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ChangeLog
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libmaus2 (2.0.420-1) unstable; urgency=medium
* add splitDbRL function in DatabaseFile
-- German Tischler <[email protected]> Thu, 16 Nov 2017 17:17:07 +0100
libmaus2 (2.0.419-1) unstable; urgency=medium
* add computeTracePart variant in OverlapData
* add parallel sorting options in SortingBufferedOutputFile
* add enumerate method in IntervalTree
* add subset check function in IntegerInterval
* add aint and bint in Path/Overlap
* add parallel buffer sorting option in BufferedOutput
-- German Tischler <[email protected]> Thu, 16 Nov 2017 10:06:46 +0100
libmaus2 (2.0.418-1) unstable; urgency=medium
* add reduceParallel method in SortingBufferedOutputFile
* use unit weights in suffixPositive calls of NNPCor
* add const modifiers in IntervalTree
* add NNPCorLocalAligner
* pass NNP arguments on construction of NNPLocalAligner
* loosen check on Path output
-- German Tischler <[email protected]> Wed, 15 Nov 2017 11:48:54 +0100
libmaus2 (2.0.417-1) unstable; urgency=medium
* add DB_ADAPTER_BEFORE and DB_ADAPTER_AFTER flags in Read class
-- German Tischler <[email protected]> Fri, 10 Nov 2017 13:36:56 +0100
libmaus2 (2.0.416-1) unstable; urgency=medium
* turn failed assertion into exception in Overlap::computeTrace
* add check for correct aid in LasRangeDecoder
-- German Tischler <[email protected]> Thu, 09 Nov 2017 20:05:40 +0100
libmaus2 (2.0.415-1) unstable; urgency=medium
* add checks in Overlap class and avoid code duplication
* add getErrorSum in Path class
-- German Tischler <[email protected]> Thu, 09 Nov 2017 17:40:49 +0100
libmaus2 (2.0.414-1) unstable; urgency=medium
* add canonical method in IndexBase class
* add canonical method in Read class
-- German Tischler <[email protected]> Thu, 09 Nov 2017 14:35:27 +0100
libmaus2 (2.0.413-1) unstable; urgency=medium
* add modifyEquidist function DNABaseNoiseSpiker
-- German Tischler <[email protected]> Wed, 08 Nov 2017 11:12:04 +0100
libmaus2 (2.0.412-1) unstable; urgency=medium
* add NNPCorL class
* add alignForward/reset methods in NNPCor class
-- German Tischler <[email protected]> Tue, 07 Nov 2017 16:35:39 +0100
libmaus2 (2.0.411-1) unstable; urgency=medium
* add missing aid/aread parameter in LasRangeDecoder
-- German Tischler <[email protected]> Mon, 06 Nov 2017 11:23:24 +0100
libmaus2 (2.0.410-1) unstable; urgency=medium
* improve error message in bounds checking of Path
* fix order check in bin indexing of OverlapIndexer
-- German Tischler <[email protected]> Fri, 03 Nov 2017 15:29:58 +0100
libmaus2 (2.0.409-1) unstable; urgency=medium
* add checkBSpan method in Overlap
* check size of values in Path output
-- German Tischler <[email protected]> Fri, 03 Nov 2017 11:23:16 +0100
libmaus2 (2.0.408-1) unstable; urgency=medium
* fix EOF issue with LasRangeDecoder and allow pass through of index decoder
-- German Tischler <[email protected]> Thu, 02 Nov 2017 22:19:07 +0100
libmaus2 (2.0.407-1) unstable; urgency=medium
* add missing include directive in OverlapData
* add computeTracePart function in OverlapData
* add OverlapDataInterface class
-- German Tischler <[email protected]> Thu, 02 Nov 2017 15:14:51 +0100
libmaus2 (2.0.406-1) unstable; urgency=medium
* add LasRangeDecoder class
* add BinIndexDecoder class
* add bin indexing function in OverlapIndexer
* add bin related functions in Path/Overlap
-- German Tischler <[email protected]> Thu, 02 Nov 2017 09:02:11 +0100
libmaus2 (2.0.405-1) unstable; urgency=medium
* add getMaxDif function in Overlap class
* add flags in filtering of GraphDecoder
* add flag encoding in GraphEncoder/GraphDecoder
-- German Tischler <[email protected]> Wed, 01 Nov 2017 13:52:41 +0100
libmaus2 (2.0.404-1) unstable; urgency=medium
* use exception instead of assertion when checking vor NaN in DoubleCode
* add cutTrace method in NP and NPL
-- German Tischler <[email protected]> Wed, 25 Oct 2017 11:36:04 +0200
libmaus2 (2.0.403-1) unstable; urgency=medium
* fix overflow check in binom class
-- German Tischler <[email protected]> Thu, 19 Oct 2017 15:29:49 +0200
libmaus2 (2.0.402-1) unstable; urgency=medium
* add option maxalign in NNPLocalAligner
