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);
}
}
}
}
/**
* Outputs all intervals that are behind the current reference locus
*
* @param refLocus the current reference locus
* @param refBase the reference allele
*/
private void outputFinishedIntervals(final GenomeLoc refLocus, final byte refBase) {
// output any intervals that were finished
final List<GenomeLoc> toRemove = new LinkedList<>();
for (GenomeLoc key : intervalMap.keySet()) {
if (key.isBefore(refLocus)) {
final IntervalStratification intervalStats = intervalMap.get(key);
outputStatsToVCF(intervalStats, Allele.create(refBase, true));
if (hasMissingLoci(intervalStats)) {
outputMissingInterval(intervalStats);
}
toRemove.add(key);
}
}
for (GenomeLoc key : toRemove) {
intervalMap.remove(key);
}
}
private void writeAndPurgeAllEqualVariants(
final List<VariantContext> sourceVCs1,
final List<VariantContext> sourceVCs2,
final String status) {
int currentIndex1 = 0, currentIndex2 = 0;
int size1 = sourceVCs1.size(), size2 = sourceVCs2.size();
VariantContext current1 = (currentIndex1 < size1 ? sourceVCs1.get(currentIndex1) : null);
VariantContext current2 = (currentIndex2 < size2 ? sourceVCs2.get(currentIndex2) : null);
while (current1 != null && current2 != null) {
final GenomeLoc loc1 = getToolkit().getGenomeLocParser().createGenomeLoc(current1);
final GenomeLoc loc2 = getToolkit().getGenomeLocParser().createGenomeLoc(current2);
if (loc1.equals(loc2)
|| (loc1.getStart() == loc2.getStart()
&& (current1.getAlternateAlleles().size() > 1
|| current2.getAlternateAlleles().size() > 1))) {
// test the alleles
if (determineAndWriteOverlap(current1, current2, status)) {
sourceVCs1.remove(currentIndex1);
sourceVCs2.remove(currentIndex2);
size1--;
size2--;
} else {
currentIndex1++;
currentIndex2++;
}
current1 = (currentIndex1 < size1 ? sourceVCs1.get(currentIndex1) : null);
current2 = (currentIndex2 < size2 ? sourceVCs2.get(currentIndex2) : null);
} else if (loc1.isBefore(loc2)) {
currentIndex1++;
current1 = (currentIndex1 < size1 ? sourceVCs1.get(currentIndex1) : null);
} else {
currentIndex2++;
current2 = (currentIndex2 < size2 ? sourceVCs2.get(currentIndex2) : null);
}
}
}