d/patches/*: refresh patches.

diff --git a/debian/patches/clean_less b/debian/patches/clean_less
index 3ab4e1e2406327911ec1203e086b4e00b262dbf3..fcf062a346129b611e394eb74cc2ae43ff0e7d66 100644 (file)
--- 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 ff374f8c6a96b5cd77a0a558b7daeeddb1f0c3f0..ed375886c63a1960b6db3e3cb6f5e2f1ecbd90a0 100644 (file)
--- 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",
      ]