/** @{inheritDoc} */
@Override
public SAMRecordIterator query(
final String sequence, final int start, final int end, final boolean contained) {
GenomeLoc region = genomeLocParser.createGenomeLoc(sequence, start, end);
List<SAMRecord> coveredSubset = new ArrayList<SAMRecord>();
for (SAMRecord read : reads) {
GenomeLoc readPosition = genomeLocParser.createGenomeLoc(read);
if (contained && region.containsP(readPosition)) coveredSubset.add(read);
else if (!contained && readPosition.overlapsP(region)) coveredSubset.add(read);
}
final Iterator<SAMRecord> iterator = coveredSubset.iterator();
return new SAMRecordIterator() {
public boolean hasNext() {
return iterator.hasNext();
}
public SAMRecord next() {
return iterator.next();
}
public void close() {}
public void remove() {
iterator.remove();
}
public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder) {
return this;
}
};
}
@BeforeTest
public void before() {
// Create GenomeLoc
IndexedFastaSequenceFile fasta =
CachingIndexedFastaSequenceFile.checkAndCreate(
new File(privateTestDir + "iupacFASTA.fasta"));
GenomeLocParser genomeLocParser = new GenomeLocParser(fasta);
chr1 = fasta.getSequenceDictionary().getSequence(0).getSequenceName();
genomeLoc = genomeLocParser.createGenomeLoc(chr1, 5, 10);
}
/**
* Updating the location of this CalledBaseState by the new stop location
*
* @param newStop
*/
public void update(GenomeLoc newStop) {
loc = genomeLocParser.createGenomeLoc(loc.getContig(), loc.getStart(), newStop.getStop());
}
@BeforeClass
public void beforeClass() {
header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
loc = genomeLocParser.createGenomeLoc("chr1", 1);
}