[med-svn] [Git][med-team/python-pysam][master] 2 commits: sga already removed python2

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / python-pysam


Commits:
9a68cba7 by Michael R. Crusoe at 2020-01-02T15:27:17+01:00
sga already removed python2

- - - - -
52b5020d by Michael R. Crusoe at 2020-01-03T21:27:27+01:00
Remove hts_utell, no longer in libhts3

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/hts1.10
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,14 +1,16 @@
-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 at gmail.com>  Tue, 06 Aug 2019 19:37:44 +0200
+ -- Michael R. Crusoe <michael.crusoe at gmail.com>  Fri, 03 Jan 2020 21:25:33 +0100
 
 python-pysam (0.15.2+ds-2) unstable; urgency=medium
 


=====================================
debian/patches/hts1.10
=====================================
@@ -0,0 +1,47 @@
+Author: Michael R. Crusoe <michael.crusoe at 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))


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 skip_test_remote.patch
 spelling
+hts1.10



View it on GitLab: https://salsa.debian.org/med-team/python-pysam/compare/f325a888db8cba2d4de66309c7d00ffd32f3b6a9...52b5020d5ac19e63e1229d8406e75707bf41eec4

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-pysam/compare/f325a888db8cba2d4de66309c7d00ffd32f3b6a9...52b5020d5ac19e63e1229d8406e75707bf41eec4
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