd merge 
+        rmdup reheader cat targetcut 
+        phase pad2unpad"
+
+  case $prev in
+      samtools)
+          COMPREPLY=( $(compgen -W "${opts}" -- ${cur}) )
+          ;;
+  esac
+  return 0
+}
+complete -F _samtools -o default samtools

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