-- German Tischler <[email protected]> Tue, 17 Oct 2017 14:44:14 +0200
libmaus2 (2.0.401-1) unstable; urgency=medium
* add computeTrace function in OverlapData
* change active band counting in NNPLocalAligner
-- German Tischler <[email protected]> Tue, 17 Oct 2017 10:20:35 +0200
libmaus2 (2.0.400-1) unstable; urgency=medium
* add test for large indices in NPL
* avoid index overflow by changing type in NPL
* add putNumberDecimal variant for AutoArray in BamAlignmentDecoderBase
* fix formatting in AlignmentPrint
-- German Tischler <[email protected]> Mon, 16 Oct 2017 15:28:00 +0200
libmaus2 (2.0.399-1) unstable; urgency=medium
* report names of broken files in GraphEncoder
* add checkSymmetryParallel in AlignmentFileSymmetryCheck
* add getMerger method in SortingBufferedOutputFile header
* add LasIntervals class
* add AlignmentFileCat class
-- German Tischler <[email protected]> Wed, 11 Oct 2017 15:28:34 +0200
libmaus2 (2.0.398-1) unstable; urgency=medium
* avoid endless recursion loop in DecoderBase
-- German Tischler <[email protected]> Fri, 06 Oct 2017 11:01:54 +0200
libmaus2 (2.0.397-1) unstable; urgency=medium
* disable padding in tar writing
-- German Tischler <[email protected]> Thu, 05 Oct 2017 17:43:42 +0200
libmaus2 (2.0.396-1) unstable; urgency=medium
* fix comparison and improve cleanup in AlignmentFileSymmetryCheck
* improve cleanup in SortingBufferedOutputFile
* delete temp files in GraphEncoder while merging them
-- German Tischler <[email protected]> Thu, 05 Oct 2017 12:02:55 +0200
libmaus2 (2.0.395-1) unstable; urgency=medium
* add support for mask tracks in DatabaseFile
-- German Tischler <[email protected]> Wed, 04 Oct 2017 17:36:32 +0200
libmaus2 (2.0.394-1) unstable; urgency=medium
* fix compilation without libarchive
-- German Tischler <[email protected]> Wed, 04 Oct 2017 14:41:33 +0200
libmaus2 (2.0.393-1) unstable; urgency=medium
* remove debug messages in TarWriter
-- German Tischler <[email protected]> Wed, 04 Oct 2017 13:26:10 +0200
libmaus2 (2.0.392-1) unstable; urgency=medium
* add TarWriter class based on libarchive
-- German Tischler <[email protected]> Wed, 04 Oct 2017 12:38:43 +0200
libmaus2 (2.0.391-1) unstable; urgency=medium
* make verbosity optional in AlignmentFileSymmetryCheck
-- German Tischler <[email protected]> Fri, 29 Sep 2017 15:17:40 +0200
libmaus2 (2.0.390-1) unstable; urgency=medium
* fix SerialisingSortingBufferedOutputFileArray
* add swappedStraight method in OverlapInfo
-- German Tischler <[email protected]> Fri, 29 Sep 2017 14:32:01 +0200
libmaus2 (2.0.389-1) unstable; urgency=medium
* add AlignmentFileSymmetryCheck class
-- German Tischler <[email protected]> Fri, 29 Sep 2017 09:08:58 +0200
libmaus2 (2.0.388-1) unstable; urgency=medium
* add SerialisingSortingBufferedOutputFileArray class
* parallelise GraphEncoder class
* implement method variants using preloaded index in OverlapIndexer
* fix computation of number of index entries in DalignerIndexDecoder
-- German Tischler <[email protected]> Thu, 28 Sep 2017 10:12:22 +0200
libmaus2 (2.0.387-1) unstable; urgency=medium
* fix comparison in BamEntryContainer
* add BamAlignmentTagComparator and update API accordingly
-- German Tischler <[email protected]> Wed, 27 Sep 2017 10:10:27 +0200
libmaus2 (2.0.386-1) unstable; urgency=medium
* do not fail on >16 bit cigar field length in BamAlignmentEncoderBase
* filter out 32 bit cigar flag when formatting BamAlignment for SAM output
* call computeBin in BamAlignment::getBin when 32 bit cigar field flag is set
-- German Tischler <[email protected]> Tue, 26 Sep 2017 11:43:25 +0200
libmaus2 (2.0.385-1) unstable; urgency=medium
* improve threshold comparison in Matrix::inverse
-- German Tischler <[email protected]> Mon, 25 Sep 2017 15:06:01 +0200
libmaus2 (2.0.384-1) unstable; urgency=medium
* add missing include directive in LogNormalRandom.hpp
-- German Tischler <[email protected]> Mon, 25 Sep 2017 13:59:09 +0200
libmaus2 (2.0.383-1) unstable; urgency=medium
* add computeParameters function in LogNormalRandom class
* add Matrix class
-- German Tischler <[email protected]> Mon, 25 Sep 2017 13:15:15 +0200
libmaus2 (2.0.382-1) unstable; urgency=medium
* fix parameter estimation in LogNormalRandom
* fix comparator in OverlapInfo
