public void setValidationStringency(ValidationStringency validationStringency) { this.validationStringency = validationStringency; if (alignmentIterator != null) { alignmentIterator.setValidationStringency(validationStringency); } if (unalignmentIterator != null) { unalignmentIterator.setValidationStringency(validationStringency); } } }
/** * @return true if contained string is an SRA accession */ public boolean isValid() { return SRAAccession.isValid(acc); }
private SRALazyRecord(final SAMFileHeader header, SRAAccession accession, String readId, boolean isAligned) { super(header); this.accession = accession; this.isAligned = isAligned; this.sraReadId = readId; setReadName(readId); setReadUnmappedFlag(!isAligned); }
@Override public void loadValue(SRALazyRecord self) { self.getAlignmentStart(); } },
@Override public void loadValue(SRALazyRecord self) { self.getMateReferenceName(); } },
@Override public void loadValue(SRALazyRecord self) { self.getCigarString(); } },
@Override public boolean getFlag(SRALazyRecord self) { return self.getMateNegativeStrandFlag(); } },
@Override public void loadValue(SRALazyRecord self) { self.getMateAlignmentStart(); } },
@Override public boolean getFlag(SRALazyRecord self) { return self.getFirstOfPairFlag(); } },
@Override public void close() { if (lastRecord != null) { lastRecord.detachFromIterator(); lastRecord = null; } alignedIterator = null; } }
@Override public void loadValue(SRALazyRecord self) { self.getReferenceName(); } },
@Override public void loadValue(SRALazyRecord self) { self.getReadBases(); } },
@Override public void loadValue(SRALazyRecord self) { self.getInferredInsertSize(); } };
@Override public boolean getFlag(SRALazyRecord self) { return self.isSecondaryAlignment(); } },
@Override public boolean getFlag(SRALazyRecord self) { return self.getReadNegativeStrandFlag(); } },
public void setValidationStringency(ValidationStringency validationStringency) { this.validationStringency = validationStringency; if (alignmentIterator != null) { alignmentIterator.setValidationStringency(validationStringency); } if (unalignmentIterator != null) { unalignmentIterator.setValidationStringency(validationStringency); } } }
@Override public void loadValue(SRALazyRecord self) { self.getAlignmentStart(); } },
@Override public void loadValue(SRALazyRecord self) { self.getMateReferenceName(); } },
@Override public void loadValue(SRALazyRecord self) { self.getCigarString(); } },
@Override public boolean getFlag(SRALazyRecord self) { return self.getMateNegativeStrandFlag(); } },