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Commits on Source (2)
python-pysam (0.15.3+ds-1) UNRELEASED; urgency=medium
python-pysam (0.15.3+ds-1) unstable; urgency=medium
* Team upload.
* New upstream release. Not yet dropping py2 due to paleomix, sga, others
* New upstream release. Not yet dropping py2 due to paleomix and pbsuite
* debhelper-compat 12
* Standards-Version: 4.4.0
* Trim trailing whitespace.
* Use secure URI in Homepage field.
* Set upstream metadata fields: Repository.
* New patch to remove symbols that were dropped in htslib 1.10:
hts_utell, hts_useek (Closes: #947426)
-- Michael R. Crusoe <michael.crusoe@gmail.com> Tue, 06 Aug 2019 19:37:44 +0200
-- Michael R. Crusoe <michael.crusoe@gmail.com> Fri, 03 Jan 2020 21:25:33 +0100
python-pysam (0.15.2+ds-2) unstable; urgency=medium
......
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Description: Remove symbol that was removed in libhts3
--- python-pysam.orig/pysam/htslib_util.h
+++ python-pysam/pysam/htslib_util.h
@@ -5,9 +5,6 @@
#include "htslib/vcf.h"
#include "htslib/khash.h"
-int hts_useek(htsFile *fp, long uoffset, int where);
-long hts_utell(htsFile *fp);
-
int hts_set_verbosity(int verbosity);
int hts_get_verbosity(void);
--- python-pysam.orig/pysam/libchtslib.pxd
+++ python-pysam/pysam/libchtslib.pxd
@@ -632,8 +632,6 @@
int8_t HTS_FMT_CRAI
BGZF *hts_get_bgzfp(htsFile *fp)
- int hts_useek(htsFile *fp, long uoffset, int where)
- long hts_utell(htsFile *fp)
ctypedef struct hts_idx_t
--- python-pysam.orig/pysam/libchtslib.pyx
+++ python-pysam/pysam/libchtslib.pyx
@@ -489,9 +489,6 @@
if self.htsfile.format.compression == bgzf:
with nogil:
ret = bgzf_seek(hts_get_bgzfp(self.htsfile), offset, SEEK_SET)
- elif self.htsfile.format.compression == no_compression:
- with nogil:
- ret = hts_useek(self.htsfile, <int>offset, SEEK_SET)
else:
raise NotImplementedError("seek not implemented in files compressed by method {}".format(
self.htsfile.format.compression))
@@ -508,9 +505,6 @@
if self.htsfile.format.compression == bgzf:
with nogil:
ret = bgzf_tell(hts_get_bgzfp(self.htsfile))
- elif self.htsfile.format.compression == no_compression:
- with nogil:
- ret = hts_utell(self.htsfile)
elif self.htsfile.format.format == cram:
with nogil:
ret = htell(cram_fd_get_fp(self.htsfile.fp.cram))
skip_test_remote.patch
spelling
hts1.10