biobambam2 (2.0.185-1) unstable; urgency=medium * Add missing include directives for gcc13 -- German Tischler-Höhle Sun, 11 Dec 2022 13:21:00 +0100 biobambam2 (2.0.184-1) unstable; urgency=medium * Add tagonly sort option in bamsort * Adapt to change in libmaus2 (renaming of GetObject to GetCObject) -- German Tischler-Höhle Mon, 19 Sep 2022 13:40:22 +0200 biobambam2 (2.0.183-1) unstable; urgency=medium * Adapt to change in libmaus2 (rename GetObject to GetCObject) -- German Tischler-Höhle Mon, 02 Aug 2021 17:54:00 +0200 biobambam2 (2.0.182-1) unstable; urgency=medium * Add O (output file) option for bamfastcat -- German Tischler-Höhle Sun, 11 Apr 2021 23:40:35 +0200 biobambam2 (2.0.181-1) unstable; urgency=medium * Add clipslashid and patchne flags in fastqtobam2 -- German Tischler-Höhle Fri, 02 Apr 2021 15:57:51 +0200 biobambam2 (2.0.180-1) unstable; urgency=medium * bump libmaus2 version due to fixes for io_lib(cram) and tmp file generation in libmaus2 -- German Tischler-Höhle Mon, 15 Mar 2021 23:05:17 +0100 biobambam2 (2.0.178-1) unstable; urgency=medium * Add bamaddne * bump libmaus2 version -- German Tischler-Höhle Mon, 23 Nov 2020 14:39:27 +0100 biobambam2 (2.0.177-1) unstable; urgency=medium * Versioning cleanup -- German Tischler-Höhle Thu, 12 Nov 2020 10:39:59 +0100 biobambam2 (2.0.176-1) unstable; urgency=medium * Adapt UpdateNumericalIndex to new libmaus2 api * Fix output of orphaned read 2 instances in bamtofastq when splitting by readgroup * Remove references to non functional IRODS interface in libmaus2 * Add bamdifference program -- German Tischler-Höhle Thu, 12 Nov 2020 09:43:13 +0100 biobambam2 (2.0.175-1) unstable; urgency=medium * Add fastaselectreg -- German Tischler-Höhle Thu, 27 Aug 2020 10:08:12 +0200 biobambam2 (2.0.174-1) unstable; urgency=medium * Fix wrong operator for deallocating memory in bamconsensus -- German Tischler-Höhle Mon, 10 Aug 2020 11:26:08 +0200 biobambam2 (2.0.173-1) unstable; urgency=medium * Fix for libmaus2 update -- German Tischler-Höhle Wed, 05 Aug 2020 14:41:16 +0200 biobambam2 (2.0.172-1) unstable; urgency=medium * update libmaus2 version -- German Tischler-Höhle Thu, 30 Jul 2020 09:10:25 +0200 biobambam2 (2.0.171-1) unstable; urgency=medium * replace UNIQUE_PTR_MOVE by std::move -- German Tischler-Höhle Tue, 21 Jul 2020 17:47:31 +0200 biobambam2 (2.0.170-1) unstable; urgency=medium * update libmaus2 version -- German Tischler-Höhle Mon, 20 Jul 2020 13:34:09 +0200 biobambam2 (2.0.169-1) unstable; urgency=medium * update libmaus2 version -- German Tischler-Höhle Fri, 17 Jul 2020 11:47:30 +0200 biobambam2 (2.0.168-1) unstable; urgency=medium * update libmaus2 version -- German Tischler-Höhle Tue, 07 Jul 2020 17:00:28 +0200 biobambam2 (2.0.167-1) unstable; urgency=medium * bump decompress buffer size when necessary in bamauxmerge2 -- German Tischler-Höhle Fri, 19 Jun 2020 12:49:56 +0200 biobambam2 (2.0.166-1) unstable; urgency=medium * make gz non value argument in vcfreplacecontigsmap -- German Tischler-Höhle Tue, 09 Jun 2020 13:21:54 +0200 biobambam2 (2.0.165-1) unstable; urgency=medium * Add vcfreplacecontigsmap program -- German Tischler-Höhle Mon, 08 Jun 2020 16:56:00 +0200 biobambam2 (2.0.164-1) unstable; urgency=medium * Add vcffilterfilterflags -- German Tischler-Höhle Thu, 07 May 2020 13:45:25 +0200 biobambam2 (2.0.163-1) unstable; urgency=medium * do not use assert in parallel loop of