[med-svn] [Git][med-team/libseqlib][master] 7 commits: New upstream version 1.1.2+git20201210+dfsg

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / libseqlib


Commits:
438a32ff by Michael R. Crusoe at 2020-12-17T12:16:09+01:00
New upstream version 1.1.2+git20201210+dfsg
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c20efbaf by Michael R. Crusoe at 2020-12-17T12:16:10+01:00
Update upstream source from tag 'upstream/1.1.2+git20201210+dfsg'

Update to upstream version '1.1.2+git20201210+dfsg'
with Debian dir fbf7fa0084431e381afda473f9d89cd3f5b649cb
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7766ff6d by Michael R. Crusoe at 2020-12-17T12:16:35+01:00
Snapshot from upstream.

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e73e0866 by Michael R. Crusoe at 2020-12-17T12:19:24+01:00
Refresh patches

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cd26a2f3 by Michael R. Crusoe at 2020-12-17T12:26:54+01:00
build-deps: libbz2-dev

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5920d711 by Michael R. Crusoe at 2020-12-17T12:36:29+01:00
Added patch to fix compat with libjsoncpp 1.8.4+. Closes #976414

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7555d3ac by Michael R. Crusoe at 2020-12-17T12:45:43+01:00
TODO: upstream uses libfml-dev r50, but debian's package is r41

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30 changed files:

- .gitmodules
- Makefile.am
- Makefile.in
- SeqLib/BWAWrapper.h
- SeqLib/BamReader.h
- SeqLib/BamRecord.h
- SeqLib/BamWalker.h
- SeqLib/BamWriter.h
- SeqLib/FastqReader.h
- SeqLib/FermiAssembler.h
- SeqLib/GenomicRegion.h
- SeqLib/GenomicRegionCollection.cpp
- SeqLib/ReadFilter.h
- + SeqLib/ThreadPool.h
- SeqLib/UnalignedSequence.h
- autogen.sh
- configure
- configure.ac
- debian/changelog
- debian/control
- debian/patches/adapt_to_debian_fermi-lite.patch
- debian/patches/dynamic_lib.patch
- − debian/patches/fix_private_htslib_usage.patch
- debian/patches/fml_include_path.patch
- + debian/patches/libjsoncpp_1_8_4_compat
- debian/patches/pkg-config.patch
- debian/patches/series
- debian/patches/use_debian_packaged_libs.patch
- src/BWAWrapper.cpp
- src/BamReader.cpp


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/libseqlib/-/compare/6cb334050d63d90bb8dcece24a62205fe1dacf73...7555d3ac0922a0421d4cb1c0ad9c37a64f0186eb

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View it on GitLab: https://salsa.debian.org/med-team/libseqlib/-/compare/6cb334050d63d90bb8dcece24a62205fe1dacf73...7555d3ac0922a0421d4cb1c0ad9c37a64f0186eb
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