[med-svn] [python-pysam] 03/08: Fix error in sam_mpileup.patch

[Afif Elghraoui]

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commit 6ba7fa2e8a0c06cd4ea6572a189df4e42eb4dce4
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Fri Jul 24 00:32:08 2015 -0700

    Fix error in sam_mpileup.patch
    
    See the patch header for details.
---
 debian/patches/sam_mpileup.patch | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/debian/patches/sam_mpileup.patch b/debian/patches/sam_mpileup.patch
index 776afd6..a11a5d0 100644
--- a/debian/patches/sam_mpileup.patch
+++ b/debian/patches/sam_mpileup.patch
@@ -1,18 +1,27 @@
 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
+Description: Update depricated command in test suite
+ [Andreas]
  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
+ [Afif]
+ --Simply replacing pileup with mpileup introduced a new error:
+ samtools mpileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+ mpileup: invalid option -- 'c'
+ Invalid option: '?'
+ --See:
+ samtools man page, under mpileup: "In the pileup format (without -u or -g),"
+ http://www.htslib.org/doc/samtools.html
+ https://www.biostars.org/p/42094/
+ The solution is to remove the "-c" flag
+--- python-pysam.orig/tests/pysam_data/Makefile
++++ python-pysam/tests/pysam_data/Makefile
+@@ -48,7 +48,7 @@
  		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
++		samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
  
  ex2_truncated.bam: ex2.bam
  	head -c 124000 ex2.bam > ex2_truncated.bam

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