-- German Tischler <[email protected]> Fri, 22 Sep 2017 10:08:29 +0200
libmaus2 (2.0.381-1) unstable; urgency=medium
* add init method in WaveletTree and several memory allocation optimisations
* add init method in ERank222B to allow reinitialisation without reallocation
-- German Tischler <[email protected]> Thu, 14 Sep 2017 11:24:56 +0200
libmaus2 (2.0.380-1) unstable; urgency=medium
* allow reinitialisation in QuickDynamicRMQ
* avoid memory reallocation in SimdX86GlobalAlignmentTemplate if possible
* round size to next power of two in AlignmentTraceContainer::push
* move Vlen array to class scope in AlignmentOneAgainstManyAVX2 to avoid reallocation
* pre allocate memory in computeTrace variants of Overlap class
-- German Tischler <[email protected]> Thu, 14 Sep 2017 08:54:14 +0200
libmaus2 (2.0.379-1) unstable; urgency=medium
* fix compilation on Darwin
-- German Tischler <[email protected]> Sun, 03 Sep 2017 20:33:35 +0200
libmaus2 (2.0.378-1) unstable; urgency=medium
* add failids argument in CommandContainer::check
-- German Tischler <[email protected]> Wed, 23 Aug 2017 09:47:28 +0200
libmaus2 (2.0.377-1) unstable; urgency=medium
* avoid outputting empty string in RealTimeClock::formatTime
* store elapsed time as double in Command::dispatch
-- German Tischler <[email protected]> Tue, 22 Aug 2017 21:20:00 +0200
libmaus2 (2.0.376-1) unstable; urgency=medium
* append run-time in error file of Command object
-- German Tischler <[email protected]> Tue, 22 Aug 2017 17:43:31 +0200
libmaus2 (2.0.375-1) unstable; urgency=medium
* make directory removal in TempFileNameGenerator more efficient
-- German Tischler <[email protected]> Tue, 22 Aug 2017 17:21:55 +0200
libmaus2 (2.0.374-1) unstable; urgency=medium
* print failed commands in CommandContainer check
-- German Tischler <[email protected]> Tue, 22 Aug 2017 16:43:59 +0200
libmaus2 (2.0.373-1) unstable; urgency=medium
* add mem and threads fields in CommandContainer
-- German Tischler <[email protected]> Sun, 20 Aug 2017 22:39:13 +0200
libmaus2 (2.0.372-1) unstable; urgency=medium
* change ArgParser interface to faciliate init by string vector
* implement indexing interface for serialised object sorting
-- German Tischler <[email protected]> Thu, 17 Aug 2017 15:14:02 +0200
libmaus2 (2.0.371-1) unstable; urgency=medium
* add maxattempt field in CommandContainer
* make dirmod and filemod settable parameters in TempFileNameGenerator
* add rdepid field in CommandContainer
* add check method for CommandContainer and id/attempt fields in CommandContainer
* add returncode field and output operator for Command class
* add ContainerDescription/ContainerDescriptionList
-- German Tischler <[email protected]> Wed, 16 Aug 2017 14:38:20 +0200
libmaus2 (2.0.370-1) unstable; urgency=medium
* add fcntl based advisory locking in PosixFdInputOutputStreamBuffer
* add detection for fcntl function
-- German Tischler <[email protected]> Tue, 15 Aug 2017 12:12:50 +0200
libmaus2 (2.0.369-1) unstable; urgency=medium
* add input operator for AlignmentStatistics
* use last colon in CramRange to delimit sequence name from interval
-- German Tischler <[email protected]> Mon, 14 Aug 2017 19:48:20 +0200
libmaus2 (2.0.368-1) unstable; urgency=medium
* add test program produce constant sum vectors in lexicographically increasing order
* add ConstantSumCombinatorics class
* add GmpInteger specialisation for Faulhaber class
* use BernoulliCache in Faulhaber class
* add RationalPolynomialSupport class
* reimplement operator- in GmpInteger
* make fillBinomialVector slightly less slow
* implement BernouilliNumber specialisation for GmpInteger and add BernoulliNumberCache class
-- German Tischler <[email protected]> Fri, 11 Aug 2017 16:06:13 +0200
libmaus2 (2.0.367-1) unstable; urgency=medium
* pass through arguments in GraphEncoder
-- German Tischler <[email protected]> Wed, 09 Aug 2017 14:49:02 +0200
libmaus2 (2.0.366-1) unstable; urgency=medium
* parallelise gathering of statistics in GraphEncoder
-- German Tischler <[email protected]> Wed, 09 Aug 2017 11:25:07 +0200
libmaus2 (2.0.365-1) unstable; urgency=medium
* add rcsupport in FragmentAlignmentBufferRewriteWorkPackageDispatcher and FragmentAlignmentBufferRewriteReadEndsWorkPackageDispatcher
