* 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
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
--- /dev/null
+--- 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
--- /dev/null
+no-pileup-tests.patch
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