[med-svn] [Git][med-team/community/helper-scripts][master] automatic update
Andreas Tille pushed to branch master at Debian Med / community / helper-scripts Commits: d4ede14e by Andreas Tille at 2022-12-28T01:42:20+00:00 automatic update - - - - - 4 changed files: - debian-med-tests.txt - debian-science-tests.txt - outdated_med-packages.txt - python-team-tests.txt Changes: = debian-med-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Tue, 27 Dec 2022 13:42:04 + +Last-Update: Wed, 28 Dec 2022 01:42:04 + Source| Vote | Tasks | Tags ---++-+-- = debian-science-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Tue, 27 Dec 2022 13:42:06 + +Last-Update: Wed, 28 Dec 2022 01:42:04 + Source | Vote | Tasks |Tags -+++ = outdated_med-packages.txt = The diff for this file was not included because it is too large. = python-team-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Tue, 27 Dec 2022 13:42:07 + +Last-Update: Wed, 28 Dec 2022 01:42:05 + Source | Vote | Tags --++ View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/d4ede14e17fff873440b7fbeb815800f2b1e66dd -- View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/d4ede14e17fff873440b7fbeb815800f2b1e66dd You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/htsjdk][pristine-tar] pristine-tar data for htsjdk_3.0.4+dfsg.orig.tar.xz
Pierre Gruet pushed to branch pristine-tar at Debian Med / htsjdk Commits: dc018705 by Pierre Gruet at 2022-12-27T20:22:14+01:00 pristine-tar data for htsjdk_3.0.4+dfsg.orig.tar.xz - - - - - 2 changed files: - + htsjdk_3.0.4+dfsg.orig.tar.xz.delta - + htsjdk_3.0.4+dfsg.orig.tar.xz.id Changes: = htsjdk_3.0.4+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/htsjdk_3.0.4+dfsg.orig.tar.xz.delta differ = htsjdk_3.0.4+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +bd4d549aad99013a9525485bf4b0ad94a9756b59 View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/commit/dc01870557641ae5881b7eb6221ca1e21a91af2e -- View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/commit/dc01870557641ae5881b7eb6221ca1e21a91af2e You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/htsjdk][upstream] New upstream version 3.0.4+dfsg
Pierre Gruet pushed to branch upstream at Debian Med / htsjdk
Commits:
8cb4ced7 by Pierre Gruet at 2022-12-27T20:21:23+01:00
New upstream version 3.0.4+dfsg
- - - - -
2 changed files:
- src/main/java/htsjdk/samtools/BAMFileReader.java
- src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec30And21QueryTest.java
Changes:
=
src/main/java/htsjdk/samtools/BAMFileReader.java
=
@@ -175,10 +175,12 @@ public class BAMFileReader extends
SamReader.ReaderImplementation {
throws IOException {
this(useAsynchronousIO ? new AsyncBlockCompressedInputStream(file,
inflaterFactory) : new BlockCompressedInputStream(file, inflaterFactory),
indexFile!=null ? indexFile : SamFiles.findIndex(file),
eagerDecode, useAsynchronousIO, file.getAbsolutePath(), validationStringency,
samRecordFactory);
-if (mIndexFile != null && mIndexFile.lastModified() <
file.lastModified()) {
+
+if (mIndexFile != null && mIndexFile.lastModified() <
file.lastModified() - 5000) {
System.err.println("WARNING: BAM index file " +
mIndexFile.getAbsolutePath() +
" is older than BAM " + file.getAbsolutePath());
}
+
// Provide better error message when there is an error reading.
