[med-svn] [beagle] 03/04: Merge tag 'upstream/4.1_160222-8ef'
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Sat Mar 26 08:07:13 UTC 2016
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bob.dybian-guest pushed a commit to branch master
in repository beagle.
commit 01c6480e6b1f309ed7005e3d9f59bd614067f9f4
Merge: 01f281c 486aca4
Author: Dylan Aïssi <bob.dybian at gmail.com>
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(+)
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