SEPARATOR_CHAR
ReadReader
SPARK_BRANCH
spark
SPARK_BUILD_DATE
spark
SPARK_BUILD_USER
spark
SPARK_REPO_URL
spark
SPARK_REVISION
spark
SPARK_VERSION
spark
SeqTenderAlignment
alignment
SeqTenderVCF
annotation
saveAsBAMFile
CustomRDDSAMRecordFunctions
saveAsVCFFile
CustomVariantContextFunctions
saveDISQAsVCFFile
CustomVariantContextFunctions
saveRddToSAMFile
AlignmentTools
secondRead
InterleavedFastqRead
sequence
FastaRead
setFastaReadAndReturnReadBytes
ReadReader
setFastqReadAndReturnReadBytes
ReadReader
setFirstRead
InterleavedFastqRead
setName
FastaRead
setQuality
FastqRead
setSecondRead
InterleavedFastqRead
setSequence
FastaRead
setUpProcessAndTaskDirectory
BioPipedRDD
setValidRead
FastaReadRecordReader
FastqReadRecordReader
InterleavedFastqReadRecordReader
ReadRecordReader
snapToolName
Constants
spark
apache
split
FastaReadRecordReader
FastqReadRecordReader
InterleavedFastqReadRecordReader
ReadRecordReader
starToolName
Constants
start
ReadRecordReader
startStdErrReaderThread
BioPipedRDD
startWriterThread
BioPipedRDD