Adapt patches to new upstream version. Patches targeting at version 1.10 were deacti...

diff --git a/debian/patches/clean_less b/debian/patches/clean_less
index 58588a2565e940352ff68e55f842a3ac1a377fb8..393b90a152be2228ae9b191887ed5e28497b5bee 100644 (file)
--- a/debian/patches/clean_less
+++ b/debian/patches/clean_less
@@ -2,9 +2,9 @@ Author: Michael R. Crusoe
 Last-Update: 2020-01-23 14:31:06 +0100
 Description: Do not clean *.bam files
 
---- python-pysam.orig/tests/pysam_data/Makefile
-+++ python-pysam/tests/pysam_data/Makefile
-@@ -87,7 +87,7 @@
+--- a/tests/pysam_data/Makefile
++++ b/tests/pysam_data/Makefile
+@@ -89,7 +89,7 @@ explicit_index.cram: ex1.cram
        cp ex1.cram $@
  
  clean:

diff --git a/debian/patches/series b/debian/patches/series
index ed8ac5a44a62264693a8786a7e7685250f9b26e2..f6eec3ba057c9ea876c974d50431a8887d2ed284 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,7 +1,7 @@
 skip_test_remote.patch
 spelling
-hts1.10
-samtools_v1.10_full
+#hts1.10
+#samtools_v1.10_full
 # samtools_v1.10
-bcftools_v1.10_full
+#bcftools_v1.10_full
 clean_less

diff --git a/debian/patches/skip_test_remote.patch b/debian/patches/skip_test_remote.patch
index d9f3c1e01397d62626f204539317accf092d3fcc..232630efd15582dcf4b665886a5a3d366b40215e 100644 (file)
--- a/debian/patches/skip_test_remote.patch
+++ b/debian/patches/skip_test_remote.patch
@@ -2,9 +2,9 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Tue, 11 Sep 2018 14:12:55 +0200
 Description: Skip tests trying to access remote site
 
---- python-pysam.orig/tests/AlignmentFile_test.py
-+++ python-pysam/tests/AlignmentFile_test.py
-@@ -1631,6 +1631,7 @@
+--- a/tests/AlignmentFile_test.py
++++ b/tests/AlignmentFile_test.py
+@@ -1616,6 +1616,7 @@ class TestDoubleFetchCRAMWithReference(T
      reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa')
  
  
@@ -12,9 +12,9 @@ Description: Skip tests trying to access remote site
  class TestRemoteFileFTP(unittest.TestCase):
  
      '''test remote access.
---- python-pysam.orig/tests/tabix_test.py
-+++ python-pysam/tests/tabix_test.py
-@@ -1014,6 +1014,7 @@
+--- a/tests/tabix_test.py
++++ b/tests/tabix_test.py
+@@ -1014,6 +1014,7 @@ for vcf_file in vcf_files:
      globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
  
  
@@ -22,7 +22,7 @@ Description: Skip tests trying to access remote site
  class TestRemoteFileHTTP(unittest.TestCase):
  
      url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"
-@@ -1053,25 +1054,28 @@
+@@ -1053,25 +1054,28 @@ class TestRemoteFileHTTP(unittest.TestCa
          self.assertEqual(list(self.local_file.header), [])
  
  

diff --git a/debian/patches/spelling b/debian/patches/spelling
index e832c94e3492d9a73ba969b8b1dbd6c3eadc73c8..34e82d646867860a3652b1c4fdd9ced2e002e531 100644 (file)
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -1,8 +1,8 @@
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: Fix spelling typos, courtesy of lintian
---- python-pysam.orig/bcftools/filter.c
-+++ python-pysam/bcftools/filter.c
-@@ -993,7 +993,7 @@
+--- a/bcftools/filter.c
++++ b/bcftools/filter.c
+@@ -1053,7 +1053,7 @@ static void filters_set_nmissing(filter_
  }
  static int func_npass(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
  {
@@ -11,9 +11,9 @@ Subject: Fix spelling typos, courtesy of lintian
      token_t *tok = stack[nstack - 1];
      if ( !tok->nsamples ) error("The function %s works with FORMAT fields\n", rtok->tag);
  
---- python-pysam.orig/bcftools/filter.c.pysam.c
-+++ python-pysam/bcftools/filter.c.pysam.c
-@@ -995,7 +995,7 @@
+--- a/bcftools/filter.c.pysam.c
++++ b/bcftools/filter.c.pysam.c
+@@ -1055,7 +1055,7 @@ static void filters_set_nmissing(filter_
  }
  static int func_npass(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
  {
@@ -22,9 +22,9 @@ Subject: Fix spelling typos, courtesy of lintian
      token_t *tok = stack[nstack - 1];
      if ( !tok->nsamples ) error("The function %s works with FORMAT fields\n", rtok->tag);
  
---- python-pysam.orig/pysam/libcalignedsegment.pyx
-+++ python-pysam/pysam/libcalignedsegment.pyx
-@@ -2238,7 +2238,7 @@
+--- a/pysam/libcalignedsegment.pyx
++++ b/pysam/libcalignedsegment.pyx
+@@ -2242,7 +2242,7 @@ cdef class AlignedSegment:
          *value*.
  