* pass through rcsupport flag in BlockControl class
* fix missing parameter pass-through in serialised sorting
-- German Tischler <[email protected]> Tue, 08 Aug 2017 16:02:18 +0200
libmaus2 (2.0.364-1) unstable; urgency=medium
* add OverlapInfoIndexer
* add single file sort interface in SortingOverlapOutputBuffer
-- German Tischler <[email protected]> Tue, 08 Aug 2017 13:05:27 +0200
libmaus2 (2.0.363-1) unstable; urgency=medium
* add binomialCoefficientGmp function in Binom class
* add pow_ui, mul_2exp, div_2exp, log and exp methods in GmpFloat class
* add abs operator in GmpFloat and refactor unary operator-
-- German Tischler <[email protected]> Mon, 07 Aug 2017 23:16:37 +0200
libmaus2 (2.0.362-1) unstable; urgency=medium
* add fanin/number of thread arguments in AlignmentWriterArray::merge
* add sortAndMergeThread function in SortingOverlapOutputBuffer featuring separate arguments for number of sort and merge threads
* add serialisation in OverlapInfo class
* bug fix in difference function of IntegerInterval class
-- German Tischler <[email protected]> Fri, 04 Aug 2017 10:48:09 +0200
libmaus2 (2.0.361-1) unstable; urgency=medium
* add mc field in opt duplicate marking
* add matecoordinate field in OptName class
-- German Tischler <[email protected]> Thu, 03 Aug 2017 11:40:07 +0200
libmaus2 (2.0.360-1) unstable; urgency=medium
* add getFrontHardClipping and getBackHardClipping in BamAlignment/BamAlignmentDecoderBase
-- German Tischler <[email protected]> Wed, 02 Aug 2017 08:51:35 +0200
libmaus2 (2.0.359-1) unstable; urgency=medium
* complete removeFileAndIndex in SortingOverlapOutputBuffer
-- German Tischler <[email protected]> Tue, 01 Aug 2017 17:38:23 +0200
libmaus2 (2.0.358-1) unstable; urgency=medium
* fix binomRowUpperGmpFloat for p=1
-- German Tischler <[email protected]> Thu, 20 Jul 2017 13:38:54 +0200
libmaus2 (2.0.357-1) unstable; urgency=medium
* fix error checking in parallel merging of SortingOverlapOutputBuffer
* fix for Darwin (lgamma not found in namespace std)
* add locking in error printing of MemoryFileAdapter
-- German Tischler <[email protected]> Fri, 14 Jul 2017 16:05:21 +0200
libmaus2 (2.0.356-1) unstable; urgency=medium
* remove useless argument from getSwapped in Overlap class
* add windowErrorLargeDetail function in AlignmentTraceContainer class
* update getSwapped method in Overlap class
-- German Tischler <[email protected]> Thu, 13 Jul 2017 13:29:59 +0200
libmaus2 (2.0.355-1) unstable; urgency=medium
* add a_sync_match function in AlignmentTraceContainer
-- German Tischler <[email protected]> Wed, 12 Jul 2017 10:44:22 +0200
libmaus2 (2.0.354-1) unstable; urgency=medium
* replace assertion by exception in GraphDecoderContext
* replace --with-asan by --enable-asan in configure script
* add OverlapInfo class
-- German Tischler <[email protected]> Wed, 12 Jul 2017 10:11:01 +0200
libmaus2 (2.0.353-1) unstable; urgency=medium
* add fillSpanHistogram/fillErrorHistogram variants in Overlap class
* add coordinates in AlignmentPrint class
-- German Tischler <[email protected]> Mon, 10 Jul 2017 16:54:58 +0200
libmaus2 (2.0.352-1) unstable; urgency=medium
* add searchNoFailure method in LinearHashTrie
-- German Tischler <[email protected]> Sat, 08 Jul 2017 15:43:47 +0200
libmaus2 (2.0.351-1) unstable; urgency=medium
* add static printMultiLine function in Pattern class
* add getBforAOffset function in Overlap class
-- German Tischler <[email protected]> Fri, 07 Jul 2017 17:05:43 +0200
libmaus2 (2.0.350-1) unstable; urgency=medium
* add fillErrorHistogram with double errors in Overlap class
* fix error message about unsupported flags in PosixFdInputOutputStreamBuffer
* add sort/sortUnique in SortingBufferedOutputFile
* add InputOutputStreamInstance class and support classes
-- German Tischler <[email protected]> Wed, 05 Jul 2017 23:01:57 +0200
libmaus2 (2.0.349-1) unstable; urgency=medium
* update testgamma to reflect new merging interfaces
* improve error checking in BwtMergeSortTemplate
* add checking in mergeToDense method of SparseGammaGapMultiFileSet
* add checking in mergeToDense method of SparseGammaGapMultiFileLevelSet
* add getAlignmentAt function in OverlapIndexer class