bamfilterk -- German Tischler-Höhle Wed, 22 Apr 2020 09:13:28 +0200 biobambam2 (2.0.162-1) unstable; urgency=medium * Add mapped/unmapped in bamcountflags -- German Tischler-Höhle Mon, 30 Mar 2020 15:11:34 +0200 biobambam2 (2.0.161-1) unstable; urgency=medium * Add bamcountflags -- German Tischler-Höhle Mon, 30 Mar 2020 14:31:52 +0200 biobambam2 (2.0.160-1) unstable; urgency=medium * Add bamdepthmerge for merging several depth tracks into a single table * Add merging framework in DepthIntervalGetter.hpp * Explicitely init DepthInterval in constructor * change/fix loop bounds in bamfeaturecount * Check for exception in parallel loop of bamexondepth -- German Tischler-Höhle Wed, 25 Mar 2020 18:00:57 +0100 biobambam2 (2.0.159-1) unstable; urgency=medium * Add cram compression mode option in bamsormadup * refactor bamexondepth * bump libmaus2 version * add gc content based analysis in bamexondepth * parallelise bamexondepth * change serialised form of DepthInterval and add comparator classes * fix warning in bamadapterfind -- German Tischler-Höhle Mon, 16 Mar 2020 13:35:22 +0100 biobambam2 (2.0.158-1) unstable; urgency=medium * bump libmaus2 version * Output coverage information in bamexondepth * Fix default depth setting in bamdepth * add avl tree tracking in bamexondepth * fix warnings -- German Tischler-Höhle Mon, 09 Mar 2020 09:02:03 +0100 biobambam2 (2.0.157-1) unstable; urgency=medium * Adapt bamexondepth from new code for bamdepth * bump libmaus2 version * Refactor bamdepth * Add program bamsimpledepth * Fix bamdepth (do not output multiple adjacent intervals for same depth) * update ignore file * Add vcfdiff program * Print complete alignment in case of exception in bamfeaturecount * Add bamexondepth and bamheadercat programs * add bammarkduplicatesoptdist * fix warnings * add print method in DepthInterval class * be more verbose in fastqtobam2 inflate failure case -- German Tischler-Höhle Wed, 04 Mar 2020 09:12:21 +0100 biobambam2 (2.0.156-1) unstable; urgency=medium * Add program bamexploderg for splitting an alignment file by read groups -- German Tischler-Höhle Mon, 24 Feb 2020 08:08:51 +0100 biobambam2 (2.0.155-1) unstable; urgency=medium * adapt cigar string on the fly in bamconsensus -- German Tischler-Höhle Fri, 21 Feb 2020 13:13:11 +0100 biobambam2 (2.0.154-1) unstable; urgency=medium * add bamfilterbyname and vcffiltersamples programs -- German Tischler-Höhle Tue, 18 Feb 2020 12:45:33 +0100 biobambam2 (2.0.153-1) unstable; urgency=medium * check for failure of parallel loop in bamfeaturecount and change sort buffer size -- German Tischler-Höhle Fri, 24 Jan 2020 12:29:53 +0100 biobambam2 (2.0.152-1) unstable; urgency=medium * update libmaus2 version to 2.0.694 -- German Tischler-Höhle Wed, 22 Jan 2020 09:58:27 +0100 biobambam2 (2.0.151-1) unstable; urgency=medium * bump libmaus2 version -- German Tischler-Höhle Tue, 21 Jan 2020 16:41:38 +0100 biobambam2 (2.0.150-1) unstable; urgency=medium * Add cols (line wrapping) option in bamtofastq -- German Tischler-Höhle Tue, 07 Jan 2020 16:37:02 +0100 biobambam2 (2.0.149-1) unstable; urgency=medium * use kmerCallbackPosFR instead of kmerCallbackPos in bamfilterk * Add vcfreplacecontigs program -- German Tischler-Höhle Tue, 07 Jan 2020 09:02:29 +0100 biobambam2 (2.0.148-1) unstable; urgency=medium * compute maximum depth in bamfeaturecount * fix output of wrong reference id in bamfeaturecount