samtools says: The `pileup' command has been removed. Please use `mpileup' instead.

diff --git a/debian/patches/sam_mpileup.patch b/debian/patches/sam_mpileup.patch
new file mode 100644 (file)
index 0000000..776afd6
--- /dev/null
+++ b/debian/patches/sam_mpileup.patch
@@ -0,0 +1,18 @@
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 20 Jul 2015 17:29:25 +0200
+Description: Follow the following hint when running the test suite
+ samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+ [main] The `pileup' command has been removed. Please use `mpileup' instead.
+
+
+--- a/tests/pysam_data/Makefile
++++ b/tests/pysam_data/Makefile
+@@ -48,7 +48,7 @@ ex1.bam:ex1.sam.gz ex1.fa.fai
+               samtools index $<
+ 
+ ex1.pileup.gz:ex1.bam ex1.fa
+-              samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
++              samtools mpileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+ 
+ ex2_truncated.bam: ex2.bam
+       head -c 124000 ex2.bam > ex2_truncated.bam

diff --git a/debian/patches/series b/debian/patches/series
index 869d4afd72c718b2df5c04501b5edbdd2b09de9d..951529b3a75f5ffbe935ecc9992f6c8bfb8a24d5 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ adding-include-hts-dirs
 correct-spelling-errors.patch
 ignore-htslib-dir.patch
 improve-python3-compatibility.patch
+sam_mpileup.patch