-- German Tischler <[email protected]> Tue, 04 Jul 2017 12:32:41 +0200
libmaus2 (2.0.348-1) unstable; urgency=medium
* add bbpos and bepos fields in ContainmentInfo
* add transitiveCross function in AlignmentTraceContainer
* add getu method in DatabaseFile
* add getAlignments functions in OverlapIndexer class
* add tripleCross function in AlignmentTraceContainer
-- German Tischler <[email protected]> Mon, 03 Jul 2017 15:38:25 +0200
libmaus2 (2.0.347-1) unstable; urgency=medium
* add methods thresLow, thresLowInv, poissonViaLog, thresLowInvLog, getVectorViaLog, lowerSum and function gamma_q in Poisson class
-- German Tischler <[email protected]> Thu, 22 Jun 2017 22:58:58 +0200
libmaus2 (2.0.346-1) unstable; urgency=medium
* remove libmaus2lsf from debian packaging files
-- German Tischler <[email protected]> Tue, 20 Jun 2017 16:57:22 +0200
libmaus2 (2.0.345-1) unstable; urgency=medium
* remove unused code
-- German Tischler <[email protected]> Tue, 20 Jun 2017 11:57:38 +0200
libmaus2 (2.0.344-1) unstable; urgency=medium
* add toString method in DNAIndexMetaDataBigBandBiDir::Coordinates
-- German Tischler <[email protected]> Fri, 02 Jun 2017 10:52:11 +0200
libmaus2 (2.0.343-1) unstable; urgency=medium
* add fillMapping method in AlignmentTraceContainer
* add inv method in OverlapNode
* reorder fields in OverlapHeader class and add constructor by values
* add searchFrom and searchTo methods in StringGraph class
* add suffix parameter in get method of LocalTempContainer class
* remove unneeded length field from OverlapNodeBase
-- German Tischler <[email protected]> Thu, 01 Jun 2017 11:27:55 +0200
libmaus2 (2.0.342-1) unstable; urgency=medium
* add LocalTempFileContainer
-- German Tischler <[email protected]> Mon, 29 May 2017 16:03:53 +0200
libmaus2 (2.0.341-1) unstable; urgency=medium
* add Poisson class
-- German Tischler <[email protected]> Wed, 24 May 2017 00:21:31 +0200
libmaus2 (2.0.340-1) unstable; urgency=medium
* add operator== in OverlapHeader
* return 0 edges for nodes outside graph saved in GraphDecoder
* change gmp default from no to auto detect
-- German Tischler <[email protected]> Tue, 23 May 2017 15:07:28 +0200
libmaus2 (2.0.339-1) unstable; urgency=medium
* add Enumerator class
-- German Tischler <[email protected]> Mon, 22 May 2017 14:25:12 +0200
libmaus2 (2.0.338-1) unstable; urgency=medium
* add LogNormalRandom class and test
-- German Tischler <[email protected]> Fri, 12 May 2017 10:34:31 +0200
libmaus2 (2.0.337-1) unstable; urgency=medium
* add getReadLengthSum/getReadLengthAverage in DatabaseFile class
* add getHeader method in Overlap class
* fix erroneous switch fall through
-- German Tischler <[email protected]> Thu, 11 May 2017 15:57:32 +0200
libmaus2 (2.0.336-1) unstable; urgency=medium
* comment out broken function calls in RlToHwtBase (fix compilation with gcc 7.1.0)
-- German Tischler <[email protected]> Thu, 04 May 2017 11:41:50 +0200
libmaus2 (2.0.335-1) unstable; urgency=medium
* add iseq and walk fields in Edge class
-- German Tischler <[email protected]> Fri, 28 Apr 2017 15:23:25 +0200
libmaus2 (2.0.334-1) unstable; urgency=medium
* update getReferenceInterval function in BamAlignment to take fron deletions into account
* only use statfs output if f_iosize field is present for determining optimal block transfer size
-- German Tischler <[email protected]> Wed, 26 Apr 2017 11:30:40 +0200
libmaus2 (2.0.333-1) unstable; urgency=medium
* fix compilation on FreeBSD/NetBSD
* add shared_ptr_type typedef in SerialisedSortingBufferedOutputFile
* add ClusteredBernoulli class
* add GeneralisedClusterBernoulli class
* add GeneralisedBernoulli class
-- German Tischler <[email protected]> Tue, 25 Apr 2017 13:28:26 +0200
libmaus2 (2.0.332-1) unstable; urgency=medium
* use LIBMAUS2_HAVE_STATFS_F_BSIZE and LIBMAUS2_HAVE_STATFS_F_IOSIZE in PosixFdInput
* detect f_bsize and f_iosize fields of statfs in configure.in
* change default arg for snappy in configure.in from no to empty
* add LIBMAUS2_HAVE_STATFS_F_BSIZE and LIBMAUS2_HAVE_STATFS_F_IOSIZE in LibMausConfig.hpp.in
-- German Tischler <[email protected]> Fri, 21 Apr 2017 14:12:38 +0200
libmaus2 (2.0.331-1) unstable; urgency=medium
* add dispatch method with filename parameter in CommandContainer
