[med-svn] [SCM] samtools branch, master, updated. debian/0.1.16-1-6-g5075acd

[Charles Plessy]

The following commit has been merged in the master branch:
commit 2347ad62090e036841008e054c234868e21f7a80
Author: Charles Plessy <plessy at debian.org>
Date:   Mon Jul 11 21:02:37 2011 +0900

    Patched the example makefile to not use samtools pileup, deprecated.

diff --git a/debian/changelog b/debian/changelog
index 3b575bd..656ed10 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,9 @@ samtools (0.1.17-1) UNRELEASED; urgency=low
 
   * New upstream release 0.1.17 (6 July, 2011).
   * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
+  * Patched the example makefile to not use samtools pileup, deprecated.
+    (debian/control, debian/rules, debian/patches/series,
+    debian/patches/no-pileup-tests.patch)
 
  -- Charles Plessy <plessy at debian.org>  Mon, 11 Jul 2011 20:22:01 +0900
 
diff --git a/debian/control b/debian/control
index 26ba80e..82e03de 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 (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), 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/patches/no-pileup-tests.patch b/debian/patches/no-pileup-tests.patch
new file mode 100644
index 0000000..26532ab
--- /dev/null
+++ b/debian/patches/no-pileup-tests.patch
@@ -0,0 +1,22 @@
+--- a/examples/Makefile
++++ b/examples/Makefile
+@@ -1,5 +1,5 @@
+ all:../libbam.a ../samtools ../bcftools/bcftools \
+-	ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.glfview.gz ex1.bcf calDepth
++	ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.bcf calDepth
+ 		@echo; echo \# You can now launch the viewer with: \'samtools tview ex1.bam ex1.fa\'; echo;
+ 
+ ex1.fa.fai:ex1.fa
+@@ -8,12 +8,6 @@
+ 		../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
+ ex1.bam.bai:ex1.bam
+ 		../samtools index ex1.bam
+-ex1.pileup.gz:ex1.bam ex1.fa
+-		../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+-ex1.glf:ex1.bam ex1.fa
+-		../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+-ex1.glfview.gz:ex1.glf
+-		../samtools glfview ex1.glf | gzip > ex1.glfview.gz
+ ex1a.bam:ex1.bam
+ 		../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"a";print}}' | ../samtools view -bS - > $@
+ ex1b.bam:ex1.bam
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..ed908a5
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+no-pileup-tests.patch
diff --git a/debian/rules b/debian/rules
index 93bf3aa..d6d4267 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,6 +2,7 @@
 
 include /usr/share/cdbs/1/rules/debhelper.mk
 include /usr/share/cdbs/1/class/makefile.mk
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
 
 CFLAGS += -fPIC
 

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