mStream.setInputFileName(file.getAbsolutePath());
}
=
src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec30And21QueryTest.java
=
@@ -586,18 +586,18 @@ public class HtsCRAMCodec30And21QueryTest extends
HtsjdkTest {
public Object[][] alignmentStartQueries() {
return new Object[][] {
// cram file, reference, query contig, alignment start query,
number of reads with matching alignment start
-{cramQueryWithCRAI, cramQueryReference, "20", 100013, 2},
-{cramQueryWithLocalCRAI, cramQueryReference, "20", 100013, 2},
-{cramQueryWithBAI, cramQueryReference, "20", 100013, 2},
+{cramQueryWithCRAI, cramQueryReference, "20", 100013L, 2},
+{cramQueryWithLocalCRAI, cramQueryReference, "20", 100013L, 2},
+{cramQueryWithBAI, cramQueryReference, "20", 100013L, 2},
// tests to ensure that query results on inputs that have
matching reads that are followed by reads
// in the same container that don't match the alignment start
are properly constrained to only the
// matching reads
{new HtsPath(TEST_DATA_DIR + "mitoAlignmentStartTest.cram"),
new HtsPath(TEST_DATA_DIR +
"mitoAlignmentStartTest.fa"),
-"Mito", 631, 24},
+"Mito", 631L, 24},
{new HtsPath(TEST_DATA_DIR +
"mitoAlignmentStartTestGATKGen.cram"),
new HtsPath(TEST_DATA_DIR +
"mitoAlignmentStartTest.fa"),
-"Mito", 631, 24},
+"Mito", 631L, 24},
};
}
View it on GitLab:
https://salsa.debian.org/med-team/htsjdk/-/commit/8cb4ced7b5d70cdb80339c6516311d5656151b0d
--
View it on GitLab:
https://salsa.debian.org/med-team/htsjdk/-/commit/8cb4ced7b5d70cdb80339c6516311d5656151b0d
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[med-svn] [Git][med-team/htsjdk][master] 6 commits: New upstream version 3.0.4+dfsg
Pierre Gruet pushed to branch master at Debian Med / htsjdk
Commits:
8cb4ced7 by Pierre Gruet at 2022-12-27T20:21:23+01:00
New upstream version 3.0.4+dfsg
- - - - -
7edb8199 by Pierre Gruet at 2022-12-27T20:22:14+01:00
Update upstream source from tag 'upstream/3.0.4+dfsg'
Update to upstream version '3.0.4+dfsg'
with Debian dir a782c8937dcdc1dc9fb32d3557524067f1216874
- - - - -
fc0f99ce by Pierre Gruet at 2022-12-27T20:24:28+01:00
Refreshing patches, one having been upstreamed
- - - - -
3ed4136c by Pierre Gruet at 2022-12-27T20:24:52+01:00
Raising Standards version to 4.6.2 (no change)
- - - - -
d4488418 by Pierre Gruet at 2022-12-27T20:25:13+01:00
Updating changelog
- - - - -
2d751565 by Pierre Gruet at 2022-12-27T20:26:08+01:00
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- − debian/patches/130-data-types-in-tests.patch
- debian/patches/series
- src/main/java/htsjdk/samtools/BAMFileReader.java
- src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec30And21QueryTest.java
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+htsjdk (3.0.4+dfsg-1) unstable; urgency=medium
+
+ * New upstream version 3.0.4+dfsg
+ * Refreshing patches
+ * Raising Standards version to 4.6.2 (no change)
+
+ -- Pierre Gruet Tue, 27 Dec 2022 20:25:59 +0100
+
htsjdk (3.0.2+dfsg-1) unstable; urgency=medium
* Adding missing DEP-3 headers to patches
=
debian/control
=
@@ -28,7 +28,7 @@ Build-Depends: default-jdk,
libcommons-lang3-java,
libjimfs-java,
scala-library
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/htsjdk
Vcs-Git: https://salsa.debian.org/med-team/htsjdk.git
Homepage: https://samtools.github.io/htsjdk/
=
debian/patches/130-data-types-in-tests.patch deleted
=
@@ -1,31 +0,0 @@
-Description: in this test, long is expected instead of int
-Author: Pierre Gruet
-Forwarded: https://github.com/samtools/htsjdk/issues/1631
-Last-Update: 2022-10-31
-
a/src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec30And21QueryTest.java
-+++
b/src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec30And21QueryTest.java
-@@ -586,18 +586,18 @@
- public Object[][] alignmentStartQueries() {
- return new Object[][] {
- // cram file, reference, query contig, alignment start query,
number of reads with matching alignment start
--{cramQueryWithCRAI, cramQueryReference, "20", 100013, 2},
--{cramQueryWithLocalCRAI, cramQueryReference, "20", 100013, 2},
--{cramQueryWithBAI, cramQueryReference, "20", 100013, 2},
-+{cramQueryWithCRAI, cramQueryReference, "20", 100013L, 2},
-+{cramQueryWithLocalCRAI, cramQueryReference, "20", 100013L,
2},
-+{cramQueryWithBAI, cramQueryReference, "20", 100013L, 2},
