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ChangeLog
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libmaus2 (2.0.499-1) unstable; urgency=medium
* add access for true/haplo flag in OverlapData/Interface
-- German Tischler <[email protected]> Wed, 06 Jun 2018 12:11:14 +0200
libmaus2 (2.0.498-1) unstable; urgency=medium
* add haplo flag for dazzler alignments
-- German Tischler <[email protected]> Tue, 05 Jun 2018 17:02:44 +0200
libmaus2 (2.0.497-1) unstable; urgency=medium
* fix warning
-- German Tischler <[email protected]> Tue, 05 Jun 2018 15:23:54 +0200
libmaus2 (2.0.496-1) unstable; urgency=medium
* fix warning
-- German Tischler <[email protected]> Mon, 04 Jun 2018 16:52:01 +0200
libmaus2 (2.0.495-1) unstable; urgency=medium
* fix min call by cast
-- German Tischler <[email protected]> Fri, 25 May 2018 15:23:32 +0200
libmaus2 (2.0.494-1) unstable; urgency=medium
* add missing include in ArgParser.cpp
-- German Tischler <[email protected]> Fri, 25 May 2018 14:41:21 +0200
libmaus2 (2.0.493-1) unstable; urgency=medium
* add getTracePoints function OverlapData
-- German Tischler <[email protected]> Wed, 23 May 2018 18:28:25 +0200
libmaus2 (2.0.492-1) unstable; urgency=medium
* add pointer types in FastaPeeker
-- German Tischler <[email protected]> Wed, 23 May 2018 09:45:21 +0200
libmaus2 (2.0.491-1) unstable; urgency=medium
* add putARead and putBRead in OverlapData
-- German Tischler <[email protected]> Fri, 18 May 2018 10:13:34 +0200
libmaus2 (2.0.490-1) unstable; urgency=medium
* update debian control files
-- German Tischler <[email protected]> Thu, 17 May 2018 10:34:55 +0200
libmaus2 (2.0.489-1) unstable; urgency=medium
* add typedef in SortingBufferedOutputFile
-- German Tischler <[email protected]> Tue, 15 May 2018 20:17:36 +0200
libmaus2 (2.0.488-1) unstable; urgency=medium
* add OverlapAdapter class
-- German Tischler <[email protected]> Tue, 15 May 2018 12:10:21 +0200
libmaus2 (2.0.487-1) unstable; urgency=medium
* add missing pass through of comparator in MergingReadBack
-- German Tischler <[email protected]> Mon, 14 May 2018 10:24:36 +0200
libmaus2 (2.0.486-1) unstable; urgency=medium
* add sortthreads option in reduce/sort methods in SortingBufferedOutputFile
-- German Tischler <[email protected]> Wed, 09 May 2018 13:58:39 +0200
libmaus2 (2.0.485-1) unstable; urgency=medium
* add missing initialisation of slotfilled field in GenericPeeker
-- German Tischler <[email protected]> Wed, 09 May 2018 11:11:52 +0200
libmaus2 (2.0.484-1) unstable; urgency=medium
* avoid endless loop in thresLow of Poisson
-- German Tischler <[email protected]> Tue, 08 May 2018 12:16:26 +0200
libmaus2 (2.0.483-1) unstable; urgency=medium
* add getOffset and checkSize in ContainerDescriptionList
-- German Tischler <[email protected]> Mon, 07 May 2018 17:31:30 +0200
libmaus2 (2.0.482-1) unstable; urgency=medium
* add output of modcall flag in Command
-- German Tischler <[email protected]> Mon, 07 May 2018 09:54:25 +0200
libmaus2 (2.0.481-1) unstable; urgency=medium
* add getAbsProgName in ArgParser
* add getCurDir in PathTools
* update getAbsProgName in ArgInfo
-- German Tischler <[email protected]> Sun, 06 May 2018 10:06:55 +0200
libmaus2 (2.0.480-1) unstable; urgency=medium
* add modcall field in Command class
-- German Tischler <[email protected]> Sat, 05 May 2018 22:23:06 +0200
