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 |