if GTF chrom set is a subset of BAM chrom set -- German Tischler-Höhle Wed, 13 Nov 2019 12:53:00 +0100 biobambam2 (2.0.147-1) unstable; urgency=medium * fix heap comparisons in bamconsensus -- German Tischler-Höhle Tue, 05 Nov 2019 10:19:07 +0100 biobambam2 (2.0.146-1) unstable; urgency=medium * add explicit flush in bamtofastq * bump libmaus2 version * explicitely call flush on BamToFastqOutputFileSet objects in bamtofastq (try to avoid triggering exceptions in object destructor) * allow disabling adapter detection/clipping in fastqtobam2 * use dynamic scheduling in bamfilterk -- German Tischler-Höhle Wed, 30 Oct 2019 10:48:48 +0100 biobambam2 (2.0.145-1) unstable; urgency=medium * refactor vcfsort * add kmer end position on reference in bamconsensus * fixes after libmaus2 changes -- German Tischler-Höhle Fri, 11 Oct 2019 12:46:33 +0200 biobambam2 (2.0.144-1) unstable; urgency=medium * update list of uncommon programs -- German Tischler-Höhle Fri, 27 Sep 2019 13:37:44 +0200 biobambam2 (2.0.143-1) unstable; urgency=medium * fix newline issue in Makefile -- German Tischler-Höhle Fri, 27 Sep 2019 13:11:19 +0200 biobambam2 (2.0.142-1) unstable; urgency=medium * add install-uncommon configure option to deselect some programs from standard installation -- German Tischler-Höhle Fri, 27 Sep 2019 12:58:23 +0200 biobambam2 (2.0.141-1) unstable; urgency=medium * bump libmaus2 version -- German Tischler-Höhle Fri, 27 Sep 2019 11:24:14 +0200 biobambam2 (2.0.140-1) unstable; urgency=medium * update libmaus2 version -- German Tischler-Höhle Fri, 27 Sep 2019 08:57:03 +0200 biobambam2 (2.0.139-1) unstable; urgency=medium * add bamheap3 program -- German Tischler-Höhle Thu, 19 Sep 2019 14:09:13 +0200 biobambam2 (2.0.138-1) unstable; urgency=medium * add exportcdna option in bamfeaturecount -- German Tischler-Höhle Wed, 28 Aug 2019 15:50:12 +0200 biobambam2 (2.0.137-1) unstable; urgency=medium * add manual page for bamfeaturecount * add manual page for filtergtf * add filtergtf program * implement simplified transcript level analysis in bamfeaturecount -- German Tischler-Höhle Wed, 28 Aug 2019 10:04:09 +0200 biobambam2 (2.0.136-1) unstable; urgency=medium * add bamfixpairinfo program -- German Tischler-Höhle Thu, 22 Aug 2019 14:44:39 +0200 biobambam2 (2.0.135-1) unstable; urgency=medium * add UniqueInterval class in bamfeaturecount * add readgroup and program header lines in bamconsensus * fix border check in bamrecalculatecigar * fix computation of MD/NM fields in bamconsensus * make exclude flags user settable in bamconsensus * change default verbose setting in bamfillquery * update synopsis in bamconsensus help message * make bamconsensus output BAM file containing alignments of consensus with the reference instead of just the consensus as FastA * construct fasta index in bamrecalculatecigar if needed * add unmapped option for bamfilterlength * add bamconsensus to list of installed programs and add documentation * improve scaling in bamconsensus * make running dot optional in bamconsensus -- German Tischler-Höhle Thu, 22 Aug 2019 10:47:00 +0200 biobambam2 (2.0.134-1) unstable; urgency=medium * bump libmaus2 version * be more verbose in bamrecalculatecigar when the input is not suitably sorted *add fragmergepar option in bamsormadup to allow (some) control concerning the number of simultaneously open files used in duplicate marking -- German Tischler-Höhle