Package ngs
Interface AlignmentIterator
Iterates across a list of Alignments
-
Field Summary
Fields inherited from interface ngs.Alignment
all, clipLeft, clipRight, maxMapQuality, minMapQuality, noWraparound, passDuplicates, passFailed, primaryAlignment, secondaryAlignment, startWithinSlice -
Method Summary
Modifier and TypeMethodDescriptionbooleanAdvance to first alignment on initial invocation Advance to next Alignment subsequentlyMethods inherited from interface ngs.Alignment
getAlignedFragmentBases, getAlignmentCategory, getAlignmentId, getAlignmentLength, getAlignmentPosition, getClippedFragmentBases, getClippedFragmentQualities, getIsReversedOrientation, getLongCigar, getMappingQuality, getMateAlignment, getMateAlignmentId, getMateIsReversedOrientation, getMateReferenceSpec, getReadGroup, getReadId, getReferenceBases, getReferenceSpec, getRNAOrientation, getShortCigar, getSoftClip, getTemplateLength, hasMateMethods inherited from interface ngs.Fragment
getFragmentBases, getFragmentBases, getFragmentBases, getFragmentId, getFragmentQualities, getFragmentQualities, getFragmentQualities, isAligned, isPaired
-
Method Details
-
nextAlignment
Advance to first alignment on initial invocation Advance to next Alignment subsequently- Returns:
- false if no more Alignments are available.
- Throws:
ErrorMsg- if more Alignments should be available, but could not be accessed.
-