ESAT
 All Classes Namespaces Files Functions Variables Enumerator Pages
umms.core.readers.PairedEndReader Member List

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.PairedEndReaderstatic
getAlignmentType()umms.core.readers.PairedEndReader
getHeader()umms.core.readers.PairedEndReader
getOrCreatePairedEndFile(String fileToCheck, TranscriptionRead txnRead)umms.core.readers.PairedEndReaderstatic
getPairedEndFile(String fileToCheck)umms.core.readers.PairedEndReaderstatic
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.PairedEndReaderstatic
iterator()umms.core.readers.PairedEndReader
main(String[] args)umms.core.readers.PairedEndReaderstatic
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