Package ngs
Interface AlignmentIterator
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Field Summary
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Fields inherited from interface ngs.Alignment
all, clipLeft, clipRight, maxMapQuality, minMapQuality, noWraparound, passDuplicates, passFailed, primaryAlignment, secondaryAlignment, startWithinSlice
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description boolean
nextAlignment()
Advance to first alignment on initial invocation Advance to next Alignment subsequently-
Methods 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, hasMate
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Methods inherited from interface ngs.Fragment
getFragmentBases, getFragmentBases, getFragmentBases, getFragmentId, getFragmentQualities, getFragmentQualities, getFragmentQualities, isAligned, isPaired
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