From b89d84a7266d0e114952f6a427b94cdd2561caf3 Mon Sep 17 00:00:00 2001 From: =?utf8?q?=C3=89tienne=20Mollier?= Date: Wed, 5 Feb 2025 21:20:11 +0100 Subject: [PATCH] d/patches/*: refresh patches. --- debian/patches/clean_less | 10 +++++----- debian/patches/skip-test-on-32-bit.patch | 8 ++++---- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/debian/patches/clean_less b/debian/patches/clean_less index 3ab4e1e..fcf062a 100644 --- a/debian/patches/clean_less +++ b/debian/patches/clean_less @@ -3,14 +3,14 @@ Last-Update: 2020-01-23 14:31:06 +0100 Description: Do not clean *.bam files Forwarded: not-needed ---- a/tests/pysam_data/Makefile -+++ b/tests/pysam_data/Makefile +--- python-pysam.orig/tests/pysam_data/Makefile ++++ python-pysam/tests/pysam_data/Makefile @@ -100,7 +100,7 @@ cp ex1.cram $@ clean: -- rm -fr [a-z]*.bam *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ -+ rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ - all.stamp *~ calDepth *.dSYM pysam_*.sam \ +- rm -fr [A-Za-z]*.bam *.bai *.csi *.fai *.gzi *.pileup* [A-Za-z]*.cram *.crai \ ++ rm -fr *.bai *.csi *.fai *.gzi *.pileup* [A-Za-z]*.cram *.crai \ + all.lock all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ diff --git a/debian/patches/skip-test-on-32-bit.patch b/debian/patches/skip-test-on-32-bit.patch index ff374f8..ed37588 100644 --- a/debian/patches/skip-test-on-32-bit.patch +++ b/debian/patches/skip-test-on-32-bit.patch @@ -13,16 +13,16 @@ Last-Update: 2021-10-15 def setUpModule(): make_data_files(BAM_DATADIR) -@@ -85,7 +86,7 @@ - "idxstats ex1.bam > %(out)s_ex1.idxstats", - "fixmate ex1.bam %(out)s_ex1.fixmate.bam", +@@ -86,7 +87,7 @@ + # TODO: fixmate behaviour changed in 1.21 + #"fixmate ex1.bam %(out)s_ex1.fixmate.bam", "flagstat ex1.bam > %(out)s_ex1.flagstat", - "calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam", + #"calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam", # use -s option, otherwise the following error in samtools 1.2: # Samtools-htslib-API: bam_get_library() not yet implemented # causes downstream problems -@@ -111,6 +112,9 @@ +@@ -112,6 +113,9 @@ # ("addreplacerg -r 'RG\tID:ga\tSM:hs' ex1.bam > %(out)s_ex1.addreplacerg", ] -- 2.39.5