[med-svn] [Git][med-team/bowtie2][master] 8 commits: New upstream version 2.3.4.2

[Alexandre Mestiashvili]

Alexandre Mestiashvili pushed to branch master at Debian Med / bowtie2


Commits:
157dbc20 by Alexandre Mestiashvili at 2018-08-14T09:16:33Z
New upstream version 2.3.4.2
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c6c16067 by Alexandre Mestiashvili at 2018-08-14T09:17:08Z
Update upstream source from tag 'upstream/2.3.4.2'

Update to upstream version '2.3.4.2'
with Debian dir c8219b584a3f214c8e384c1d1d64f3f8580722ec
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25a75367 by Alexandre Mestiashvili at 2018-08-14T09:20:01Z
Bump Standards-Version to 4.2.0

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9a3ac321 by Alexandre Mestiashvili at 2018-08-14T09:48:24Z
Refresh patches

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6b58808a by Alexandre Mestiashvili at 2018-08-14T11:03:58Z
Add patch fixing interpreter for bowite2 scripts

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d7c4ead5 by Alexandre Mestiashvili at 2018-08-14T11:27:03Z
Add patch removing reference to js lib for ie9...

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dc419df9 by Alexandre Mestiashvili at 2018-08-14T11:31:44Z
Update uploader's email

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d5e59a9c by Alexandre Mestiashvili at 2018-08-14T11:32:13Z
Update changelog, upload to unstable

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30 changed files:

- + CMakeLists.txt
- MANUAL
- MANUAL.markdown
- Makefile
- NEWS
- VERSION
- aln_sink.cpp
- bowtie2-build
- bowtie2-inspect
- bt2_idx.h
- bt2_search.cpp
- debian/changelog
- debian/control
- + debian/patches/drop-not-needed-js-from-manual.patch
- debian/patches/reproducible.patch
- debian/patches/series
- debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch
- + debian/patches/wrong-interpreter-path.patch
- doc/manual.html
- doc/website/manual.ssi
- doc/website/recent_news.ssi
- doc/website/rhsidebar.ssi
- + example/reads/combined_reads.bam
- formats.h
- opts.h
- pat.cpp
- pat.h
- presets.cpp
- read.h
- ref_read.cpp


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/bowtie2/compare/e55726211b2d7276e9ddcdac1ef98e36ccbe7839...d5e59a9ca4138dce566729d5b36c81f20dce4ff9

-- 
View it on GitLab: https://salsa.debian.org/med-team/bowtie2/compare/e55726211b2d7276e9ddcdac1ef98e36ccbe7839...d5e59a9ca4138dce566729d5b36c81f20dce4ff9
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