/**
* Read all of the VCF records from source into memory, returning the header and the
* VariantContexts
*
* <p>SHOULD ONLY BE USED FOR UNIT/INTEGRATION TESTING PURPOSES!
*
* @param source the file to read, must be in VCF4 format
* @return
* @throws java.io.IOException
*/
public static Pair<VCFHeader, List<VariantContext>> readVCF(final File source)
throws IOException {
// read in the features
final List<VariantContext> vcs = new ArrayList<VariantContext>();
final VCFCodec codec = new VCFCodec();
PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(source));
final LineIterator vcfSource = codec.makeSourceFromStream(pbs);
try {
final VCFHeader vcfHeader = (VCFHeader) codec.readActualHeader(vcfSource);
while (vcfSource.hasNext()) {
final VariantContext vc = codec.decode(vcfSource);
if (vc != null) vcs.add(vc);
}
return new Pair<VCFHeader, List<VariantContext>>(vcfHeader, vcs);
} finally {
codec.close(vcfSource);
}
}
public void initialize() {
for (final Tranche t : Tranche.readTranches(TRANCHES_FILE)) {
if (t.ts >= TS_FILTER_LEVEL) {
tranches.add(t);
}
logger.info(String.format("Read tranche " + t));
}
Collections.reverse(
tranches); // this algorithm wants the tranches ordered from best (lowest truth sensitivity)
// to worst (highest truth sensitivity)
for (final RodBinding rod : input) {
inputNames.add(rod.getName());
}
if (IGNORE_INPUT_FILTERS != null) {
ignoreInputFilterSet.addAll(Arrays.asList(IGNORE_INPUT_FILTERS));
}
// setup the header fields
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
addVQSRStandardHeaderLines(hInfo);
final TreeSet<String> samples = new TreeSet<String>();
samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames));
if (tranches.size() >= 2) {
for (int iii = 0; iii < tranches.size() - 1; iii++) {
final Tranche t = tranches.get(iii);
hInfo.add(
new VCFFilterHeaderLine(
t.name,
String.format(
"Truth sensitivity tranche level for "
+ t.model.toString()
+ " model at VQS Lod: "
+ t.minVQSLod
+ " <= x < "
+ tranches.get(iii + 1).minVQSLod)));
}
}
if (tranches.size() >= 1) {
hInfo.add(
new VCFFilterHeaderLine(
tranches.get(0).name + "+",
String.format(
"Truth sensitivity tranche level for "
+ tranches.get(0).model.toString()
+ " model at VQS Lod < "
+ tranches.get(0).minVQSLod)));
} else {
throw new UserException(
"No tranches were found in the file or were above the truth sensitivity filter level "
+ TS_FILTER_LEVEL);
}
logger.info("Keeping all variants in tranche " + tranches.get(tranches.size() - 1));
final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
vcfWriter.writeHeader(vcfHeader);
}