private void outputMissingInterval(final IntervalStratification stats) {
final GenomeLoc interval = stats.getInterval();
final boolean missing[] = new boolean[interval.size()];
Arrays.fill(missing, true);
for (AbstractStratification sample : stats.getElements()) {
if (hasMissingStatuses(sample)) {
int pos = 0;
for (AbstractStratification locus : sample.getElements()) {
if (locus.callableStatuses().isEmpty()) {
missing[pos] = false;
}
pos++;
}
}
}
int start = -1;
boolean insideMissing = false;
for (int i = 0; i < missing.length; i++) {
if (missing[i] && !insideMissing) {
start = interval.getStart() + i;
insideMissing = true;
} else if (!missing[i] && insideMissing) {
final int stop = interval.getStart() + i - 1;
outputMissingInterval(interval.getContig(), start, stop);
insideMissing = false;
}
}
if (insideMissing) {
outputMissingInterval(interval.getContig(), start, interval.getStop());
}
}
/**
* Takes the interval, finds it in the stash, prints it to the VCF
*
* @param stats The statistics of the interval
* @param refAllele the reference allele
*/
private void outputStatsToVCF(final IntervalStratification stats, final Allele refAllele) {
GenomeLoc interval = stats.getInterval();
final List<Allele> alleles = new ArrayList<>();
final Map<String, Object> attributes = new HashMap<>();
final ArrayList<Genotype> genotypes = new ArrayList<>();
for (String sample : samples) {
final GenotypeBuilder gb = new GenotypeBuilder(sample);
SampleStratification sampleStat = stats.getSampleStatistics(sample);
gb.attribute(
GATKVCFConstants.AVG_INTERVAL_DP_BY_SAMPLE_KEY,
sampleStat.averageCoverage(interval.size()));
gb.attribute(GATKVCFConstants.LOW_COVERAGE_LOCI, sampleStat.getNLowCoveredLoci());
gb.attribute(GATKVCFConstants.ZERO_COVERAGE_LOCI, sampleStat.getNUncoveredLoci());
gb.filters(statusToStrings(stats.getSampleStatistics(sample).callableStatuses(), false));
genotypes.add(gb.make());
}
alleles.add(refAllele);
alleles.add(SYMBOLIC_ALLELE);
VariantContextBuilder vcb =
new VariantContextBuilder(
"DiagnoseTargets",
interval.getContig(),
interval.getStart(),
interval.getStop(),
alleles);
vcb = vcb.log10PError(VariantContext.NO_LOG10_PERROR);
vcb.filters(new LinkedHashSet<>(statusToStrings(stats.callableStatuses(), true)));
attributes.put(VCFConstants.END_KEY, interval.getStop());
attributes.put(GATKVCFConstants.AVG_INTERVAL_DP_KEY, stats.averageCoverage(interval.size()));
attributes.put(GATKVCFConstants.INTERVAL_GC_CONTENT_KEY, stats.gcContent());
vcb = vcb.attributes(attributes);
vcb = vcb.genotypes(genotypes);
vcfWriter.add(vcb.make());
}
public Event(GenomeLoc loc, int furthestStopPos, EVENT_TYPE type) {
this.loc = loc;
this.furthestStopPos = furthestStopPos;
this.type = type;
if (type == EVENT_TYPE.INDEL_EVENT || type == EVENT_TYPE.BOTH) {
eventStartPos = loc.getStart();
eventStopPos = loc.getStop();
} else {
eventStartPos = -1;
eventStopPos = -1;
}
if (type == EVENT_TYPE.POINT_EVENT || type == EVENT_TYPE.BOTH) {
pointEvents.add(loc.getStart());
}
}
public void onTraversalDone(EventPair sum) {
if (sum.left != null && sum.left.isReportableEvent()) sum.intervals.add(sum.left.getLoc());
if (sum.right != null && sum.right.isReportableEvent()) sum.intervals.add(sum.right.getLoc());
if (FilenameUtils.getExtension(out.getName()).equals("interval_list")) {
final SAMFileHeader masterSequenceDictionaryHeader = new SAMFileHeader();
masterSequenceDictionaryHeader.setSequenceDictionary(
getToolkit().getMasterSequenceDictionary());
final IntervalList intervalList = new IntervalList(masterSequenceDictionaryHeader);
for (GenomeLoc loc : sum.intervals) {
intervalList.add(new Interval(loc.getContig(), loc.getStart(), loc.getStop()));
}
intervalList.write(out);
} else {
try (BufferedWriter bufferedWriter = IOUtil.openFileForBufferedWriting(out)) {
for (GenomeLoc loc : sum.intervals) {
bufferedWriter.write(loc.toString());
bufferedWriter.newLine();
}
} catch (final IOException e) {
throw new GATKException("Error writing out intervals to file: " + out.getAbsolutePath(), e);
}
}
}
public String toString() {
return String.format(
"%s\t%d\t%d\t%s", loc.getContig(), loc.getStart() - 1, loc.getStop(), state);
}
/**
* 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());
}
