private boolean compareSequenceRecord(final SAMSequenceRecord sequenceRecord1, final SAMSequenceRecord sequenceRecord2, final int which) { if (!sequenceRecord1.getSequenceName().equals(sequenceRecord2.getSequenceName())) { reportDifference(sequenceRecord1.getSequenceName(), sequenceRecord2.getSequenceName(), "Name of sequence record " + which); return false; } boolean ret = compareValues(sequenceRecord1.getSequenceLength(), sequenceRecord2.getSequenceLength(), "Length of sequence " + sequenceRecord1.getSequenceName()); ret = compareValues(sequenceRecord1.getSpecies(), sequenceRecord2.getSpecies(), "Species of sequence " + sequenceRecord1.getSequenceName()) && ret; ret = compareValues(sequenceRecord1.getAssembly(), sequenceRecord2.getAssembly(), "Assembly of sequence " + sequenceRecord1.getSequenceName()) && ret; ret = compareValues(sequenceRecord1.getAttribute("M5"), sequenceRecord2.getAttribute("M5"), "MD5 of sequence " + sequenceRecord1.getSequenceName()) && ret; ret = compareValues(sequenceRecord1.getAttribute("UR"), sequenceRecord2.getAttribute("UR"), "URI of sequence " + sequenceRecord1.getSequenceName()) && ret; return ret; }
private boolean compareSequenceRecord(final SAMSequenceRecord sequenceRecord1, final SAMSequenceRecord sequenceRecord2, final int which) { if (!sequenceRecord1.getSequenceName().equals(sequenceRecord2.getSequenceName())) { reportDifference(sequenceRecord1.getSequenceName(), sequenceRecord2.getSequenceName(), "Name of sequence record " + which); return false; } boolean ret = compareValues(sequenceRecord1.getSequenceLength(), sequenceRecord2.getSequenceLength(), "Length of sequence " + sequenceRecord1.getSequenceName()); ret = compareValues(sequenceRecord1.getSpecies(), sequenceRecord2.getSpecies(), "Species of sequence " + sequenceRecord1.getSequenceName()) && ret; ret = compareValues(sequenceRecord1.getAssembly(), sequenceRecord2.getAssembly(), "Assembly of sequence " + sequenceRecord1.getSequenceName()) && ret; ret = compareValues(sequenceRecord1.getAttribute("M5"), sequenceRecord2.getAttribute("M5"), "MD5 of sequence " + sequenceRecord1.getSequenceName()) && ret; ret = compareValues(sequenceRecord1.getAttribute("UR"), sequenceRecord2.getAttribute("UR"), "URI of sequence " + sequenceRecord1.getSequenceName()) && ret; return ret; }
private boolean compareSequenceRecord(final SAMSequenceRecord sequenceRecord1, final SAMSequenceRecord sequenceRecord2, final int which) throws Exception { if (!sequenceRecord1.getSequenceName().equals(sequenceRecord2.getSequenceName())) { reportDifference(sequenceRecord1.getSequenceName(), sequenceRecord2.getSequenceName(), "Name of sequence record " + which); return false; } boolean ret = compareValues(sequenceRecord1.getSequenceLength(), sequenceRecord2.getSequenceLength(), "Length of sequence " + sequenceRecord1.getSequenceName()); if (!options.ignoreSequenceProperties) { ret = compareValues(sequenceRecord1.getSpecies(), sequenceRecord2.getSpecies(), "Species of sequence " + sequenceRecord1.getSequenceName()) && ret; ret = compareValues(sequenceRecord1.getAssembly(), sequenceRecord2.getAssembly(), "Assembly of sequence " + sequenceRecord1.getSequenceName()) && ret; ret = compareValues(sequenceRecord1.getAttribute("M5"), sequenceRecord2.getAttribute("M5"), "MD5 of sequence " + sequenceRecord1.getSequenceName()) && ret; ret = compareValues(sequenceRecord1.getAttribute("UR"), sequenceRecord2.getAttribute("UR"), "URI of sequence " + sequenceRecord1.getSequenceName()) && ret; } return ret; }
private boolean compareSequenceRecord(final SAMSequenceRecord sequenceRecord1, final SAMSequenceRecord sequenceRecord2, final int which) throws Exception { if (!sequenceRecord1.getSequenceName().equals(sequenceRecord2.getSequenceName())) { reportDifference(sequenceRecord1.getSequenceName(), sequenceRecord2.getSequenceName(), "Name of sequence record " + which); return false; } boolean ret = compareValues(sequenceRecord1.getSequenceLength(), sequenceRecord2.getSequenceLength(), "Length of sequence " + sequenceRecord1.getSequenceName()); if (!options.ignoreSequenceProperties) { ret = compareValues(sequenceRecord1.getSpecies(), sequenceRecord2.getSpecies(), "Species of sequence " + sequenceRecord1.getSequenceName()) && ret; ret = compareValues(sequenceRecord1.getAssembly(), sequenceRecord2.getAssembly(), "Assembly of sequence " + sequenceRecord1.getSequenceName()) && ret; ret = compareValues(sequenceRecord1.getAttribute("M5"), sequenceRecord2.getAttribute("M5"), "MD5 of sequence " + sequenceRecord1.getSequenceName()) && ret; ret = compareValues(sequenceRecord1.getAttribute("UR"), sequenceRecord2.getAttribute("UR"), "URI of sequence " + sequenceRecord1.getSequenceName()) && ret; } return ret; }