-- German Tischler <[email protected]> Tue, 11 Apr 2017 11:36:46 +0200
libmaus2 (2.0.330-1) unstable; urgency=medium
* allow random access in CommandContainer
-- German Tischler <[email protected]> Mon, 10 Apr 2017 16:39:01 +0200
libmaus2 (2.0.329-1) unstable; urgency=medium
* add Command/CommandContainer
-- German Tischler <[email protected]> Mon, 10 Apr 2017 16:22:52 +0200
libmaus2 (2.0.328-1) unstable; urgency=medium
* add verbosity in SMEMProcessor
-- German Tischler <[email protected]> Thu, 06 Apr 2017 14:17:00 +0200
libmaus2 (2.0.327-1) unstable; urgency=medium
* add serialisation for NNPAlignResult
* add serialisation for DNAIndexMetaDataBigBandBiDir::Coordinates
-- German Tischler <[email protected]> Wed, 05 Apr 2017 17:56:06 +0200
libmaus2 (2.0.326-1) unstable; urgency=medium
* fix error occuring with empty files in GammaIntervalDecoder
* add getAlignments method in ChainNodeInfoSet and SMEMProcessor
* add TraversalElement class
* add getAOffsets and getBOffsets functions in AlignmentTraceContainer
* update template parameter for slide in NP class
* add ContainmentInfo class
* add push variant in AutoArray
* fix data type in NPL
* remove unneeded length field from terminal nodes of string graph edges
* fix warning about misguiding indentation in huffman.hpp
* fix NPL class for case of empty A or empty B string
* add string graph data structures
* add serialisation for block sorting merge tree
-- German Tischler <[email protected]> Wed, 05 Apr 2017 17:20:02 +0200
libmaus2 (2.0.325-1) unstable; urgency=medium
* add advanceMaxB function in AlignmentTraceContainer
* add methods baseMatch, baseMatchPrime, getReadPrime, getRefPosForReadPos, getRefStart, getReferenceUsed, getReferenceUsedPrime and getRefPosForReadPosChecked in BamAlignment class
* fix MD/NM calculation in case of delete operations ahead of the first match/mismatch
* add getReferenceRegionViaMd and checkCigar in BamAlignment
* make sure substituted base is not same as original base in DNABaseNoiseSpiker
* add decodeReadS function in BamAlignmentDecoderBase
-- German Tischler <[email protected]> Thu, 23 Mar 2017 17:46:23 +0100
libmaus2 (2.0.324-1) unstable; urgency=medium
* improve cleanup in GraphEncoder
-- German Tischler <[email protected]> Thu, 16 Mar 2017 09:53:26 +0100
libmaus2 (2.0.323-1) unstable; urgency=medium
* add decode variant for (a,b) pair in GraphDecoder
* add static trueOverlap variant in TrueOverlap class
* add getReadLengthArrayParallel variants in DatabaseFile
* add clear method setting new length in RangeSet
-- German Tischler <[email protected]> Wed, 15 Mar 2017 13:59:35 +0100
libmaus2 (2.0.322-1) unstable; urgency=medium
* add graph encoder/decoder
* add EscapeCanonicalEncoder constructor variant for symbol,freq maps
* add copyToArray function supporting tracks in DatabaseFile class
* fix null pointer dereferencing bug in CanonicalEncoder when alphabet is empty
* add binomVectorDouble function in Binom class
-- German Tischler <[email protected]> Tue, 14 Mar 2017 14:05:06 +0100
libmaus2 (2.0.321-1) unstable; urgency=medium
* avoid using temporaries in BwtMergeTempFileNameSet, implement explicit assignment operator and copy constructor
* get explicit copy of histfn in BwtMergeSortTemplate before loading histogram
* avoid warning about shift larger than size of data type in FastWriteBitWriter
-- German Tischler <[email protected]> Wed, 08 Mar 2017 12:01:26 +0100
libmaus2 (2.0.320-1) unstable; urgency=medium
* add binomSingleGmp function in Binom class
-- German Tischler <[email protected]> Tue, 07 Mar 2017 16:05:26 +0100
libmaus2 (2.0.319-1) unstable; urgency=medium
* Added AdapterInfo copy constructor to ensure pointer to C string is correctly maintained (patch by Andrew Whitwham)
* remove unnecessary typename keyword in KmerCount
-- German Tischler <[email protected]> Tue, 07 Mar 2017 16:00:58 +0100
libmaus2 (2.0.318-1) unstable; urgency=medium
* change BamAlignment::getRefPosForReadPos so it only returns a result one it is on an actual read position (not because it reached the respective query position)
* add debugging/verbosity code in NP class
* add index_type parameter in ConstIterator class
-- German Tischler <[email protected]> Thu, 23 Feb 2017 15:49:40 +0100
