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Project: dataflow-java
(GitHub Link)
dataflow-java-master
EclipseCodeFormat.xml
run_tests.sh
src
main
java
htsjdk
samtools
BAMBlockWriter.java
SeekingBAMFileReader.java
BAMShardIndexer.java
BAMFileIndexImpl.java
SAMFileSpanImpl.java
BinaryBAMShardIndexWriter.java
com
google
cloud
genomics
dataflow
coders
DelegatingAtomicCoder.java
GenericJsonCoder.java
functions
VariantFunctions.java
JoinNonVariantSegmentsWithVariants.java
SitesToShards.java
ibs
CallSimilarityCalculator.java
AlleleSimilarityCalculator.java
SharedMinorAllelesCalculatorFactory.java
IBSCalculator.java
SharedMinorAllelesCalculator.java
SharedAllelesRatioCalculator.java
CallSimilarityCalculatorFactory.java
FormatIBSData.java
SharedAllelesRatioCalculatorFactory.java
verifybamid
ReadFunctions.java
Solver.java
LikelihoodFn.java
KeyReadsFn.java
BreakFusionTransform.java
GetReferencesFromHeaderFn.java
pca
PCoAnalysis.java
ExtractSimilarCallsets.java
OutputPCoAFile.java
ShardReadsTransform.java
utils
BAMDiff.java
GCSOutputOptions.java
GCSOptions.java
CallSetNamesOptions.java
GenomicsOptions.java
PairGenerator.java
TruncatedOutputStream.java
AnnotationUtils.java
CallFilters.java
ShardOptions.java
GCSHelper.java
writers
bam
WriteBAIFn.java
CombineShardsFn.java
WriteBAMTransform.java
WriteBAMFn.java
pipelines
ShardedBAMWriting.java
VerifyBamId.java
CalculateCoverage.java
IdentifyPrivateVariants.java
AnnotateVariants.java
IdentityByState.java
LoadReadsToBigQuery.java
VariantSimilarity.java
DeleteVariants.java
CountReads.java
model
AlleleFreq.java
ReadCounts.java
ReadBaseQuality.java
ReadQualityCount.java
PosRgsMq.java
ReadBaseWithReference.java
readers
GenomicsApiReader.java
VariantStreamer.java
ReadStreamer.java
ReadGroupStreamer.java
bam
ReaderOptions.java
Reader.java
BAMShard.java
ShardingPolicy.java
ReadBAMTransform.java
Sharder.java
SeekableGCSStream.java
BAMIO.java
HeaderInfo.java
test
resources
com
google
cloud
genomics
dataflow
pipelines
family.txt
sites.tsv
bamlist.txt
readers
bam
conversion_test.sam
java
com
google
cloud
genomics
dataflow
coders
GenericJsonCoderTest.java
functions
VariantFunctionsTest.java
JoinNonVariantSegmentsWithVariantsTest.java
ibs
AlleleSimilarityCalculatorTest.java
CallSimilarityCalculatorTest.java
verifybamid
LikelihoodFnTest.java
SolverTest.java
ReadFunctionsTest.java
SitesToShardsTest.java
pca
ExtractSimilarCallsetsTest.java
utils
PairGeneratorTest.java
GCSHelperITCase.java
AnnotationUtilsTest.java
DataUtils.java
pipelines
CountReadsITCase.java
AnnotateVariantsITCase.java
IdentityByStateITCase.java
ShardedBAMWritingITCase.java
IntegrationTestHelper.java
CalculateCoverageTest.java
CalculateCoverageITCase.java
VerifyBamIdTest.java
IdentifyPrivateVariantsITCase.java
VariantSimilarityITCase.java
readers
bam
ShardingPolicyTest.java
BAMShardTest.java
BAMIOITCase.java
results
ibs
1000Genomes-chr22
analyze-ibs-data.Rmd
analyze-ibs-data.md
figure
generate.R
.gitignore
pom.xml
LICENSE
lib
README.rst
.travis.yml
CONTRIBUTING.rst
.gitignore