Fix error in sam_mpileup.patch

See the patch header for details.

diff --git a/debian/patches/sam_mpileup.patch b/debian/patches/sam_mpileup.patch
index 776afd6b1519e9ebcffaca7195fc982220ae4a0a..a11a5d01579243689c592fb90cb33271230a994d 100644 (file)
--- a/debian/patches/sam_mpileup.patch
+++ b/debian/patches/sam_mpileup.patch
@@ -1,18 +1,27 @@
 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
+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