@Override
protected void doWork(String inputSource, VcfIterator r, VariantContextWriter w)
throws IOException {
VCFHeader header = r.getHeader();
VCFHeader h2 = new VCFHeader(header.getMetaDataInInputOrder(), header.getSampleNamesInOrder());
h2.addMetaDataLine(
new VCFInfoHeaderLine(
TAG,
VCFHeaderLineCount.UNBOUNDED,
VCFHeaderLineType.String,
"metadata added from " + TABIX + " . Format was " + FORMAT));
h2.addMetaDataLine(
new VCFHeaderLine(
getClass().getSimpleName() + "CmdLine", String.valueOf(getProgramCommandLine())));
h2.addMetaDataLine(
new VCFHeaderLine(getClass().getSimpleName() + "Version", String.valueOf(getVersion())));
h2.addMetaDataLine(
new VCFHeaderLine(
getClass().getSimpleName() + "HtsJdkVersion", HtsjdkVersion.getVersion()));
h2.addMetaDataLine(
new VCFHeaderLine(getClass().getSimpleName() + "HtsJdkHome", HtsjdkVersion.getHome()));
SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header);
w.writeHeader(h2);
while (r.hasNext()) {
VariantContext ctx = progress.watch(r.next());
Set<String> annotations = new HashSet<String>();
CloseableIterator<BedLine> iter =
this.bedReader.iterator(ctx.getContig(), ctx.getStart() - 1, ctx.getEnd() + 1);
while (iter.hasNext()) {
BedLine bedLine = iter.next();
if (!ctx.getContig().equals(bedLine.getContig())) continue;
if (ctx.getStart() - 1 >= bedLine.getEnd()) continue;
if (ctx.getEnd() - 1 < bedLine.getStart()) continue;
String newannot = this.parsedFormat.toString(bedLine);
if (!newannot.isEmpty()) annotations.add(VCFUtils.escapeInfoField(newannot));
}
CloserUtil.close(iter);
if (annotations.isEmpty()) {
w.add(ctx);
continue;
}
VariantContextBuilder vcb = new VariantContextBuilder(ctx);
vcb.attribute(TAG, annotations.toArray());
w.add(vcb.make());
incrVariantCount();
if (checkOutputError()) break;
}
progress.finish();
}
@Override
protected void doWork(String source, VcfIterator in, VariantContextWriter out)
throws IOException {
try {
VCFHeader header = in.getHeader();
VCFHeader h2 = new VCFHeader(header);
h2.addMetaDataLine(
new VCFHeaderLine(
getClass().getSimpleName() + "CmdLine", String.valueOf(getProgramCommandLine())));
h2.addMetaDataLine(
new VCFHeaderLine(getClass().getSimpleName() + "Version", String.valueOf(getVersion())));
h2.addMetaDataLine(
new VCFHeaderLine(
getClass().getSimpleName() + "HtsJdkVersion", HtsjdkVersion.getVersion()));
h2.addMetaDataLine(
new VCFHeaderLine(getClass().getSimpleName() + "HtsJdkHome", HtsjdkVersion.getHome()));
out.writeHeader(h2);
final VepPredictionParser vepParser = new VepPredictionParser(header);
final SnpEffPredictionParser snpEffparser = new SnpEffPredictionParser(header);
final MyPredictionParser myPredParser = new MyPredictionParser(header);
SAMSequenceDictionaryProgress progress =
new SAMSequenceDictionaryProgress(header.getSequenceDictionary());
while (in.hasNext()) {
this.checkKnimeCancelled();
VariantContext ctx = progress.watch(in.next());
boolean keep = false;
for (SnpEffPredictionParser.SnpEffPrediction pred : snpEffparser.getPredictions(ctx)) {
if (hasUserTem(pred.getSOTerms())) {
keep = true;
break;
}
}
if (!keep) {
for (VepPredictionParser.VepPrediction pred : vepParser.getPredictions(ctx)) {
if (hasUserTem(pred.getSOTerms())) {
keep = true;
break;
}
}
}
if (!keep) {
for (MyPredictionParser.MyPrediction pred : myPredParser.getPredictions(ctx)) {
if (hasUserTem(pred.getSOTerms())) {
keep = true;
break;
}
}
}
if (isInverseResult()) keep = !keep;
if (keep) {
incrVariantCount();
out.add(ctx);
}
if (checkOutputError()) break;
}
progress.finish();
} finally {
}
}