public static String prettyPrintSequenceRecords(SAMSequenceDictionary sequenceDictionary) {
String[] sequenceRecordNames = new String[sequenceDictionary.size()];
int sequenceRecordIndex = 0;
for (SAMSequenceRecord sequenceRecord : sequenceDictionary.getSequences())
sequenceRecordNames[sequenceRecordIndex++] = sequenceRecord.getSequenceName();
return Arrays.deepToString(sequenceRecordNames);
}
/**
* Check to ensure that the alignment makes sense based on the contents of the header.
*
* @param header The SAM file header.
* @param read The read to verify.
* @return true if alignment agrees with header, false otherwise.
*/
public static boolean alignmentAgreesWithHeader(final SAMFileHeader header, final GATKRead read) {
final int referenceIndex = getReferenceIndex(read, header);
// Read is aligned to nonexistent contig
if (!read.isUnmapped() && referenceIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
return false;
}
final SAMSequenceRecord contigHeader = header.getSequence(referenceIndex);
// Read is aligned to a point after the end of the contig
return read.isUnmapped() || read.getStart() <= contigHeader.getSequenceLength();
}
private List<String> getReferenceNames(final URL bamFile) throws IOException {
final SamReader reader =
SamReaderFactory.makeDefault().open(SamInputResource.of(bamFile.openStream()));
final List<String> result = new ArrayList<String>();
final List<SAMSequenceRecord> seqRecords =
reader.getFileHeader().getSequenceDictionary().getSequences();
for (final SAMSequenceRecord seqRecord : seqRecords) {
if (seqRecord.getSequenceName() != null) {
result.add(seqRecord.getSequenceName());
}
}
reader.close();
return result;
}
public List<String> getSequenceNames() {
if (sequenceNames == null) {
SAMFileHeader header = getFileHeader();
if (header == null) {
return null;
}
sequenceNames = new ArrayList();
List<SAMSequenceRecord> records = header.getSequenceDictionary().getSequences();
if (records.size() > 0) {
for (SAMSequenceRecord rec : header.getSequenceDictionary().getSequences()) {
String chr = rec.getSequenceName();
sequenceNames.add(chr);
}
}
}
return sequenceNames;
}
@Test
public void testSequenceDictionaryMerge() {
final String sd1 = sq1 + sq2 + sq5;
final String sd2 = sq2 + sq3 + sq4;
SAMFileReader reader1 =
new SAMFileReader(new ByteArrayInputStream(StringUtil.stringToBytes(sd1)));
SAMFileReader reader2 =
new SAMFileReader(new ByteArrayInputStream(StringUtil.stringToBytes(sd2)));
final List<SAMFileHeader> inputHeaders =
Arrays.asList(reader1.getFileHeader(), reader2.getFileHeader());
SamFileHeaderMerger merger =
new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate, inputHeaders, true);
final SAMFileHeader mergedHeader = merger.getMergedHeader();
for (final SAMFileHeader inputHeader : inputHeaders) {
int prevTargetIndex = -1;
for (final SAMSequenceRecord sequenceRecord :
inputHeader.getSequenceDictionary().getSequences()) {
final int targetIndex = mergedHeader.getSequenceIndex(sequenceRecord.getSequenceName());
Assert.assertNotSame(targetIndex, -1);
Assert.assertTrue(prevTargetIndex < targetIndex);
prevTargetIndex = targetIndex;
}
}
}