- // tests to ensure that query results on inputs that have
matching reads that are followed by reads
- // in the same container that don't match the alignment start
are properly constrained to only the
- // matching reads
- {new HtsPath(TEST_DATA_DIR + "mitoAlignmentStartTest.cram"),
- new HtsPath(TEST_DATA_DIR +
"mitoAlignmentStartTest.fa"),
--"Mito", 631, 24},
-+"Mito", 631L, 24},
- {new HtsPath(TEST_DATA_DIR +
"mitoAlignmentStartTestGATKGen.cram"),
- new HtsPath(TEST_DATA_DIR +
"mitoAlignmentStartTest.fa"),
--"Mito", 631, 24},
-+"Mito", 631L, 24},
- };
- }
-
=
debian/patches/series
=
@@ -11,6 +11,5 @@
110-debian-lib-version.patch
disable-network-tests.diff
120-fix-build.patch
-130-data-types-in-tests.patch
140-skip-testFlushNotSpammed.patch
150-use-rhino-as-JS-engine.patch
=
src/main/java/htsjdk/samtools/BAMFileReader.java
=
@@ -175,10 +175,12 @@ public class BAMFileReader extends
SamReader.ReaderImplementation {
throws IOException {
this(useAsynchronousIO ? new AsyncBlockCompressedInputStream(file,
inflaterFactory) : new BlockCompressedInputStream(file, inflaterFactory),
indexFile!=null ? indexFile : SamFiles.findIndex(file),
eagerDecode, useAsynchronousIO, file.getAbsolutePath(), validationStringency,
samRecordFactory);
-if (mIndexFile != null && mIndexFile.lastModified() <
file.lastModified()) {
+
+if (mIndexFile != null && mIndexFile.lastModified() <
file.lastModified() - 5000) {
System.err.p
[med-svn] [Git][med-team/htsjdk] Pushed new tag debian/3.0.4+dfsg-1
Pierre Gruet pushed new tag debian/3.0.4+dfsg-1 at Debian Med / htsjdk -- View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/tree/debian/3.0.4+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/htsjdk] Pushed new tag upstream/3.0.4+dfsg
Pierre Gruet pushed new tag upstream/3.0.4+dfsg at Debian Med / htsjdk -- View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/tree/upstream/3.0.4+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb] Pushed new tag debian/3.0.2+dfsg-1
Aaron M. Ucko pushed new tag debian/3.0.2+dfsg-1 at Debian Med / ncbi-vdb -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/tree/debian/3.0.2+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb][master] 2 commits: routine-update: Standards-Version: 4.6.2
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-vdb Commits: a7296f4d by Aaron M. Ucko at 2022-12-27T11:52:37-05:00 routine-update: Standards-Version: 4.6.2 - - - - - 01fdd846 by Aaron M. Ucko at 2022-12-27T12:01:45-05:00 Finalize ncbi-vdb 3.0.2+dfsg-1 (still targeting experimental for now). - - - - - 2 changed files: - debian/changelog - debian/control Changes: = debian/changelog = @@ -1,6 +1,6 @@ -ncbi-vdb (3.0.2+dfsg-1) UNRELEASED; urgency=medium +ncbi-vdb (3.0.2+dfsg-1) experimental; urgency=medium - * New upstream release. (NOT RELEASED YET.) + * New upstream release. * debian/control: Drop libkdf5-* and corresponding libhdf5-dev build-dep. * debian/copyright: Drop references to content removed upstream, both in Files-Excluded and in special cases. @@ -13,8 +13,9 @@ ncbi-vdb (3.0.2+dfsg-1) UNRELEASED; urgency=medium - Dropping several static libraries (which had been installed on principle). - Dropping libkdf5. + * Standards-Version: 4.6.2 (routine-update) - -- Aaron M. Ucko Sat, 17 Dec 2022 23:17:00 -0500 + -- Aaron M. Ucko Tue, 27 Dec 2022 12:01:29 -0500 ncbi-vdb (3.0.0+dfsg2-4) experimental; urgency=medium = debian/control = @@ -19,7 +19,7 @@ Build-Depends-Arch: cmake, doxygen, graphviz, chrpath -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/ncbi-vdb Vcs-Git: https://salsa.debian.org/med-team/ncbi-vdb.git Homepage: https://github.com/ncbi/ncbi-vdb View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/eaa562b0b0d3e664d8a3af46464c6c7245688486...01fdd8463d3baf3b68a25cf4f40077b7cba3d1cf -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/eaa562b0b0d3e664d8a3af46464c6c7245688486...01fdd8463d3baf3b68a25cf4f40077b7cba3d1cf You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-pysam] Pushed new tag debian/0.20.0+ds-2
Étienne Mollier pushed new tag debian/0.20.0+ds-2 at Debian Med / python-pysam -- View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/tree/debian/0.20.0+ds-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-pysam][master] 6 commits: disable-tests-python3.11.patch: add; work around test failure.
