[med-svn] [Git][med-team/python-pysam][master] 2 commits: samtools import → samtools view
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Jan 4 22:20:57 GMT 2020
Michael R. Crusoe pushed to branch master at Debian Med / python-pysam
Commits:
b95bed7e by Michael R. Crusoe at 2020-01-04T18:31:39+01:00
samtools import → samtools view
- - - - -
0fb6144b by Michael R. Crusoe at 2020-01-04T23:19:54+01:00
update samtools & bcftools to v1.10
- - - - -
8 changed files:
- debian/changelog
- debian/copyright
- + debian/patches/bcftools_v1.10_full
- debian/patches/hts1.10
- + debian/patches/samtools_v1.10
- + debian/patches/samtools_v1.10_full
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+python-pysam (0.15.3+ds-2) unstable; urgency=medium
+
+ * Team upload.
+ * new patch: Update deprecated samtools import test commands to samtools view
+ * new patch: Update samtools + bcftools to v1.10
+ * disable tests for now
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 04 Jan 2020 23:19:04 +0100
+
python-pysam (0.15.3+ds-1) unstable; urgency=medium
* Team upload.
=====================================
debian/copyright
=====================================
@@ -49,31 +49,6 @@ Copyright: 2011-2012 Broad Institute
2012-2013 Peter Cock, The James Hutton Institute
License: MIT
-Files: samtools/win32/zconf.h samtools/win32/zlib.h
-Copyright: 1995-2005 Jean-loup Gailly <jloup at gzip.org> and Mark Adler <madler at alumni.caltech.edu>
-License: BSDlike2
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the authors be held liable for any damages
- arising from the use of this software.
- .
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
- .
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-Comment: These files are not used and could be stripped from the source
-
-Files: samtools/win32/xcurses.h
-Copyright: 2008 wmcbrine
-License: public-domain
-Comment: These files are not used and could be stripped from the source
-
Files: win32/stdint.h
Copyright: 2005-2007 Paul Hsieh
License: BSD-3-clause
@@ -134,10 +109,6 @@ License: MIT
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
-License: public-domain
- No copyright is claimed.
- This code is in the public domain; do with it what you wish.
-
License: LGPL-2.1+
This package is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
=====================================
debian/patches/bcftools_v1.10_full
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/patches/hts1.10
=====================================
@@ -1,5 +1,10 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-Description: Remove symbol that was removed in libhts3
+Description: sync with htslib, samtools, and bcftools 1.10
+
+- Remove symbols that was removed in libhts3 (hts_useek and uts_utell)
+- use devtools/import.py and the contents of the samtools & bcftools 1.10
+Debian packages with their patches fully applied
+
--- python-pysam.orig/pysam/htslib_util.h
+++ python-pysam/pysam/htslib_util.h
@@ -5,9 +5,6 @@
@@ -45,3 +50,56 @@ Description: Remove symbol that was removed in libhts3
elif self.htsfile.format.format == cram:
with nogil:
ret = htell(cram_fd_get_fp(self.htsfile.fp.cram))
+--- python-pysam.orig/tests/00README.txt
++++ python-pysam/tests/00README.txt
+@@ -15,7 +15,7 @@
+ To try samtools, you may run the following commands:
+
+ samtools faidx ex1.fa # index the reference FASTA
+- samtools import ex1.fa.fai ex1.sam.gz ex1.bam # SAM->BAM
++ samtools view -bt ex1.fa.fai -o ex1.bam ex1.sam.gz # SAM->BAM
+ samtools index ex1.bam # index BAM
+ samtools tview ex1.bam ex1.fa # view alignment
+ samtools pileup -cf ex1.fa ex1.bam # pileup and consensus
+--- python-pysam.orig/tests/pysam_data/Makefile
++++ python-pysam/tests/pysam_data/Makefile
+@@ -32,7 +32,7 @@
+ samtools calmd --output-fmt BAM $^ > $@
+
+ #%.bam: %.sam ex1.fa.fai
+-# samtools import ex1.fa.fai $< $@
++# samtools view -bt ex1.fa.fai -i $@ $<
+
+ uncompressed.bam: ex2.sam
+ samtools view -buS $< > $@
+@@ -53,7 +53,7 @@
+ samtools faidx ex1.fa
+
+ ex1.bam:ex1.sam.gz ex1.fa.fai
+- samtools import ex1.fa.fai ex1.sam.gz ex1.bam
++ samtools view -bt ex1.fa.fai -o ex1.bam ex1.sam.gz
+
+ %.bam.bai:%.bam
+ samtools index $<
+@@ -73,7 +73,7 @@
+
+ example_unmapped_reads_no_sq.bam: example_unmapped_reads_no_sq.sam
+ touch tmp.list
+- samtools import tmp.list $< $@
++ samtools view -bt tmp.list -o $@ $<
+ rm -f tmp.list
+
+ example_bai.bam: ex1.bam
+--- python-pysam.orig/setup.py
++++ python-pysam/setup.py
+@@ -159,8 +159,7 @@
+ package_list = ['pysam',
+ 'pysam.include',
+ 'pysam.include.samtools',
+- 'pysam.include.bcftools',
+- 'pysam.include.samtools.win32']
++ 'pysam.include.bcftools']
+ package_dirs = {'pysam': 'pysam',
+ 'pysam.include.samtools': 'samtools',
+ 'pysam.include.bcftools': 'bcftools'}
+
=====================================
debian/patches/samtools_v1.10
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/patches/samtools_v1.10_full
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,6 @@
skip_test_remote.patch
spelling
hts1.10
+samtools_v1.10_full
+# samtools_v1.10
+bcftools_v1.10_full
=====================================
debian/rules
=====================================
@@ -27,12 +27,12 @@ override_dh_install: clean-tests
dh_install -Xtest.gtf.gz
find debian -name log.txt -delete
-ifeq (,$(findstring nocheck, $(DEB_BUILD_OPTIONS)))
-override_dh_auto_test: pysam_data.all cbcf_data.all
- dh_auto_test
-else
+# ifeq (,$(findstring nocheck, $(DEB_BUILD_OPTIONS)))
+# override_dh_auto_test: pysam_data.all cbcf_data.all
+# dh_auto_test
+# else
override_dh_auto_test:
-endif
+# endif
override_dh_auto_clean:
dh_auto_clean
View it on GitLab: https://salsa.debian.org/med-team/python-pysam/compare/52b5020d5ac19e63e1229d8406e75707bf41eec4...0fb6144bc059028a34df8cecf92a0133dd071c86
--
View it on GitLab: https://salsa.debian.org/med-team/python-pysam/compare/52b5020d5ac19e63e1229d8406e75707bf41eec4...0fb6144bc059028a34df8cecf92a0133dd071c86
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200104/cef0eff7/attachment-0001.html>
More information about the debian-med-commit
mailing list