umms.core.writers.PairedEndWriter Member List

This is the complete list of members for umms.core.writers.PairedEndWriter, including all inherited members.

addAlignment(final Alignment alignment)	umms.core.writers.PairedEndWriter
addRecord(final SAMRecord record)	umms.core.writers.PairedEndWriter
close()	umms.core.writers.PairedEndWriter
convertInputToPairedEnd()	umms.core.writers.PairedEndWriter
convertInputToPairedEnd(TranscriptionRead txnRead)	umms.core.writers.PairedEndWriter
getDefaultFile(String file)	umms.core.writers.PairedEndWriter	static
getOutputFile()	umms.core.writers.PairedEndWriter
mateCigarFlag	umms.core.writers.PairedEndWriter	static
mateLineFlag	umms.core.writers.PairedEndWriter	static
mateSequenceFlag	umms.core.writers.PairedEndWriter	static
PAIRED_END_EXTENSION	umms.core.writers.PairedEndWriter	static
PairedEndWriter(File bamFile)	umms.core.writers.PairedEndWriter
PairedEndWriter(File bamFile, String output)	umms.core.writers.PairedEndWriter
readCigarFlag	umms.core.writers.PairedEndWriter	static
readStartFlag	umms.core.writers.PairedEndWriter	static
setMaxAllowableInsert(int x)	umms.core.writers.PairedEndWriter