libmaus2 (2.0.479-1) unstable; urgency=medium
* add Base64 class
-- German Tischler <[email protected]> Sat, 05 May 2018 20:25:36 +0200
libmaus2 (2.0.478-1) unstable; urgency=medium
* avoid unnecessary clearing of buffer in BufferedOutput
-- German Tischler <[email protected]> Sat, 05 May 2018 00:43:44 +0200
libmaus2 (2.0.477-1) unstable; urgency=medium
* use absolute paths for symlink sources in DatabaseFile
* add PathTools
-- German Tischler <[email protected]> Fri, 04 May 2018 14:36:37 +0200
libmaus2 (2.0.476-1) unstable; urgency=medium
* fix serialise in ContainerDescriptionList
-- German Tischler <[email protected]> Wed, 02 May 2018 15:43:25 +0200
libmaus2 (2.0.475-1) unstable; urgency=medium
* add LIBMAUS2_USE_ASSEMBLY in AlignmentOneAgainstManyFactory check
-- German Tischler <[email protected]> Wed, 02 May 2018 12:39:40 +0200
libmaus2 (2.0.474-1) unstable; urgency=medium
* add replace method in ContainerDescriptionList
* add serialisedSize method in ContainerDescription
* only try to use I386CacheLineSize if assembly is enabled
-- German Tischler <[email protected]> Wed, 02 May 2018 10:42:14 +0200
libmaus2 (2.0.473-1) unstable; urgency=medium
* rewrite Command dispatching
-- German Tischler <[email protected]> Mon, 30 Apr 2018 10:20:37 +0200
libmaus2 (2.0.472-1) unstable; urgency=medium
* fix splitting in splitDbRLTwo
-- German Tischler <[email protected]> Fri, 27 Apr 2018 17:10:44 +0200
libmaus2 (2.0.471-1) unstable; urgency=medium
* add writeSplitDatabase in DatabaseFile
-- German Tischler <[email protected]> Thu, 26 Apr 2018 17:30:20 +0200
libmaus2 (2.0.470-1) unstable; urgency=medium
* add splitDbRLTwo in DatabaseFile
-- German Tischler <[email protected]> Thu, 26 Apr 2018 13:45:10 +0200
libmaus2 (2.0.469-1) unstable; urgency=medium
* add libmaus2/util/FileEnumerator.hpp in Makefile.am
* add enumerateTracks method in DatabaseFile class
* add splitDbRLPrefixStrict in DatabaseFile
-- German Tischler <[email protected]> Thu, 26 Apr 2018 11:32:38 +0200
libmaus2 (2.0.468-1) unstable; urgency=medium
* fix NPLNoTrace for case one input string is empty
* add serialise method in DatabaseFile
-- German Tischler <[email protected]> Wed, 25 Apr 2018 13:50:50 +0200
libmaus2 (2.0.467-1) unstable; urgency=medium
* add testnnplocalaligner
-- German Tischler <[email protected]> Fri, 13 Apr 2018 16:53:21 +0200
libmaus2 (2.0.466-1) unstable; urgency=medium
* add prepend method in AlignmentTraceContainer
-- German Tischler <[email protected]> Thu, 12 Apr 2018 16:47:50 +0200
libmaus2 (2.0.465-1) unstable; urgency=medium
* add prepend function in AlignmentTraceContainer
-- German Tischler <[email protected]> Thu, 12 Apr 2018 16:32:01 +0200
libmaus2 (2.0.464-1) unstable; urgency=medium
* add simpler file vector constructor for concat SimpleOverlapParser
* add file constructors for LasFileRange
-- German Tischler <[email protected]> Thu, 12 Apr 2018 09:27:04 +0200
libmaus2 (2.0.463-1) unstable; urgency=medium
* add advanceMaxA function in AlignmentTraceContainer
* add static serialise functions in Overlap and Path
-- German Tischler <[email protected]> Thu, 12 Apr 2018 09:01:11 +0200
libmaus2 (2.0.462-1) unstable; urgency=medium
* update testnpl for NNPCor
* use linear memory NNPCor methods in NNPCorL
* add alignLinMemForward in NNPCor