Étienne Mollier pushed to branch master at Debian Med / python-pysam Commits: 80e9e2fd by Étienne Mollier at 2022-12-27T11:35:48+01:00 disable-tests-python3.11.patch: add; work around test failure. Thanks: John Marshall and Graham Inggs Closes: #1024425 - - - - - a8954aa9 by Étienne Mollier at 2022-12-27T11:37:21+01:00 d/control: restore dependency on python3-all-dev. - - - - - a76ba743 by Étienne Mollier at 2022-12-27T11:38:43+01:00 d/control: restore autodep8-python autopkgtest. - - - - - d6912281 by Étienne Mollier at 2022-12-27T11:39:50+01:00 update changelog - - - - - 95ddab52 by Étienne Mollier at 2022-12-27T11:40:54+01:00 routine-update: Standards-Version: 4.6.2 - - - - - ecb253ac by Étienne Mollier at 2022-12-27T11:49:02+01:00 routine-update: Ready to upload to unstable - - - - - 4 changed files: - debian/changelog - debian/control - + debian/patches/disable-tests-python3.11.patch - debian/patches/series Changes: = debian/changelog = @@ -1,3 +1,13 @@ +python-pysam (0.20.0+ds-2) unstable; urgency=medium + + * disable-tests-python3.11.patch: add; work around test failure. +Thanks to John Marshall and Graham Inggs (Closes: #1024425) + * d/control: restore dependency on python3-all-dev. + * d/control: restore autodep8-python autopkgtest. + * Standards-Version: 4.6.2 (routine-update) + + -- Étienne Mollier Tue, 27 Dec 2022 11:41:25 +0100 + python-pysam (0.20.0+ds-1) unstable; urgency=medium * New upstream version = debian/control = @@ -4,22 +4,21 @@ Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Section: python -# FIXME: restore Testsuite: autopkgtest-pkg-python when #1024425 is resolved. +Testsuite: autopkgtest-pkg-python Priority: optional Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, libhts-dev (>= 1.14~), zlib1g-dev, -# FIXME: restore python3-all-dev when #1024425 is resolved. - python3-dev, + python3-all-dev, python3-setuptools, cython3, tabix , samtools , bcftools , python3-pytest -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/python-pysam Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git Homepage: https://pysam.readthedocs.org/en/latest = debian/patches/disable-tests-python3.11.patch = @@ -0,0 +1,28 @@ +Description: skip tests bound to fail past python3.11. + Thanks John Marshall and Graham Inggs for the independent suggestion. +Author: Étienne Mollier +Bug: https://github.com/pysam-developers/pysam/issues/1151 +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024425 +Last-Update: 2022-12-27 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- python-pysam.orig/tests/AlignmentFilePileup_test.py python-pysam/tests/AlignmentFilePileup_test.py +@@ -1,5 +1,6 @@ + """Benchmarking module for AlignmentFile functionality""" + import os ++import sys + import pysam + import unittest + from TestUtils import make_data_files, BAM_DATADIR, IS_PYTHON3, force_str, flatten_nested_list +@@ -206,6 +207,10 @@ + def tearDown(self): + self.samfile.close() + ++@unittest.skipIf((sys.version_info.major == 3 ++ and sys.version_info.minor >= 11) ++ or sys.version_info.major >= 4, ++ "Test known to fail past python3.11.") + def testIteratorOutOfScope(self): + '''test if exception is raised if pileup col is accessed after + iterator is exhausted.''' = debian/patches/series = @@ -1,3 +1,4 @@ skip_test_remote.patch clean_less skip-test-on-32-bit.patch +disable-tests-python3.11.patch View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/33f64515dfa4757a76900275d21e5104b5427b75...ecb253ac5c723737a3f3cf9646b2ef0c8e90a12c -- View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/33f64515dfa4757a76900275d21e5104b5427b75...ecb253ac5c723737a3f3cf9646b2ef0c8e90a12c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star] Pushed new tag upstream/2.7.10b+dfsg
