[med-svn] [Git][med-team/bedtools][master] 14 commits: routine-update: New upstream version

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / bedtools


Commits:
d3b073f7 by Étienne Mollier at 2021-01-27T15:11:52+01:00
routine-update: New upstream version

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b6cb1870 by Étienne Mollier at 2021-01-27T15:11:54+01:00
New upstream version 2.30.0+dfsg
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8e2a0b2e by Étienne Mollier at 2021-01-27T15:12:37+01:00
Update upstream source from tag 'upstream/2.30.0+dfsg'

Update to upstream version '2.30.0+dfsg'
with Debian dir ef4d8263068b691b4523f0cc81247527235d2f63
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2d5ed086 by Étienne Mollier at 2021-01-27T15:17:51+01:00
refresh 2to3.patch

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91def4b6 by Étienne Mollier at 2021-01-27T15:18:47+01:00
refresh hardening patch

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864f8856 by Étienne Mollier at 2021-01-27T16:32:58+01:00
remove test related patches

The test suite has been reviewed by upstream, following John
Marshall's intervention on Debian Med:

	https://lists.debian.org/debian-med/2021/01/msg00189.html

Thanks John

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39ec1ebc by Étienne Mollier at 2021-01-27T16:36:54+01:00
32-bit-fixes.patch applied upstream

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119bc1d5 by Étienne Mollier at 2021-01-27T16:37:35+01:00
spelling patch applied upstream

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21c7ab34 by Étienne Mollier at 2021-01-27T16:40:47+01:00
remove references to htsutil

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d41d79ab by John Marshall at 2021-01-27T17:11:35+01:00
add htsutil patch

This patch inlines the htsutil test tool to reduce the memory footprint
of the bedtools package, compared to adding it as a side program.

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8495d818 by Étienne Mollier at 2021-01-27T17:16:14+01:00
d/rules: set htsutil to use subcommand

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852d8af6 by Étienne Mollier at 2021-01-27T17:16:34+01:00
d/t/run-unit-test: use htsutil subcommand

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d2e90e8a by Étienne Mollier at 2021-01-27T17:24:08+01:00
updated changelog

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e8ffe8bd by Étienne Mollier at 2021-01-27T17:27:59+01:00
routine-update: Ready to upload to unstable

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30 changed files:

- .github/workflows/main.yml
- .gitignore
- Makefile
- README.md
- − debian/bedtools-test.links
- debian/bedtools.install
- debian/changelog
- debian/patches/2to3.patch
- − debian/patches/32-bit-fixes.patch
- − debian/patches/fix_intersect_test.patch
- − debian/patches/fix_test_script.patch
- debian/patches/hardening
- + debian/patches/htsutil
- − debian/patches/no-samtools
- debian/patches/series
- − debian/patches/spelling
- debian/rules
- debian/tests/run-unit-test
- docs/conf.py
- docs/content/advanced-usage.rst
- docs/content/general-usage.rst
- docs/content/history.rst
- docs/content/installation.rst
- docs/content/tools/getfasta.rst
- docs/content/tools/intersect.rst
- docs/content/tools/multicov.rst
- src/annotateBed/annotateBed.cpp
- src/annotateBed/annotateMain.cpp
- src/bamToFastq/bamToFastq.cpp
- src/bedpeToBam/bedpeToBam.cpp


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/bedtools/-/compare/98d1fa4c90623052f1a8ac357a2ba6a61ca52f2f...e8ffe8bdde9782b2f23945a2d033f5739cff42f2

-- 
View it on GitLab: https://salsa.debian.org/med-team/bedtools/-/compare/98d1fa4c90623052f1a8ac357a2ba6a61ca52f2f...e8ffe8bdde9782b2f23945a2d033f5739cff42f2
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