CommandBuilder

alignment

Constants

alignment

CustomRDDSAMRecordFunctions

alignment

CustomRDDTextFunctions

utils

CustomVariantContextFunctions

annotation

childThreadException

ProcessDetails

cleanupTaskDirectory

BioPipedRDD

clear

FastaRead FastqRead InterleavedFastqRead

close

ReadRecordReader

codec

ReadRecordReader

codecFactory

ReadRecordReader

compute

AlignmentsPipedRDD BioPipedRDD VariantsPipedRDD

conf

FastaReadRecordReader FastqReadRecordReader InterleavedFastqReadRecordReader ReadRecordReader biodatageeks

context

VariantContextWithHeader

createRecordReader

FastaReadInputFormat FastqReadInputFormat InterleavedFastqReadInputFormat

currentValue

ReadRecordReader