Package ngs
Interface AlignmentIterator
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Field Summary
Fields inherited from interface ngs.Alignment
all, clipLeft, clipRight, maxMapQuality, minMapQuality, noWraparound, passDuplicates, passFailed, primaryAlignment, secondaryAlignment, startWithinSlice
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Method Summary
Modifier and TypeMethodDescriptionboolean
Advance 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, hasMate
Methods inherited from interface ngs.Fragment
getFragmentBases, getFragmentBases, getFragmentBases, getFragmentId, getFragmentQualities, getFragmentQualities, getFragmentQualities, isAligned, isPaired
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Method Details
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nextAlignment
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