API for jefferys/SamSeq
Work with aligned reads from a SAM file

Global functions
BinaryFlagDescriptor Source code
HeaderOnlyException Man page Source code
HeaderOnlyMsg Source code
MISSING_HEADER_Exception Man page Source code
MISSING_HEADER_Msg Source code
Sam Man page Source code
SamFileFormatException Man page Source code
SamFileHeaderException Man page Source code
SamFileHeaderMsg Source code
SamFileReadException Man page Source code
SamFileReadMsg Source code
SamHeader Man page Source code
SamHeader.Sam Man page Source code
SamHeader.character Man page Source code
SamReads Man page
SamReads.Sam Man page Source code
SamReads.character Man page Source code
SamSeq Man page
SamSeq-package Man page
SamSource Man page
SamSource.NULL Man page
SamSource.Sam Man page
SamSource.SamHeader Man page
SamSource.SamReads Man page
SamSource.SamSource Man page
SamSource.character Man page
SamSource.list Man page
allSetSamFlags Man page Source code
allUnsetSamFlags Man page Source code
anySetSamFlags Man page Source code
anyUnsetSamFlags Man page Source code
areHeaderTagsParsed Man page Source code
areHeaderTagsParsed.Sam Man page Source code
areHeaderTagsParsed.SamHeader Man page Source code
areReadFlags Man page Source code
areReadFlagsSet Man page Source code
areReadFlagsUnset Man page Source code
areReadTagsParsed Man page Source code
areReadTagsParsed.Sam Man page Source code
areReadTagsParsed.SamReads Man page Source code
areTagsParsed Man page
as.data.frame.SamHeader Man page Source code
as.data.frame.SamReads Man page Source code
countAllReads Man page Source code
countAllReads.Sam Source code
countAllReads.SamReads Source code
matchSamFlags Man page Source code
pairHasRef Man page Source code
pairIsAligned Man page Source code
pairIsChimeric Man page Source code
pairIsNotChimeric Man page Source code
pairIsPrimary Man page Source code
pairedEndReadTests Man page
pairedReads Man page Source code
parseSamHeaderLines Man page Source code
parseSamReadLines Man page Source code
parseSamReadTags Man page Source code
readHasRef Man page Source code
readMateHasRef Man page Source code
readTests Man page
samFlags Man page Source code
samFlags.NULL Man page Source code
samFlags.character Man page Source code
samFlags.numeric Man page Source code
samReadCount Man page Source code
samReadFilter Man page Source code
samReadMatch Man page Source code
samSourceHost Man page
samSourceName Man page
samSourceType Man page
testSamFlags Man page
jefferys/SamSeq documentation built on May 19, 2019, 3:59 a.m.