Mon, 19 Aug 2019 15:18:51 +0200 biobambam2 (2.0.133-1) unstable; urgency=medium * update libmaus2 version -- German Tischler-Höhle Fri, 16 Aug 2019 13:32:26 +0200 biobambam2 (2.0.132-1) unstable; urgency=medium * use heaviest path per connected component as representative in bamconsensus -- German Tischler-Höhle Fri, 16 Aug 2019 13:14:32 +0200 biobambam2 (2.0.131-1) unstable; urgency=medium * update help message in bamfilterk * add bamfilterk -- German Tischler-Höhle Tue, 13 Aug 2019 09:36:30 +0200 biobambam2 (2.0.130-1) unstable; urgency=medium * support numerical indexing in fastqtobam2 -- German Tischler-Höhle Thu, 08 Aug 2019 11:13:12 +0200 biobambam2 (2.0.129-1) unstable; urgency=medium * rename fastaexplode to fastaexplod -- German Tischler-Höhle Thu, 08 Aug 2019 09:29:48 +0200 biobambam2 (2.0.128-1) unstable; urgency=medium * remove manual page for removed kmerprob * remove bamrefdepth and bamrefdepthpeaks -- German Tischler-Höhle Wed, 31 Jul 2019 14:10:27 +0200 biobambam2 (2.0.127-1) unstable; urgency=medium * add bamdepthintersect program * add bamdepth program * add DepthInterval class * remove hard coded Z_DEFAULT_COMPRESSION default and replace by DeflateDefaults::getDefaultLevel() -- German Tischler-Höhle Wed, 31 Jul 2019 12:53:58 +0200 biobambam2 (2.0.126-1) unstable; urgency=medium * allow output to standard output in bamnumericalindex -- German Tischler-Höhle Tue, 30 Jul 2019 11:11:47 +0200 biobambam2 (2.0.125-1) unstable; urgency=medium * add construction of numerical index from numerical indexes of input files in bamfastcat -- German Tischler-Höhle Fri, 26 Jul 2019 17:17:43 +0200 biobambam2 (2.0.124-1) unstable; urgency=medium * update numerical index in bamreplacechecksums * update numerical index in bamreheader * put header and data in separate blocks in ReadHeader -- German Tischler-Höhle Thu, 25 Jul 2019 15:29:48 +0200 biobambam2 (2.0.123-1) unstable; urgency=medium * avoid explicitely invoking BamDecoder class (use factory instead) * use output factory to allow SAM/BAM/CRAM output in bam12auxmerge * use input factories in bam12auxmerge to support SAM and CRAM input * add manual page for bamclipXT * remove filtersam and kmerprob -- German Tischler-Höhle Thu, 25 Jul 2019 11:10:33 +0200 biobambam2 (2.0.122-1) unstable; urgency=medium * add bamnumericalindexstats -- German Tischler-Höhle Wed, 24 Jul 2019 15:01:14 +0200 biobambam2 (2.0.121-1) unstable; urgency=medium * add numerical indexing in bamsormadup -- German Tischler-Höhle Wed, 24 Jul 2019 14:34:22 +0200 biobambam2 (2.0.120-1) unstable; urgency=medium * add vcfsort program * remove bamclipextract * simplify bamdisthist -- German Tischler-Höhle Wed, 24 Jul 2019 11:02:17 +0200 biobambam2 (2.0.119-1) unstable; urgency=medium * add manual page for bambisect * fix manual page for bamchecksort * update help message in bamauxmerge2 * remove bamcheckalignments * add manual page for bamauxmerge2 * add manual page for bamauxmerge * clean up bamauxmerge * change input order in bamalignfrac * add documentation for regex option in manual page for bamalignfrac * remove bamalignmentoffsets program * add manual page for bamalignfrac * rewrite bamalignfrac to produce more useful output -- German Tischler-Höhle Tue, 23 Jul 2019 21:55:28 +0200 biobambam2 (2.0.118-1) unstable; urgency=medium * avoid writing empty BGZF blocks in ReadHeader * remove bamlastfilter * remove deprecated bamcollate