libmaus2 (2.0.317-1) unstable; urgency=medium
* add clean method in IntervalTree class
-- German Tischler <[email protected]> Mon, 20 Feb 2017 16:21:51 +0100
libmaus2 (2.0.316-1) unstable; urgency=medium
* add registerMatches method in NNPTraceContainer
* allow memory pool sharing in IntervalTree class
* fix detection of pthread getname/setname functions in configure.ac
-- German Tischler <[email protected]> Mon, 20 Feb 2017 15:52:48 +0100
libmaus2 (2.0.315-1) unstable; urgency=medium
* add IntervalTree class
-- German Tischler <[email protected]> Sat, 18 Feb 2017 13:21:36 +0100
libmaus2 (2.0.314-1) unstable; urgency=medium
* add KmerCount class plus test
* delete temporary file at end of SerialisingSortingBufferedOutputFile::reduce
* add constructor variant accepting file name in LineBufferFastAReader
* add stack protection/asan for debugging in configure.ac
-- German Tischler <[email protected]> Thu, 16 Feb 2017 12:29:33 +0100
libmaus2 (2.0.313-1) unstable; urgency=medium
* add NNPCor class (NNP plus clipping at furthest reaching points satisfying a correlation bound)
* return number of clipped bases on A and B sequence in NNPTraceContainer::suffixPositive
* add byteSize method in DatabaseFile::ReadDataRange
* add clipEndWindowError method in NNPTraceContainer class
* restore previous default for local error threshold in NNP
* fix off by one error when checking maximum local error count in NNP
-- German Tischler <[email protected]> Fri, 10 Feb 2017 16:03:36 +0100
libmaus2 (2.0.312-1) unstable; urgency=medium
* add unique term val option for NNP class
* add termval option for decodeReadIntervalParallel method in DatabaseFile
-- German Tischler <[email protected]> Wed, 08 Feb 2017 00:17:07 +0100
libmaus2 (2.0.311-1) unstable; urgency=medium
* add parallel decoding in DatabaseFile
-- German Tischler <[email protected]> Tue, 07 Feb 2017 18:01:24 +0100
libmaus2 (2.0.310-1) unstable; urgency=medium
* do not recode underscore symbol in argument list of ArgParser
-- German Tischler <[email protected]> Thu, 02 Feb 2017 11:20:36 +0100
libmaus2 (2.0.309-1) unstable; urgency=medium
* allow adding aux tags in convertUnmapped function of LASToBamConverterBase
-- German Tischler <[email protected]> Wed, 01 Feb 2017 12:55:58 +0100
libmaus2 (2.0.308-1) unstable; urgency=medium
* add AuxTagCopyAddRequest class in LASToBamConverterBase
* add enumerateAuxTags variants in BamAlignmentDecoderBase
* add commandlinecoded attribute in ArgParser class
* add pointer types in LineBufferFastAReader
-- German Tischler <[email protected]> Tue, 31 Jan 2017 16:27:58 +0100
libmaus2 (2.0.307-1) unstable; urgency=medium
* implement SimpleThreadPool based parallelism in InterleavedRadixSort
* add removeDispatcher method in SimpleThreadPool class
* change threading in parallel decoding of FastaBPDecoder from OpenMP to thread pooling via SimpleThreadPool
* add locking to dispatcher handling in SimpleThreadPool
-- German Tischler <[email protected]> Tue, 31 Jan 2017 13:15:19 +0100
libmaus2 (2.0.306-1) unstable; urgency=medium
* avoid failure in rename over device boundaries in PosixFdOutputStreamFactory
-- German Tischler <[email protected]> Mon, 30 Jan 2017 13:56:21 +0100
libmaus2 (2.0.305-1) unstable; urgency=medium
* add HD line field merging in BamCatHeader
-- German Tischler <[email protected]> Fri, 27 Jan 2017 11:21:54 +0100
libmaus2 (2.0.304-1) unstable; urgency=medium
* add BamAlignmentDecoder ref based constructor in BamPeeker class
-- German Tischler <[email protected]> Thu, 26 Jan 2017 17:32:47 +0100
libmaus2 (2.0.303-1) unstable; urgency=medium
* add NPL class
* add option to avoid suffixPositive call in NPL
-- German Tischler <[email protected]> Tue, 17 Jan 2017 15:21:06 +0100
libmaus2 (2.0.302-1) unstable; urgency=medium
* add copying of dazzler Database to array memory
-- German Tischler <[email protected]> Thu, 05 Jan 2017 10:57:13 +0100
libmaus2 (2.0.301-1) unstable; urgency=medium
* add support for opening file via Daligner index (.idx) files
-- German Tischler <[email protected]> Wed, 04 Jan 2017 18:03:06 +0100
libmaus2 (2.0.300-1) unstable; urgency=medium
* allow passing of index file name in OverlapIndexer
-- German Tischler <[email protected]> Wed, 04 Jan 2017 15:41:49 +0100
