From 6ba7fa2e8a0c06cd4ea6572a189df4e42eb4dce4 Mon Sep 17 00:00:00 2001 From: Afif Elghraoui Date: Fri, 24 Jul 2015 00:32:08 -0700 Subject: [PATCH] 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 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 -- 2.30.2