This is the complete list of members for umms.core.readers.PairedEndReader, including all inherited members.

close()	umms.core.readers.PairedEndReader
getAlignmentType(SAMFileHeader header)	umms.core.readers.PairedEndReader	static
getAlignmentType()	umms.core.readers.PairedEndReader
getHeader()	umms.core.readers.PairedEndReader
getOrCreatePairedEndFile(String fileToCheck, TranscriptionRead txnRead)	umms.core.readers.PairedEndReader	static
getPairedEndFile(String fileToCheck)	umms.core.readers.PairedEndReader	static
getRefSequenceLengths(String chr)	umms.core.readers.PairedEndReader
getRefSequenceLengths()	umms.core.readers.PairedEndReader
getSequenceNames()	umms.core.readers.PairedEndReader
hasIndex()	umms.core.readers.PairedEndReader
isPairedEndFormat(String fileToCheck)	umms.core.readers.PairedEndReader	static
iterator()	umms.core.readers.PairedEndReader
main(String[] args)	umms.core.readers.PairedEndReader	static
PairedEndReader(File bam)	umms.core.readers.PairedEndReader
PairedEndReader(File bam, TranscriptionRead read)	umms.core.readers.PairedEndReader
PairedEndReader(File bam, TranscriptionRead read, boolean fra)	umms.core.readers.PairedEndReader
query(Annotation a, boolean contained)	umms.core.readers.PairedEndReader
setFragmentFlag(boolean fra)	umms.core.readers.PairedEndReader