libmaus2 (2.0.299-1) unstable; urgency=medium
* add tracklist in DatabaseFile::copyToPrefix
* add getErrorForBase/getMaxErrorForRange methods in OverlapProperCheck class
-- German Tischler <[email protected]> Wed, 21 Dec 2016 14:57:51 +0100
libmaus2 (2.0.298-1) unstable; urgency=medium
* change return type of OverlapProperCheck to return more information
-- German Tischler <[email protected]> Tue, 20 Dec 2016 20:37:28 +0100
libmaus2 (2.0.297-1) unstable; urgency=medium
* add OverlapProperCheck class
-- German Tischler <[email protected]> Mon, 19 Dec 2016 23:27:40 +0100
libmaus2 (2.0.296-1) unstable; urgency=medium
* rewrite fillErrorHistogram in Overlap class
-- German Tischler <[email protected]> Thu, 15 Dec 2016 14:50:19 +0100
libmaus2 (2.0.295-1) unstable; urgency=medium
* update character escaping in ArgParser
-- German Tischler <[email protected]> Wed, 14 Dec 2016 14:59:02 +0100
libmaus2 (2.0.294-1) unstable; urgency=medium
* add printArgs method in ArgParser class
-- German Tischler <[email protected]> Wed, 14 Dec 2016 14:05:31 +0100
libmaus2 (2.0.293-1) unstable; urgency=medium
* fix getDiagonalBand and add new variant of it in AlignmentTraceContainer
* add KmerEnumerator class in DNARankSMEMComputation
* add chain domination updates in SMEMProcessor
* add domsamerefid flag in ChainNodeInfoSet
* add refid field in ChainAlignment class
* add refid field in Chain class
-- German Tischler <[email protected]> Mon, 12 Dec 2016 12:26:02 +0100
libmaus2 (2.0.292-1) unstable; urgency=medium
* add getTraceBlocks method in Overlap class
-- German Tischler <[email protected]> Thu, 08 Dec 2016 16:27:09 +0100
libmaus2 (2.0.291-1) unstable; urgency=medium
* fix typo in BamAlignment::getErrorRatePair
-- German Tischler <[email protected]> Wed, 07 Dec 2016 11:04:42 +0100
libmaus2 (2.0.290-1) unstable; urgency=medium
* add BamAccessor
* add AlignmentWriterArray class
* add argument free and istream constructor in ApproximateRun class
* add SerialisedPeeker class
-- German Tischler <[email protected]> Tue, 06 Dec 2016 10:45:35 +0100
libmaus2 (2.0.289-1) unstable; urgency=medium
* add operator==/operator!=/isLeaf and size methods in CompressedSuffixTree::Node
* change semantics of CompressedSuffixTree::sdepth to return infinity/max for leafs
* add AutoArray based CompressedSuffixTree::enumerateChildren method
* add CompressedSuffixTree::printNodeContext
* check for sorting thread failure in sortAndMerge function of SortingOverlapOutputBuffer
* add getTracePoints and true overlap flag in Overlap class
* add runtime reporting in BlockMergeControl
* add priorisation of packages in BlockSortControl/BlockMergeControl
* add lock for accessing blockid in GenericInputSingleData
-- German Tischler <[email protected]> Mon, 05 Dec 2016 16:36:13 +0100
libmaus2 (2.0.288-1) unstable; urgency=medium
* move output operator for DuplicationMetrics to libmaus2::bambam namespace
* fix buffer overflows in coordinate parsing (tile,x,y) of ReadEndsBase
-- German Tischler <[email protected]> Tue, 29 Nov 2016 12:20:08 +0100
libmaus2 (2.0.287-1) unstable; urgency=medium
* use input factories in opt dup marking of DupMarkBase where possible and add mate cigar insertion option
-- German Tischler <[email protected]> Tue, 29 Nov 2016 10:33:43 +0100
libmaus2 (2.0.286-1) unstable; urgency=medium
* add optminpixeldif argument in BlockSortControl/PairReadEndsMergeWorkPackageDispatcher
* add mergePairs method in ReadEndsBlockIndexSet to allow passing optminpixeldif argument
* be more deterministic about which read pairs are marked as duplicates/optical duplicates
* use align in/out factories in marking optical routines
* add OptName/OptNameReader classes
* fix tile,x,y parsing for larger number of read name fields in ReadEndsBase
* add BamAlignmentInputCallbackBamRef and BamAlignmentInputCallbackSnappyRef classes
-- German Tischler <[email protected]> Mon, 28 Nov 2016 17:53:29 +0100
libmaus2 (2.0.285-1) unstable; urgency=medium
* add notes about releases to README.md
-- German Tischler <[email protected]> Mon, 28 Nov 2016 10:31:25 +0100
libmaus2 (2.0.284-1) unstable; urgency=medium
* add rank of reference read for optical duplicates in DupMarkBase opt interface