/** @{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;
}
};
}
private void writeDifferences(
final List<VariantContext> source1Alleles, final List<VariantContext> source2Alleles) {
int currentIndex1 = 0, currentIndex2 = 0;
final int size1 = source1Alleles.size(), size2 = source2Alleles.size();
VariantContext current1 = source1Alleles.get(0);
VariantContext current2 = source2Alleles.get(0);
while (currentIndex1 < size1 || currentIndex2 < size2) {
if (current1 == null) {
writeOne(current2, source2, null);
currentIndex2++;
current2 = (currentIndex2 < size2 ? source2Alleles.get(currentIndex2) : null);
} else if (current2 == null) {
writeOne(current1, source1, null);
currentIndex1++;
current1 = (currentIndex1 < size1 ? source1Alleles.get(currentIndex1) : null);
} else {
final GenomeLoc loc1 = getToolkit().getGenomeLocParser().createGenomeLoc(current1);
final GenomeLoc loc2 = getToolkit().getGenomeLocParser().createGenomeLoc(current2);
if (loc1.getStart() == loc2.getStart() || loc1.overlapsP(loc2)) {
String status;
if (loc1.getStart() == loc2.getStart()) {
final String allele1 = current1.getAlternateAllele(0).getBaseString();
final String allele2 = current2.getAlternateAllele(0).getBaseString();
if (allele1.indexOf(allele2) != -1 || allele2.indexOf(allele1) != -1)
status = ONE_ALLELE_SUBSET_OF_OTHER_STATUS;
else status = SAME_START_DIFFERENT_ALLELES_STATUS;
} else {
status = OVERLAPPING_EVENTS_STATUS;
}
writeOne(current1, INTERSECTION_SET, status);
currentIndex1++;
currentIndex2++;
current1 = (currentIndex1 < size1 ? source1Alleles.get(currentIndex1) : null);
current2 = (currentIndex2 < size2 ? source2Alleles.get(currentIndex2) : null);
} else if (loc1.isBefore(loc2)) {
writeOne(current1, source1, null);
currentIndex1++;
current1 = (currentIndex1 < size1 ? source1Alleles.get(currentIndex1) : null);
} else {
writeOne(current2, source2, null);
currentIndex2++;
current2 = (currentIndex2 < size2 ? source2Alleles.get(currentIndex2) : null);
}
}
}
}