* make sure window error functions in AlignmentTraceContainer return value inside [0,1]
* add OverlapDataInterfaceBAComparator class
-- German Tischler <[email protected]> Wed, 11 Apr 2018 14:15:34 +0200
libmaus2 (2.0.461-1) unstable; urgency=medium
* add linear space variant in NNPCor
* add lastGoodWindowBack method/function in AlignmentTraceContainer
* fix clang warning about parentheses in noise spiker
* add reduceParallel in SortingBufferedOutputFile
* add BgzfDeflateBaseAllocator class
* add BgzfDeflateBaseTypeInfo class
-- German Tischler <[email protected]> Tue, 10 Apr 2018 16:28:21 +0200
libmaus2 (2.0.460-1) unstable; urgency=medium
* use BamParallelThreadPoolDecoderWrapper in BamAlignmentDecoderFactory
* use BamParallelThreadPoolDecoder in testthreadpoolbgzfdecode
* add BamParallelThreadPoolDecoder class
* add copystr in BgzfInflateThreadPoolReader
* add getReferenceLength in AlignmentStatistics
-- German Tischler <[email protected]> Fri, 06 Apr 2018 09:45:56 +0200
libmaus2 (2.0.459-1) unstable; urgency=medium
* fix include guards in SimpleThreadPoolThread.hpp
* use OverlapParser in GraphEncoder
* add data block writing in AlignmentWriter
* use LasIntervals for graph encoding
* fix graph check
* add constructIndexIf in OverlapIndexer
* add SynchronousConditionQueue class
* add full method in LockedGrowingFreeList/GrowingFreeList
* add timedWait method in PosixConditionSemaphore
* add pointer types in NPLLinMem, NPLinMem
-- German Tischler <[email protected]> Wed, 04 Apr 2018 09:19:30 +0200
libmaus2 (2.0.458-1) unstable; urgency=medium
* added NPLNoTrace,NPLLinMem
* added thread pool based bgzf decoding study
-- German Tischler <[email protected]> Wed, 28 Mar 2018 14:54:48 +0200
libmaus2 (2.0.457-1) unstable; urgency=medium
* add test for NPLinMem
* add NPNoTrace class
* add NPLinMem class
* add byteSize method in NP
-- German Tischler <[email protected]> Tue, 27 Mar 2018 09:49:49 +0200
libmaus2 (2.0.456-1) unstable; urgency=medium
* add splitDbRLPrefix method in DatabaseFile
-- German Tischler <[email protected]> Wed, 21 Mar 2018 15:08:46 +0100
libmaus2 (2.0.455-1) unstable; urgency=medium
* add SimpleOverlapParserConcat class
* add LasFileRange
* add computeMapping method in Overlap
-- German Tischler <[email protected]> Mon, 19 Mar 2018 16:46:55 +0100
libmaus2 (2.0.454-1) unstable; urgency=medium
* add getInterval method in LasIntervals
* add possibility to seek before access in SimpleOverlapParser
-- German Tischler <[email protected]> Mon, 19 Mar 2018 14:11:45 +0100
libmaus2 (2.0.453-1) unstable; urgency=medium
* add pointer types in bit vector classes
-- German Tischler <[email protected]> Fri, 09 Mar 2018 10:20:27 +0100
libmaus2 (2.0.452-1) unstable; urgency=medium
* add operator==/operator!= in OverlapInfo class
-- German Tischler <[email protected]> Fri, 02 Mar 2018 11:09:14 +0100
libmaus2 (2.0.451-1) unstable; urgency=medium
* check for presence of CSI index in BamRangeDecoder
* add decoding capabilities for CSI indexes in BamIndex
-- German Tischler <[email protected]> Thu, 01 Mar 2018 12:23:39 +0100
libmaus2 (2.0.450-1) unstable; urgency=medium
* fix problems with vectors of length 1 in GraphEncoder
-- German Tischler <[email protected]> Thu, 01 Mar 2018 10:30:19 +0100
libmaus2 (2.0.449-1) unstable; urgency=medium
* force writing CSI index if indexing file name ends on .csi