program -- German Tischler-Höhle Mon, 22 Jul 2019 09:36:51 +0200 biobambam2 (2.0.117-1) unstable; urgency=medium * fix breakages after libmaus2 cleanup -- German Tischler-Höhle Fri, 19 Jul 2019 13:09:16 +0200 biobambam2 (2.0.116-1) unstable; urgency=medium * avoid copying inline EOF blocks in bamfastcat -- German Tischler-Höhle Fri, 19 Jul 2019 12:27:19 +0200 biobambam2 (2.0.115-1) unstable; urgency=medium * add bamfiltereofblocks -- German Tischler-Höhle Fri, 19 Jul 2019 11:23:28 +0200 biobambam2 (2.0.114-1) unstable; urgency=medium * bump libmaus2 version -- German Tischler-Höhle Thu, 18 Jul 2019 10:55:18 +0200 biobambam2 (2.0.113-1) unstable; urgency=medium * add bamfastsplit * add multi threaded processing in bamseqchksum * add building numerical index in bamrecompress * add vcfconcat -- German Tischler-Höhle Wed, 17 Jul 2019 16:19:52 +0200 biobambam2 (2.0.112-1) unstable; urgency=medium * fix bamrecompress for case of BAM input with inline empty BGZF blocks -- German Tischler-Höhle Tue, 16 Jul 2019 13:57:00 +0200 biobambam2 (2.0.111-1) unstable; urgency=medium * use readFileAsStream to read text header file in bamfastcat/bamreheader/bamreplacechecksums * add tryoq flag in bamseqchksum -- German Tischler-Höhle Tue, 16 Jul 2019 11:13:33 +0200 biobambam2 (2.0.110-1) unstable; urgency=medium * add headerchecksums option in bamseqchecksum -- German Tischler-Höhle Mon, 15 Jul 2019 15:59:56 +0200 biobambam2 (2.0.109-1) unstable; urgency=medium * refactor bamreheader/bamfastcat and add bamreplacechecksums -- German Tischler-Höhle Mon, 15 Jul 2019 13:52:29 +0200 biobambam2 (2.0.108-1) unstable; urgency=medium * add include and exclude options in normalisefasta * make sure we write an EOF block in bamfastexploderef even for "empty" output files * add bisect tool * add bamfastnumextract * add low recompression bam input/output variant of exploderef functionality * add populaterefcache program * add bamexploderef -- German Tischler-Höhle Fri, 12 Jul 2019 16:34:24 +0200 biobambam2 (2.0.107-1) unstable; urgency=medium * add OQ tags in fastqtobam2 * add bamfastcat * allow multi threading input and output in bamsplit * replace usage of PosixRegex by std::regex * fixes after changes in libmaus2 * remove lasToBAM * added gzip output in vcffilterinfo * added program vcfpatchcontigprepend (prepend string to all seq ids in a VCF file) * add vcffilterinfo program (filter out all INFO fields not in a given filter list from a VCF file) * add append option in bamreheader * add bamreheader * try to avoid stalling on blocked write queue in bamauxmerge2 * refactor Reference class out of bamauxmerge2 and add cigar string rewriting in bamauxmerge2 -- German Tischler-Höhle Wed, 03 Jul 2019 21:04:34 +0200 biobambam2 (2.0.106-1) unstable; urgency=medium * fix email address in version bumping script -- German Tischler-Höhle Fri, 14 Jun 2019 12:39:35 +0200 biobambam2 (2.0.105-1) unstable; urgency=medium * no change version bump after fixing bumping script -- German Tischler Fri, 14 Jun 2019 12:11:44 +0200 biobambam2 (2.0.104-1) unstable; urgency=medium * version bumping script test -- German Tischler Fri, 14 Jun 2019 12:08:38 +0200 biobambam2 (2.0.103-1) unstable; urgency=low * bump libmaus2 version * remove bamparsort * fixes after libmaus2 changes * do not replace cigar string for unmapped reads in bamauxmerge2 -- German Tischler-Höhle Thu, 14 Jun 2019 12:00:00 +0000