[med-svn] [euler-sr] 10/12: Merge tag 'upstream/1.1.2'
Andreas Tille
tille at debian.org
Tue Dec 5 15:29:46 UTC 2017
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tille pushed a commit to branch master
in repository euler-sr.
commit 2acfa7072020b4ff68c190912176587e1a3afba5
Merge: dd6d6c6 9e9c0a1
Author: Andreas Tille <tille at debian.org>
Date: Tue Dec 5 16:26:50 2017 +0100
Merge tag 'upstream/1.1.2'
Upstream version 1.1.2
CreateExecBuildCommands.pl | 54 +
LICENSE | 32 +
Makefile | 39 +
README.eulersr | 576 +
assembly/Assemble.pl | 141 +
assembly/BEdge.h | 95 +
assembly/BVertex.cpp | 15 +
assembly/BVertex.h | 282 +
assembly/BinSpectToAscii.cpp | 74 +
assembly/BitSpectrum.cpp | 13 +
assembly/BitSpectrum.h | 200 +
assembly/BuildMateTable.cpp | 176 +
assembly/CleanGraphWithMates.cpp | 552 +
assembly/CompareAssemblies.cpp | 340 +
assembly/ContigMap.cpp | 27 +
assembly/ContigMap.h | 47 +
assembly/CountIntegralTuples.cpp | 208 +
assembly/CountSpectrum.cpp | 228 +
assembly/CreateMateScaffold.cpp | 336 +
assembly/DeBruijn.cpp | 858 +
assembly/DeBruijnGraph.cpp | 15 +
assembly/DeBruijnGraph.h | 701 +
assembly/Edge.h | 15 +
assembly/EdgesToOverlapList.cpp | 73 +
assembly/ElandToFastq.cpp | 206 +
assembly/EstimateErrorDistribution.cpp | 483 +
assembly/ExecList.txt | 221 +
assembly/FilterFailedEndReads.cpp | 97 +
assembly/FilterIlluminaReads.cpp | 164 +
assembly/FilterValidMatePaths.cpp | 173 +
assembly/FixErrors.pl | 26 +
assembly/FixErrorsI.cpp | 542 +
assembly/FixErrorsIVoting.cpp | 733 +
assembly/FixErrorsSAP.cpp | 1177 +
assembly/FixErrorsStats.h | 56 +
assembly/FixErrorsVoting.cpp | 788 +
assembly/GraphExplorer.cpp | 250 +
assembly/GraphReader.cpp | 105 +
assembly/GraphReader.h | 20 +
assembly/HashedSpectrum.cpp | 112 +
assembly/HashedSpectrum.h | 78 +
assembly/IntegralCountSpectrum.cpp | 388 +
assembly/IntegralEdgesToOverlapList.cpp | 73 +
assembly/IntegralPrintReadIntervals.cpp | 452 +
assembly/IntegralTuple.cpp | 65 +
assembly/IntegralTuple.h | 586 +
assembly/IntervalGraph.cpp | 5293 +
assembly/IntervalGraph.h | 656 +
assembly/JoinSourcesAndSinks.cpp | 417 +
assembly/LastChanceReads.cpp | 136 +
assembly/ListSpectrum.cpp | 12 +
assembly/ListSpectrum.h | 145 +
assembly/Makefile | 100 +
assembly/MapContigs.cpp | 177 +
assembly/MapContigs.h | 35 +
assembly/MateLibrary.cpp | 1941 +
assembly/MateLibrary.h | 260 +
assembly/MateTable.h | 29 +
assembly/MateTransformGraph.cpp | 523 +
assembly/MultTuple.h | 61 +
assembly/NumericHashedSpectrum.h | 111 +
assembly/NumericTuple.cpp | 14 +
assembly/NumericTuple.h | 200 +
assembly/PathBranch.cpp | 29 +
assembly/PathBranch.h | 17 +
assembly/PathLib.cpp | 2793 +
assembly/PathLib.h | 243 +
assembly/PrintContigs.cpp | 60 +
assembly/PrintGraph.cpp | 56 +
assembly/PrintGraph.h | 10 +
assembly/PrintGraphSummary.cpp | 287 +
assembly/PrintMateLengthDistribution.cpp | 83 +
assembly/PrintReadIntervals.cpp | 131 +
assembly/PrintVariants.cpp | 116 +
