private String getCigarStringImpl() { try { if (isAligned) { return getCurrentAlignment().getShortCigar(false); } } catch (ErrorMsg e) { throw new RuntimeException(e); } return SAMRecord.NO_ALIGNMENT_CIGAR; }
private int getInferredInsertSizeImpl() { try { if (isAligned) { return (int) getCurrentAlignment().getTemplateLength(); } } catch (ErrorMsg e) { throw new RuntimeException(e); } return 0; }
private boolean getSecondaryAlignmentFlagImpl() { try { if (isAligned) { return getCurrentAlignment().getAlignmentCategory() == Alignment.secondaryAlignment; } } catch (ErrorMsg e) { throw new RuntimeException(e); } return false; }
private int getMappingQualityImpl() { try { if (isAligned) { return getCurrentAlignment().getMappingQuality(); } } catch (ErrorMsg e) { throw new RuntimeException(e); } return SAMRecord.NO_MAPPING_QUALITY; }
private String getCigarStringImpl() { try { if (isAligned) { return getCurrentAlignment().getShortCigar(false); } } catch (ErrorMsg e) { throw new RuntimeException(e); } return SAMRecord.NO_ALIGNMENT_CIGAR; }
private boolean getSecondaryAlignmentFlagImpl() { try { if (isAligned) { return getCurrentAlignment().getAlignmentCategory() == Alignment.secondaryAlignment; } } catch (ErrorMsg e) { throw new RuntimeException(e); } return false; }
private int getMappingQualityImpl() { try { if (isAligned) { return getCurrentAlignment().getMappingQuality(); } } catch (ErrorMsg e) { throw new RuntimeException(e); } return SAMRecord.NO_MAPPING_QUALITY; }
private boolean getReadNegativeStrandFlagImpl() { try { if (isAligned) { return getCurrentAlignment().getIsReversedOrientation(); } } catch (ErrorMsg e) { throw new RuntimeException(e); } return false; }
private String getReferenceNameImpl() { try { if (isAligned) { return getCurrentAlignment().getReferenceSpec(); } } catch (ErrorMsg e) { throw new RuntimeException(e); } return SAMRecord.NO_ALIGNMENT_REFERENCE_NAME; }
private int getAlignmentStartImpl() { try { if (isAligned) { return (int) getCurrentAlignment().getAlignmentPosition() + 1; } } catch (ErrorMsg e) { throw new RuntimeException(e); } return SAMRecord.NO_ALIGNMENT_START; }
private String getReferenceNameImpl() { try { if (isAligned) { return getCurrentAlignment().getReferenceSpec(); } } catch (ErrorMsg e) { throw new RuntimeException(e); } return SAMRecord.NO_ALIGNMENT_REFERENCE_NAME; }
private int getInferredInsertSizeImpl() { try { if (isAligned) { return (int) getCurrentAlignment().getTemplateLength(); } } catch (ErrorMsg e) { throw new RuntimeException(e); } return 0; }
private byte[] getReadBasesImpl() { try { if (isAligned) { return getCurrentAlignment().getAlignedFragmentBases().getBytes(); } else { return getCurrentUnalignedRead().getFragmentBases().getBytes(); } } catch (ErrorMsg e) { throw new RuntimeException(e); } }
private byte[] getReadBasesImpl() { try { if (isAligned) { return getCurrentAlignment().getAlignedFragmentBases().getBytes(); } else { return getCurrentUnalignedRead().getFragmentBases().getBytes(); } } catch (ErrorMsg e) { throw new RuntimeException(e); } }
private boolean getReadPairedFlagImpl() { try { if (isAligned) { return getCurrentAlignment().isPaired(); } else { return getCurrentUnalignedRead().getNumFragments() > 1; } } catch (ErrorMsg e) { throw new RuntimeException(e); } }
private boolean getReadPairedFlagImpl() { try { if (isAligned) { return getCurrentAlignment().isPaired(); } else { return getCurrentUnalignedRead().getNumFragments() > 1; } } catch (ErrorMsg e) { throw new RuntimeException(e); } }
private String getMateReferenceNameImpl() { try { if (isAligned && getReadPairedFlag() && !getMateUnmappedFlag()) { return getCurrentAlignment().getMateReferenceSpec(); } } catch (ErrorMsg e) { throw new RuntimeException(e); } return SAMRecord.NO_ALIGNMENT_REFERENCE_NAME; }
private boolean getMateNegativeStrandFlagImpl() { try { if (isAligned && getReadPairedFlag() && !getMateUnmappedFlag()) { Alignment mate = getCurrentAlignment().getMateAlignment(); return mate.getIsReversedOrientation(); } } catch (ErrorMsg e) { throw new RuntimeException(e); } return false; }
private int getMateAlignmentStartImpl() { try { if (isAligned && getReadPairedFlag() && !getMateUnmappedFlag()) { Alignment mate = getCurrentAlignment().getMateAlignment(); return (int) mate.getAlignmentPosition() + 1; } } catch (ErrorMsg e) { throw new RuntimeException(e); } return SAMRecord.NO_ALIGNMENT_START; }
private boolean getMateNegativeStrandFlagImpl() { try { if (isAligned && getReadPairedFlag() && !getMateUnmappedFlag()) { Alignment mate = getCurrentAlignment().getMateAlignment(); return mate.getIsReversedOrientation(); } } catch (ErrorMsg e) { throw new RuntimeException(e); } return false; }