From: Andreas Tille Date: Fri, 2 Oct 2020 07:08:24 +0000 (+0200) Subject: Adapt patches to new upstream version. Patches targeting at version 1.10 were deacti... X-Git-Tag: archive/raspbian/0.22.0+ds-1+rpi1~1^2^2~47 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=24db9f3ab50cae5fa204d847f24752da31175ba4;p=python-pysam.git Adapt patches to new upstream version. Patches targeting at version 1.10 were deactivated --- diff --git a/debian/patches/clean_less b/debian/patches/clean_less index 58588a2..393b90a 100644 --- 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 ed8ac5a..f6eec3b 100644 --- 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 d9f3c1e..232630e 100644 --- a/debian/patches/skip_test_remote.patch +++ b/debian/patches/skip_test_remote.patch @@ -2,9 +2,9 @@ Author: Andreas Tille 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 e832c94..34e82d6 100644 --- a/debian/patches/spelling +++ b/debian/patches/spelling @@ -1,8 +1,8 @@ From: Michael R. Crusoe 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