AlignmentIterator

All Superinterfaces:: Alignment, Fragment

public interface AlignmentIterator extends Alignment

Iterates across a list of Alignments

Field Summary

Fields inherited from interface Alignment
all, clipLeft, clipRight, maxMapQuality, minMapQuality, noWraparound, passDuplicates, passFailed, primaryAlignment, secondaryAlignment, startWithinSlice
Method Summary

Modifier and Type

Method

Description

boolean

nextAlignment()

Advance to first alignment on initial invocation Advance to next Alignment subsequently

Methods inherited from interface 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 Fragment
getFragmentBases, getFragmentBases, getFragmentBases, getFragmentId, getFragmentQualities, getFragmentQualities, getFragmentQualities, isAligned, isPaired

Method Details
- nextAlignment
  
  boolean nextAlignment() throws ErrorMsg
  
  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.