[med-svn] [python-pysam] 05/08: samtools says: The `pileup' command has been removed. Please use `mpileup' instead.

[Andreas Tille]

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tille pushed a commit to branch master
in repository python-pysam.

commit 4e5de6463bde5b091d5cd1c6201c9b2f6839b97c
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jul 20 17:30:20 2015 +0200

    samtools says:   The `pileup' command has been removed. Please use `mpileup' instead.
---
 debian/patches/sam_mpileup.patch | 18 ++++++++++++++++++
 debian/patches/series            |  1 +
 2 files changed, 19 insertions(+)

diff --git a/debian/patches/sam_mpileup.patch b/debian/patches/sam_mpileup.patch
new file mode 100644
index 0000000..776afd6
--- /dev/null
+++ b/debian/patches/sam_mpileup.patch
@@ -0,0 +1,18 @@
+Author: Andreas Tille <tille at 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 869d4af..951529b 100644
--- 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

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