          An existing value of the same *tag* will be overwritten unless
@@ -33,9 +33,9 @@ Subject: Fix spelling typos, courtesy of lintian
          tag may only appear once in the optional alignment section.
  
          If *value* is None, the tag will be deleted.
---- python-pysam.orig/pysam/libcalignmentfile.pyx
-+++ python-pysam/pysam/libcalignmentfile.pyx
-@@ -1028,7 +1028,7 @@
+--- a/pysam/libcalignmentfile.pyx
++++ b/pysam/libcalignmentfile.pyx
+@@ -1029,7 +1029,7 @@ cdef class AlignmentFile(HTSFile):
  
          See :meth:`~pysam.HTSFile.parse_region` for more information
          on how genomic regions can be specified. :term:`reference` and
@@ -44,7 +44,7 @@ Subject: Fix spelling typos, courtesy of lintian
          for :term:`contig` and `stop`, respectively.
  
          Without a `contig` or `region` all mapped reads in the file
-@@ -1211,7 +1211,7 @@
+@@ -1212,7 +1212,7 @@ cdef class AlignmentFile(HTSFile):
          """perform a :term:`pileup` within a :term:`region`. The region is
          specified by :term:`contig`, `start` and `stop` (using
          0-based indexing).  :term:`reference` and `end` are also accepted for
@@ -53,7 +53,7 @@ Subject: Fix spelling typos, courtesy of lintian
          respectively.  Alternatively, a samtools 'region' string
          can be supplied.
  
-@@ -1360,7 +1360,7 @@
+@@ -1354,7 +1354,7 @@ cdef class AlignmentFile(HTSFile):
  
          The region is specified by :term:`contig`, `start` and `stop`.
          :term:`reference` and `end` are also accepted for backward
@@ -62,7 +62,7 @@ Subject: Fix spelling typos, courtesy of lintian
          respectively.  Alternatively, a :term:`samtools` :term:`region`
          string can be supplied.
  
-@@ -1464,7 +1464,7 @@
+@@ -1458,7 +1458,7 @@ cdef class AlignmentFile(HTSFile):
  
          The region is specified by :term:`contig`, `start` and `stop`.
          :term:`reference` and `end` are also accepted for backward
@@ -71,9 +71,9 @@ Subject: Fix spelling typos, courtesy of lintian
          respectively.  Alternatively, a :term:`samtools` :term:`region`
          string can be supplied.  The coverage is computed per-base [ACGT].
  
---- python-pysam.orig/pysam/libchtslib.pxd
-+++ python-pysam/pysam/libchtslib.pxd
-@@ -2513,7 +2513,7 @@
+--- a/pysam/libchtslib.pxd
++++ b/pysam/libchtslib.pxd
+@@ -2511,7 +2511,7 @@ cdef extern from "htslib/cram.h" nogil:
      #         2 if the file is a stream and thus unseekable
      #         1 if the file contains an EOF block
      #         0 if the file does not contain an EOF block
@@ -82,9 +82,9 @@ Subject: Fix spelling typos, courtesy of lintian
      #
      #
      int cram_check_EOF(cram_fd *fd)
---- python-pysam.orig/pysam/libchtslib.pyx
-+++ python-pysam/pysam/libchtslib.pyx
-@@ -587,7 +587,7 @@
+--- a/pysam/libchtslib.pyx
++++ b/pysam/libchtslib.pyx
+@@ -585,7 +585,7 @@ cdef class HTSFile(object):
                  rval = hts_opt_apply(self.htsfile, opts)
                  if rval != 0:
                      hts_opt_free(opts)
@@ -93,7 +93,7 @@ Subject: Fix spelling typos, courtesy of lintian
                  hts_opt_free(opts)
  
      def parse_region(self, contig=None, start=None, stop=None,
-@@ -597,7 +597,7 @@
+@@ -595,7 +595,7 @@ cdef class HTSFile(object):
          either be specified by :term:`contig`, `start` and
          `stop`. `start` and `stop` denote 0-based, half-open
          intervals. :term:`reference` and `end` are also accepted for
@@ -102,9 +102,9 @@ Subject: Fix spelling typos, courtesy of lintian
          `stop`, respectively.
  
          Alternatively, a samtools :term:`region` string can be
---- python-pysam.orig/pysam/libcutils.pyx
-+++ python-pysam/pysam/libcutils.pyx
-@@ -179,7 +179,7 @@
+--- a/pysam/libcutils.pyx
++++ b/pysam/libcutils.pyx
+@@ -179,7 +179,7 @@ cpdef parse_region(contig=None,
      `end`. `start` and `end` denote 0-based, half-open intervals.
      
      :term:`reference` and `end` are also accepted for backward