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

diff --git a/debian/changelog b/debian/changelog
index 3b575bdcc6faa8671feabe7f74aaa3a8489cba07..656ed103159c38c33cd633f197b0568d62294bdb 100644 (file)
--- 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@debian.org>  Mon, 11 Jul 2011 20:22:01 +0900
 

diff --git a/debian/control b/debian/control
index 26ba80ea8501e0ca32f12f36be1ba2921ff25f4f..82e03de4c7dc0e086ec35a1fd98b3109263fd01b 100644 (file)
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy@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 (file)
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 (file)
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 93bf3aa3c1166305dfd02400d4dfe366ec9d2f79..d6d4267cbfce61ec4091a4dcf229af7028cd4df6 100755 (executable)
--- 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