assembly/QualityTrimmer.cpp | 357 +
assembly/ReadIntervals.cpp | 434 +
assembly/ReadIntervals.h | 720 +
assembly/ReadMap.cpp | 69 +
assembly/ReadMap.h | 33 +
assembly/ReadPaths.cpp | 143 +
assembly/ReadPaths.h | 95 +
assembly/ReadPos.cpp | 41 +
assembly/ReadPos.h | 121 +
assembly/ReadsToSpectrum.cpp | 466 +
assembly/ReorderIntervals.cpp | 74 +
assembly/RepeatSearch.cpp | 88 +
assembly/RepeatSearch.h | 21 +
assembly/RuleList.cpp | 83 +
assembly/RuleList.h | 26 +
assembly/RunCmd.pm | 24 +
assembly/SAP.cpp | 689 +
assembly/SAP.h | 116 +
assembly/SFF2Fasta.cpp | 301 +
assembly/Scaffold.cpp | 542 +
assembly/Scaffold.h | 60 +
assembly/SimplifyGraph.cpp | 288 +
assembly/SmallVertexDeBruijn.cpp | 1301 +
assembly/SortIntegralTupleList.cpp | 80 +
assembly/SortTupleList.cpp | 149 +
assembly/SortVertexList.cpp | 72 +
assembly/SortedTupleList.cpp | 100 +
assembly/SortedTupleList.h | 87 +
assembly/Spectrum.cpp | 16 +
assembly/Spectrum.h | 43 +
assembly/SplitLinkedClones.cpp | 319 +
assembly/StringMultTuple.h | 112 +
assembly/StringTuple.cpp | 14 +
assembly/StringTuple.h | 180 +
assembly/ThreadPath.h | 19 +
assembly/ThreadReads.cpp | 509 +
assembly/ThreadReads2.cpp | 598 +
assembly/ThreadUtils.cpp | 665 +
assembly/ThreadUtils.h | 57 +
assembly/Trace.h | 88 +
assembly/TransformGraph.cpp | 258 +
assembly/Tuple.cpp | 36 +
assembly/Tuple.h | 93 +
assembly/VectorHashedSpectrum.h | 128 +
assembly/Vertex.h | 111 +
assembly/VoteUtils.cpp | 43 +
assembly/VoteUtils.h | 10 +
assembly/Voting.cpp | 387 +
assembly/Voting.h | 53 +
assembly/assemblesec.pl | 109 +
assembly/readtitle.rules | 4 +
assembly_utils/ABIToEULER.pl | 97 +
assembly_utils/AlignmentToCoverage.pl | 22 +
assembly_utils/AlignmentToFasta.pl | 32 +
assembly_utils/AssembleToMates.pl | 27 +
assembly_utils/CalcGC.pl | 13 +
assembly_utils/CheckMatepairFile.pl | 49 +
assembly_utils/CompareCoordinatesWithGeneList.pl | 46 +
assembly_utils/CompareLikelihood.pl | 121 +
assembly_utils/ComputeAlignedCoverage.pl | 40 +
assembly_utils/ComputeAlignedErrorRate.pl | 23 +
assembly_utils/ComputeCoverage.pl | 71 +
assembly_utils/ComputeErrorProfile.pl | 40 +
assembly_utils/ComputeSolexaErrorProfile.pl | 69 +
assembly_utils/CountVoteFixableReads.pl | 65 +
assembly_utils/ExtractReadsInInterval.pl | 43 +
assembly_utils/FilterQFasta.pl | 2 +
assembly_utils/FilterReads.pl | 123 +
assembly_utils/FindGapsInCoverage.pl | 79 +
assembly_utils/FindMaxGap.pl | 22 +
assembly_utils/FullToSmallSpectrum.pl | 15 +
assembly_utils/Ilmn2Fasta.pl | 14 +
assembly_utils/IntervalsToCoverage.pl | 39 +
assembly_utils/JoinSeqLines.pl | 26 +
assembly_utils/MaskTupleList.pl | 48 +
assembly_utils/ParseFitAlignment.pl | 96 +
assembly_utils/PrepareIlluminaReads.pl | 5 +
assembly_utils/PrintContigBoundaries.pl | 44 +
assembly_utils/PrintContigEnds.pl | 33 +
assembly_utils/PrintEdgeIntvs.pl | 31 +
assembly_utils/PrintEdgeSpanningReads.pl | 47 +
assembly_utils/PrintGapPlot.pl | 11 +