Sascha Steinbiss pushed new tag upstream/2.7.10b+dfsg at Debian Med / rna-star -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/tree/upstream/2.7.10b+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star][pristine-tar] pristine-tar data for rna-star_2.7.10b+dfsg.orig.tar.xz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / rna-star Commits: bdf38bf7 by Sascha Steinbiss at 2022-12-27T02:18:29+01:00 pristine-tar data for rna-star_2.7.10b+dfsg.orig.tar.xz - - - - - 2 changed files: - + rna-star_2.7.10b+dfsg.orig.tar.xz.delta - + rna-star_2.7.10b+dfsg.orig.tar.xz.id Changes: = rna-star_2.7.10b+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/rna-star_2.7.10b+dfsg.orig.tar.xz.delta differ = rna-star_2.7.10b+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +6953f562f0b5e9a15c6d2d5310f9a4553fb9769e View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/bdf38bf7fcc8053b475f0888159459aa1f2805c7 -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/bdf38bf7fcc8053b475f0888159459aa1f2805c7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star][upstream] New upstream version 2.7.10b+dfsg
Sascha Steinbiss pushed to branch upstream at Debian Med / rna-star Commits: 89e51161 by Sascha Steinbiss at 2022-12-27T02:18:28+01:00 New upstream version 2.7.10b+dfsg - - - - - 30 changed files: - + .travis.yml - CHANGES.md - README.md - RELEASEnotes.md - doc/STARmanual.pdf - docs/STARsolo.md - extras/doc-latex/STARmanual.tex - extras/docker/Dockerfile - extras/scripts/sjFromSAMcollapseUandM.awk - extras/scripts/sjFromSAMcollapseUandM_inclOverlaps.awk - source/Genome.cpp - source/Makefile - source/OutSJ.cpp - source/OutSJ.h - source/ParametersClip_initialize.cpp - source/ParametersSolo.cpp - source/ParametersSolo.h - source/ReadAlignChunk_mapChunk.cpp - source/STAR.cpp - source/SharedMemory.cpp - source/Solo.cpp - source/SoloCommon.h - source/SoloFeature.cpp - source/SoloFeature.h - source/SoloFeature_cellFiltering.cpp - source/SoloFeature_collapseUMIall_multiMappers.cpp → source/SoloFeature_collapseUMIall.cpp - source/SoloFeature_countCBgeneUMI.cpp - source/SoloFeature_countVelocyto.cpp - source/SoloFeature_outputResults.cpp - source/SoloFeature_processRecords.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/89e511619950f991efd95a5a581ee65a840673d3 -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/89e511619950f991efd95a5a581ee65a840673d3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star][master] 3 commits: New upstream version 2.7.10b+dfsg
Sascha Steinbiss pushed to branch master at Debian Med / rna-star Commits: 89e51161 by Sascha Steinbiss at 2022-12-27T02:18:28+01:00 New upstream version 2.7.10b+dfsg - - - - - af3a5b71 by Sascha Steinbiss at 2022-12-27T02:18:29+01:00 Update upstream source from tag 'upstream/2.7.10b+dfsg' Update to upstream version '2.7.10b+dfsg' with Debian dir e281a7aa9f9d83781a8e3d2760edf7c9507d642f - - - - - a880cfe0 by Sascha Steinbiss at 2022-12-27T10:15:44+01:00 new upstream release - - - - - 30 changed files: - + .travis.yml - CHANGES.md - README.md - RELEASEnotes.md - debian/changelog - debian/patches/gcc-12.patch - doc/STARmanual.pdf - docs/STARsolo.md - extras/doc-latex/STARmanual.tex - extras/docker/Dockerfile - extras/scripts/sjFromSAMcollapseUandM.awk - extras/scripts/sjFromSAMcollapseUandM_inclOverlaps.awk - source/Genome.cpp - source/Makefile - source/OutSJ.cpp - source/OutSJ.h - source/ParametersClip_initialize.cpp - source/ParametersSolo.cpp - source/ParametersSolo.h - source/ReadAlignChunk_mapChunk.cpp - source/STAR.cpp - source/SharedMemory.cpp - source/Solo.cpp - source/SoloCommon.h - source/SoloFeature.cpp - source/SoloFeature.h - source/SoloFeature_cellFiltering.cpp - source/SoloFeature_collapseUMIall_multiMappers.cpp → source/SoloFeature_collapseUMIall.cpp - source/SoloFeature_countCBgeneUMI.cpp - source/SoloFeature_countVelocyto.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/8e58df5c0e2332e38b9ecf159d06fcf28ac99aea...a880cfe0460e2d53a0f6861b8bcbad3794c2ac8f -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/8e58df5c0e2332e38b9ecf159d06fcf28ac99aea...a880cfe0460e2d53a0f6861b8bcbad3794c2ac8f You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star] Pushed new tag debian/2.7.10b+dfsg-1
Sascha Steinbiss pushed new tag debian/2.7.10b+dfsg-1 at Debian Med / rna-star -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/tree/debian/2.7.10b+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
