Activity for janda
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Peter Johansson committed [r283] on Code
update to archive 2024.10.16
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update to latest macros.
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update release year
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merge r279 from trunk.
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with empty 1st arg, macro test for C++11 features with CXX first without added switches.
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update copyright years
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avoid deprecation warnings from yat.
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require yat 0.22
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prefer std::shared_ptr over boost version.
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update URLs to guidelines.
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update download URL (reported by Jari Hakkinen)
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fix typo causing incorrect dependency for normal.fasta file.
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previously altered generated file tandem_staggered.dir/tumour.data; here update the src file instead. Also make rules explicit and not SUFFIX based (which is confusing)
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using bwa mem to map test data; some tests have to be adjusted to PASS.
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update to autoconf-archive-2022.09.03
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upgrade to autoconf-archive 2022.02.11
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upgrade 3rd-party autoconf macros
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janda released /janda-0.10.tar.gz.MD5
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bump version to 0.10.1pre
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merge release 0.10 into trunk
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tagging version 0.10
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update copyright years
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preparing release 0.10
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fix problem in Reader: secondary reads were considered as clipped reads; and supplemantary reads were considered as discordant.
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bumping version to 0.11pre
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New stable branch 0.10
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update copyright years
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prepare 0.10-stable branch
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less log
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update copyright years
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ignore copyright in third party files
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add header file in dist
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add missing file
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avoid compiler warnings
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add missing file
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fix candidate
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turn variable split_read_threshold into an unsigned int; log a bit more frequent when few jobs remaining
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some more checks for clear stderr
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remove debug code
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respect THREADS variable
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remove debug code
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when running janda in tests, log to file and check that stderr is clean
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print log.txt into test log
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major refactor
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prefer std instead of boost
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check for options needed for thread support
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prefer std rather than boost
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fix compiler error
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marking failing tests as XFAIL_TESTS
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remove debug code
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fix compiler (gcc 6.4.0) warnings
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prefer including YAT_SAM_HEADER, to allow building against old libbam headers
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correct link order to make it work on ubuntu
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don't try to create bam when tools are not available
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add missing includes
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flush log message
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updating --version output as suggested by GCS
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remove debug code
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use count_threshold also for medium sized variants
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ignore supplementary reads in isize distribution inference; count fragments instead of reads
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update copyright years
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link against boost-chrono
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remove devel branch
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merge parallel branch into trunk
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add missing file
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merge latest trunk changes into branch
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use yat::omic::Fasta::Sequence; and fix some 0/1-based related bug in the Aligner
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correct typo
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use yat::omic::Fasta
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TESTs pass
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tests pass but still a few FIXMEs
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update to latest yat macro
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require cxx11
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remove code catering for yat prior 0.14
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require yat 0.14 because we use dna_reverse_complement in yat
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add missing dependencies
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avoid pedantic compiler warnings
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save environment variables so we can restore later
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fix some spurious test failures and merge F.U.
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bump version to 0.9.2pre
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merge release 0.9.1 into trunk
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tagging version 0.9.1
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update copyright years
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preparing release 0.9.1
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latest yat macro
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test no_normal uses data from somatic.test; add that dependency in Makefile.
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change needed to work with latest autoconf-archive
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upgrade to autoconf-archive-2019.01.06
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upgrade to latest yat
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copy flags from yat verbatimly
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fix compilations against htslib, avoid compiler warnings, and fix spurious test failures
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remove dead files
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remove dead files
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remove TmpBam
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leftover
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remove dead files
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remove class ClippedFilter
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