assembly_utils/PrintPrefix.pl | 19 +
assembly_utils/PrintReadCoords.pl | 18 +
assembly_utils/PrintReadPrefixes.pl | 17 +
assembly_utils/PrintRemovedReads.pl | 43 +
assembly_utils/PrintRetainedReads.pl | 25 +
assembly_utils/PrintUniqueEdgeIntervalCoords.pl | 28 +
assembly_utils/PrintUniqueIntervals.pl | 31 +
assembly_utils/QFastaToMaskedFasta.pl | 37 +
assembly_utils/ReleaseEulerSR.pl | 114 +
assembly_utils/RemoveGappedSequences.pl | 41 +
assembly_utils/RemoveLowQualityPairs.pl | 50 +
assembly_utils/RemoveMaskedSequence.pl | 107 +
assembly_utils/RemoveVectorSequence.pl | 91 +
assembly_utils/RunEcoliSimulation.pl | 25 +
assembly_utils/SelectMappedReads.pl | 19 +
assembly_utils/SelectReadsByCoverage.pl | 71 +
assembly_utils/TrimReadEnds.pl | 22 +
assembly_utils/TrimReads.pl | 19 +
assembly_utils/TruncateReads.pl | 24 +
assembly_utils/WindowGC.pl | 2 +
assembly_utils/abiName2ArachneName.pl | 35 +
assembly_utils/eland2fasta.pl | 22 +
assembly_utils/everyother.pl | 11 +
assembly_utils/export2fasta.pl | 24 +
assembly_utils/export2fastq.pl | 24 +
assembly_utils/fastaToReadPairing.pl | 76 +
assembly_utils/fastaToTraceinfo.pl | 47 +
assembly_utils/fq_all2std.pl | 194 +
assembly_utils/ntoa.pl | 14 +
assembly_utils/printReadInfo.pl | 23 +
assembly_utils/test.pl | 7 +
common.mak | 137 +
debian/README.Debian | 8 -
debian/README.source | 5 -
debian/changelog | 5 -
debian/compat | 1 -
debian/control | 20 -
debian/copyright | 42 -
debian/docs | 1 -
debian/install | 2 -
debian/patches/20_gcc_4.3.patch | 22 -
debian/patches/series | 1 -
debian/rules | 23 -
debian/upstream/metadata | 12 -
debian/watch | 5 -
lib/Alignment.cpp | 40 +
lib/Alignment.h | 68 +
lib/AlignmentPrinter.cpp | 144 +
lib/AlignmentPrinter.h | 39 +
lib/BinomialHeap.h | 456 +
lib/BufferedSeqReader.h | 96 +
lib/DNASequence.cpp | 276 +
lib/DNASequence.h | 362 +
lib/Makefile | 59 +
lib/Mapping.cpp | 46 +
lib/Mapping.h | 19 +
lib/PagedList.h | 273 +
lib/ParseTitle.cpp | 55 +
lib/ParseTitle.h | 48 +
lib/SeqReader.cpp | 258 +
lib/SeqReader.h | 55 +
lib/SeqUtils.cpp | 181 +
lib/SeqUtils.h | 215 +
lib/SimpleSequence.h | 45 +
lib/SimpleStats.cpp | 39 +
lib/SimpleStats.h | 139 +
lib/StatUtils.h | 49 +
lib/align/Makefile | 31 +
lib/align/alignutils.cpp | 1213 +
lib/align/alignutils.h | 268 +
lib/align/graphalign.cpp | 549 +
lib/align/graphalign.h | 122 +
lib/graph/DisjointSet.h | 66 +
lib/graph/GraphAlgo.h | 651 +
lib/graph/MSTAlgo.h | 836 +
lib/hash/HashUtils.cpp | 168 +
lib/hash/HashUtils.h | 173 +
lib/hash/Makefile | 19 +
lib/hash/PagedHashTable.h | 160 +
lib/hash/VectorHashTable.h | 266 +
lib/mctypes.h | 92 +
lib/rbtree.h | 611 +
lib/utils.cpp | 287 +
lib/utils.h | 88 +
make.rules | 42 +
mkdep.pl | 524 +
mkfiles.pl | 95 +
reads.fasta | 285716 ++++++++++++++++++++
reads.variants.fasta | 14266 +
readtitle.rules | 1 +
246 files changed, 348275 insertions(+), 147 deletions(-)
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