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commit 01c6480e6b1f309ed7005e3d9f59bd614067f9f4 Merge: 01f281c 486aca4 Author: Dylan Aïssi <[email protected]> Date: Sat Mar 26 08:38:56 2016 +0100 Merge tag 'upstream/4.1_160222-8ef' Upstream version 4.1~160222-8ef beagleutil/BasicIntInterval.java | 148 +++++ beagleutil/CenteredIntIntervalTree.java | 616 +++++++++++++++++ beagleutil/ChromIds.java | 126 ++++ beagleutil/ChromInterval.java | 343 ++++++++++ beagleutil/IntInterval.java | 42 ++ beagleutil/IntIntervalTree.java | 145 ++++ beagleutil/Phase.java | 78 +++ beagleutil/SampleIds.java | 127 ++++ beagleutil/Samples.java | 225 +++++++ beagleutil/ThreadSafeIndexer.java | 153 +++++ blbutil/ByteIndexArray.java | 85 +++ blbutil/CharIndexArray.java | 85 +++ blbutil/Const.java | 93 +++ blbutil/FileIt.java | 70 ++ blbutil/FileUtil.java | 235 +++++++ blbutil/Filter.java | 100 +++ blbutil/IndexMap.java | 195 ++++++ blbutil/IndexSet.java | 152 +++++ blbutil/InputIt.java | 320 +++++++++ blbutil/IntArray.java | 102 +++ blbutil/IntList.java | 212 ++++++ blbutil/IntPair.java | 143 ++++ blbutil/IntSet.java | 265 ++++++++ blbutil/SampleFileIt.java | 41 ++ blbutil/ShiftedByteIndexArray.java | 86 +++ blbutil/StringUtil.java | 281 ++++++++ blbutil/Utilities.java | 208 ++++++ blbutil/Validate.java | 576 ++++++++++++++++ blbutil/WrappedIntArray.java | 58 ++ dag/Dag.java | 384 +++++++++++ dag/DagLevel.java | 241 +++++++ dag/DagUtil.java | 182 +++++ dag/HighCapacityDagLevel.java | 340 ++++++++++ dag/ImmutableDag.java | 265 ++++++++ dag/LinkageEquilibriumDag.java | 301 +++++++++ dag/LowCapacityDagLevel.java | 369 +++++++++++ dag/MergeableDag.java | 406 ++++++++++++ dag/MergeableDagLevel.java | 731 +++++++++++++++++++++ dag/Score.java | 200 ++++++ gpl_license | 674 +++++++++++++++++++ haplotype/BasicHapPairs.java | 129 ++++ haplotype/BasicSampleHapPairs.java | 260 ++++++++ haplotype/BitHapPair.java | 172 +++++ haplotype/ConsensusPhaser.java | 271 ++++++++ haplotype/GLSampleHapPairs.java | 152 +++++ haplotype/GenotypeCorrection.java | 273 ++++++++ haplotype/HapPair.java | 90 +++ haplotype/HapPairs.java | 132 ++++ haplotype/HapsMarkerIterator.java | 127 ++++ haplotype/RefHapPairs.java | 189 ++++++ haplotype/RevHapPair.java | 88 +++ haplotype/RevHapPairs.java | 121 ++++ haplotype/RevSampleHapPairs.java | 138 ++++ haplotype/SampleHapPairs.java | 114 ++++ haplotype/Weights.java | 150 +++++ haplotype/WrappedHapPair.java | 88 +++ ibd/HapSegment.java | 169 +++++ ibd/HaploidIbd.java | 264 ++++++++ ibd/Haplotype.java | 242 +++++++ ibd/IbdBaum.java | 292 ++++++++ ibd/IbdSegment.java | 247 +++++++ ibd/IbsHapSegments.java | 353 ++++++++++ main/AlleleProbs.java | 162 +++++ main/BasicAlleleProbs.java | 139 ++++ main/BasicGenotypeValues.java | 116 ++++ main/ConstrainedAlleleProbs.java | 157 +++++ main/CurrentData.java | 484 ++++++++++++++ main/GeneticMap.java | 142 ++++ main/GenotypeValues.java | 134 ++++ main/HapAlleleProbs.java | 93 +++ main/HapPairSampler.java | 233 +++++++ main/LiAndStephensHapSampler.java | 158 +++++ main/LowMemHapAlleleProbs.java | 203 ++++++ main/Main.java | 451 +++++++++++++ main/MainHelper.java | 261 ++++++++ main/NuclearFamilies.java | 374 +++++++++++ main/Par.java | 550 ++++++++++++++++ main/PlinkGeneticMap.java | 369 +++++++++++ main/PositionMap.java | 84 +++ main/RecombHapPairSampler.java | 178 +++++ main/RevGenotypeValues.java | 111 ++++ main/RunStats.java | 370 +++++++++++ main/SampleGenotypeValues.java | 183 ++++++ main/SampleHapPairAlleleProbs.java | 105 +++ main/WindowWriter.java | 274 ++++++++ net/sf/samtools/Defaults.java | 49 ++ net/sf/samtools/FileTruncatedException.java | 46 ++ net/sf/samtools/SAMException.java | 44 ++ net/sf/samtools/SAMFormatException.java | 44 ++ net/sf/samtools/util/BinaryCodec.java | 662 +++++++++++++++++++ .../util/BlockCompressedFilePointerUtil.java | 101 +++ .../samtools/util/BlockCompressedInputStream.java | 484 ++++++++++++++ .../samtools/util/BlockCompressedOutputStream.java | 312 +++++++++ .../util/BlockCompressedStreamConstants.java | 118 ++++ net/sf/samtools/util/BlockGunzipper.java | 115 ++++ net/sf/samtools/util/HttpUtils.java | 102 +++ net/sf/samtools/util/IOUtil.java | 124 ++++ net/sf/samtools/util/RuntimeEOFException.java | 46 ++ net/sf/samtools/util/RuntimeIOException.java | 46 ++ net/sf/samtools/util/SeekableBufferedStream.java | 90 +++ net/sf/samtools/util/SeekableFileStream.java | 69 ++ net/sf/samtools/util/SeekableHTTPStream.java | 153 +++++ net/sf/samtools/util/SeekableStream.java | 37 ++ net/sf/samtools/util/StringUtil.java | 460 +++++++++++++ sample/ConsumeSingleSamples.java | 163 +++++ sample/DiploidStates.java | 88 +++ sample/DuoBaumLevel.java | 641 ++++++++++++++++++ sample/DuoNodes.java | 338 ++++++++++ sample/HapBaumLevel.java | 445 +++++++++++++ sample/HapNodes.java | 233 +++++++ sample/HaplotypeCoder.java | 204 ++++++ sample/ImputationData.java | 341 ++++++++++ sample/LSHapBaum.java | 324 +++++++++ sample/RecombSingleBaum.java | 326 +++++++++ sample/RecombSingleBaumLevel.java | 613 +++++++++++++++++ sample/RecombSingleNodes.java | 361 ++++++++++ sample/RefHapSeg.java | 283 ++++++++ sample/RefHapSegs.java | 221 +++++++ sample/RestrictedDag.java | 402 +++++++++++ sample/SamplerData.java | 240 +++++++ sample/SingleBaum.java | 301 +++++++++ sample/SingleBaumInterface.java | 108 +++ sample/SingleBaumLevel.java | 530 +++++++++++++++ sample/SingleNodes.java | 294 +++++++++ vcf/AL.java | 118 ++++ vcf/AllData.java | 355 ++++++++++ vcf/BasicGL.java | 193 ++++++ vcf/BasicMarker.java | 547 +++++++++++++++ vcf/BitSetGT.java | 482 ++++++++++++++ vcf/BitSetRefGT.java | 252 +++++++ vcf/Bref.java | 550 ++++++++++++++++ vcf/BrefIt.java | 350 ++++++++++ vcf/ByteArrayRefGT.java | 222 +++++++ vcf/Data.java | 249 +++++++ vcf/FilterUtil.java | 139 ++++ vcf/FuzzyGL.java | 143 ++++ vcf/GL.java | 182 +++++ vcf/GprobsStatistics.java | 313 +++++++++ vcf/HapsMarker.java | 82 +++ vcf/HbdAL.java | 117 ++++ vcf/IntervalVcfIt.java | 137 ++++ vcf/LowMafRefDiallelicGT.java | 220 +++++++ vcf/LowMafRefGT.java | 264 ++++++++ vcf/Marker.java | 177 +++++ vcf/MarkerContainer.java | 34 + vcf/Markers.java | 389 +++++++++++ vcf/MaskedEndsGL.java | 182 +++++ vcf/NoPhaseGL.java | 120 ++++ vcf/RefGL.java | 172 +++++ vcf/RefIt.java | 449 +++++++++++++ vcf/RestrictedVcfWindow.java | 285 ++++++++ vcf/RevGL.java | 121 ++++ vcf/SeqCodedRefGT.java | 178 +++++ vcf/SplicedGL.java | 167 +++++ vcf/TargetData.java | 230 +++++++ vcf/VcfEmission.java | 208 ++++++ vcf/VcfEmissionCompressor.java | 298 +++++++++ vcf/VcfHeader.java | 289 ++++++++ vcf/VcfIt.java | 396 +++++++++++ vcf/VcfMetaInfo.java | 101 +++ vcf/VcfRecGTParser.java | 300 +++++++++ vcf/VcfRecord.java | 676 +++++++++++++++++++ vcf/VcfWindow.java | 321 +++++++++ vcf/VcfWriter.java | 380 +++++++++++ 164 files changed, 38741 insertions(+) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beagle.git _______________________________________________ debian-med-commit mailing list [email protected] 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