[med-svn] [Git][med-team/ivar][master] 6 commits: routine-update: New upstream version

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / ivar


Commits:
a1495424 by Étienne Mollier at 2020-12-13T22:18:53+01:00
routine-update: New upstream version

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3c322198 by Étienne Mollier at 2020-12-13T22:18:54+01:00
New upstream version 1.3+dfsg
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4d1e809e by Étienne Mollier at 2020-12-13T22:18:55+01:00
Update upstream source from tag 'upstream/1.3+dfsg'

Update to upstream version '1.3+dfsg'
with Debian dir 3d0e78d36b4f1f4d86c0b6660351e68bacef5a7a
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72eb8928 by Étienne Mollier at 2020-12-13T22:18:55+01:00
routine-update: Standards-Version: 4.5.1

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1eeb0aca by Étienne Mollier at 2020-12-13T22:19:33+01:00
routine-update: Ready to upload to unstable

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e97c7fe5 by Étienne Mollier at 2020-12-13T23:10:15+01:00
Run the test suite in a single thread.

Run run with the host default thread count, it would seem several
tests are colliding, and leading to random failures.  The issue
has been caught on i386, but did affect amd64 as well.

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30 changed files:

- configure.ac
- + data/pair_info_2.tsv
- + data/test_amplicon.sorted.bam
- + data/test_isize.bed
- + data/test_isize.sorted.bam
- debian/changelog
- debian/control
- debian/rules
- docs/MANUAL.md
- src/Makefile.am
- + src/interval_tree.cpp
- + src/interval_tree.h
- src/ivar.cpp
- src/trim_primer_quality.cpp
- src/trim_primer_quality.h
- tests/Makefile.am
- tests/check_quality_trim.cpp
- tests/test_allele_depth.cpp
- + tests/test_amplicon_search.cpp
- tests/test_call_consensus_from_plup.cpp
- tests/test_common_variants.cpp
- tests/test_consensus_min_depth.cpp
- tests/test_consensus_seq_id.cpp
- tests/test_consensus_threshold.cpp
- tests/test_getmasked.cpp
- + tests/test_interval_tree.cpp
- + tests/test_isize_trim.cpp
- tests/test_primer_bed.cpp
- tests/test_primer_trim.cpp
- tests/test_primer_trim_edge_cases.cpp


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/dceaa07e1aba563df35db7cba5de74a8c4da21ba...e97c7fe547a34b4dd3ee98b513b508122f736a34

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View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/dceaa07e1aba563df35db7cba5de74a8c4da21ba...e97c7fe547a34b4dd3ee98b513b508122f736a34
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