* use block code instead of UTF8 for coordinate encoding in ReadEndsBase
* remove dead code from BamAlignment class
* add CSI support in BamIndexGenerator
* reformat bin computation in BamAlignmentEncoderBase and replace bin range check by truncation
* extend computeBin/getBin in BamAlignment/BamAlignmentDecoderBase to support CSI
* remove unused reg2bins variant in BamIndex class
* rewrite signedEncode/signedDecode in ReadEndsBase
* add getMaximumSequenceSize method in BamHeader class
* add CSI indexing support in BamAlignmentReg2Bin
* more changes for SAM spec updates
-- German Tischler <[email protected]> Wed, 28 Feb 2018 15:17:53 +0100
libmaus2 (2.0.448-1) unstable; urgency=medium
* adapt check of position value to updated SAM specs
-- German Tischler <[email protected]> Fri, 23 Feb 2018 14:51:33 +0100
libmaus2 (2.0.447-1) unstable; urgency=medium
* add sanity checks in NP class
* add sanity check in AlignmentTraceContainer
-- German Tischler <[email protected]> Mon, 19 Feb 2018 14:57:02 +0100
libmaus2 (2.0.446-1) unstable; urgency=medium
* add nplCheck in NNPCorL class
* add getCoveredReadIntervalPrime method in BamAlignment class
* move ProduceBitsContext to public area in WaveletTree
* add cast in GzipHeader
-- German Tischler <[email protected]> Tue, 13 Feb 2018 19:33:05 +0100
libmaus2 (2.0.445-1) unstable; urgency=medium
* add output of threads and mem in CommandContainer
* add GenericPeeker class
* add npCheck method in NNPCorL
* add swappedInverse method in OverlapInfo
-- German Tischler <[email protected]> Wed, 31 Jan 2018 10:40:25 +0100
libmaus2 (2.0.444-1) unstable; urgency=medium
* refactor configure.ac and move setting of LIBMAUSCPPFLAGS/LIBMAUSLDFLAGS into LIBS and CPPFLAGS down
-- German Tischler <[email protected]> Thu, 25 Jan 2018 16:13:43 +0100
libmaus2 (2.0.443-1) unstable; urgency=medium
* add operator() in ArgParser
-- German Tischler <[email protected]> Thu, 25 Jan 2018 13:45:02 +0100
libmaus2 (2.0.442-1) unstable; urgency=medium
* add FilterUnique class
* add getCoverOverlap method in GraphDecoder class
-- German Tischler <[email protected]> Mon, 15 Jan 2018 15:19:10 +0100
libmaus2 (2.0.441-1) unstable; urgency=medium
* add cast in testlassort
* add rename function in SortingOverlapOutputBuffer
-- German Tischler <[email protected]> Mon, 15 Jan 2018 12:24:53 +0100
libmaus2 (2.0.440-1) unstable; urgency=medium
* add U class
-- German Tischler <[email protected]> Tue, 09 Jan 2018 15:00:10 +0100
libmaus2 (2.0.439-1) unstable; urgency=medium
* fix unused parameter warning
* fix signed/unsigned comparison warnings
* initialize fields in parameterless constructors
-- German Tischler <[email protected]> Tue, 09 Jan 2018 12:01:42 +0100
libmaus2 (2.0.438-1) unstable; urgency=medium
* add testlassort program
* add SimpleOverlapParserGet class
* add OverlapDataInterfaceFullComparator
-- German Tischler <[email protected]> Mon, 08 Jan 2018 12:52:25 +0100
libmaus2 (2.0.437-1) unstable; urgency=medium
* add intended fall through markers in DupMarkBase
* add BamAlignmentNameHIComparator
* add hasAux in BamAlignmentDecoderBase
* add SortOrderCheck and GraphCheck
* add static modifier for checkEncodedGraph
* add getOverlaps variant in GraphDecoder
* add SortOrderCheck
-- German Tischler <[email protected]> Fri, 05 Jan 2018 11:42:30 +0100
libmaus2 (2.0.436-1) unstable; urgency=medium
* add isComplete and isFinished in Command and CommandContainer
* fix compilation with fftw
* avoid memset in ReadEndsBase::reset
-- German Tischler <[email protected]> Thu, 04 Jan 2018 10:10:38 +0100
libmaus2 (2.0.435-1) unstable; urgency=medium
* add lastGoodWindow function in AlignmentTraceContainer
* add pointer types in LasIntervals
-- German Tischler <[email protected]> Fri, 22 Dec 2017 13:10:28 +0100
libmaus2 (2.0.434-1) unstable; urgency=medium
* add reduceUnique and reduceUniqueParallel in SerialisingSortingBufferedOutputFileArray
-- German Tischler <[email protected]> Thu, 21 Dec 2017 14:57:01 +0100
libmaus2 (2.0.433-1) unstable; urgency=medium
* move some functions in PosixFdOutputStreamBuffer from private to public area
-- German Tischler <[email protected]> Mon, 18 Dec 2017 12:53:09 +0100
libmaus2 (2.0.432-1) unstable; urgency=medium
* print more information for Command class
-- German Tischler <[email protected]> Thu, 14 Dec 2017 14:36:26 +0100
libmaus2 (2.0.431-1) unstable; urgency=medium
* add deepsleep flag in Command
-- German Tischler <[email protected]> Thu, 14 Dec 2017 13:01:02 +0100
libmaus2 (2.0.430-1) unstable; urgency=medium
* replace uint by uint64_t in testdecimalnumberparser
* replace u_int64_t with uint64_t
* add detection of number of cpus via /proc/cpuinfo for linux in case sysconf is unavailable
* add detection for linux/sysctl.h
* use setAffinity if pthread_attr_setaffinity_np is not available in PosixThread
* add detection of pthread_attr_setaffinity_np in configure
* create a single point where we include pthread.h
-- German Tischler <[email protected]> Thu, 14 Dec 2017 11:24:27 +0100
libmaus2 (2.0.429-1) unstable; urgency=medium
* replace FFTRef calls with FFT in Convolution power classes
-- German Tischler <[email protected]> Tue, 12 Dec 2017 08:40:50 +0100
libmaus2 (2.0.428-1) unstable; urgency=medium
* add PowerCacheRussian and PowerBlockCache in Convolution class
-- German Tischler <[email protected]> Mon, 11 Dec 2017 09:26:15 +0100
libmaus2 (2.0.427-1) unstable; urgency=medium
* add PowerCache class in Convolution
-- German Tischler <[email protected]> Thu, 07 Dec 2017 14:46:37 +0100
libmaus2 (2.0.426-1) unstable; urgency=medium
* add ignorefail flag in Command
-- German Tischler <[email protected]> Wed, 06 Dec 2017 11:07:52 +0100
libmaus2 (2.0.425-1) unstable; urgency=medium
* add functions for decoding reads for given arrat of ids in DatabaseFile
-- German Tischler <[email protected]> Tue, 05 Dec 2017 00:11:23 +0100
libmaus2 (2.0.424-1) unstable; urgency=medium
* replace assertion by exception when checking order in SortingOverlapOutputBuffer
* add comparator type in AlignmentWriterArray
-- German Tischler <[email protected]> Mon, 04 Dec 2017 13:43:59 +0100
libmaus2 (2.0.423-1) unstable; urgency=medium
* add fields in Command class
-- German Tischler <[email protected]> Mon, 04 Dec 2017 11:50:44 +0100
libmaus2 (2.0.422-1) unstable; urgency=medium
* add swap method in AlignmentTraceContainer
-- German Tischler <[email protected]> Thu, 30 Nov 2017 15:02:16 +0100
libmaus2 (2.0.421-1) unstable; urgency=medium
* add untrimmed block bounds in splitDb of DatabaseFile
-- German Tischler <[email protected]> Wed, 29 Nov 2017 10:34:56 +0100
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