private void loadVCF(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException, TribbleIndexNotFoundException {
TribbleFeatureSource src = TribbleFeatureSource.getFeatureSource(locator, genome);
VCFHeader header = (VCFHeader) src.getHeader();
// Test if the input VCF file contains methylation rate data:
// This is determined by testing for the presence of two sample format fields: MR and GB, used
// in the
// rendering of methylation rate.
// MR is the methylation rate on a scale of 0 to 100% and GB is the number of bases that pass
// filter for the position. GB is needed to avoid displaying positions for which limited
// coverage
// prevents reliable estimation of methylation rate.
boolean enableMethylationRateSupport =
(header.getFormatHeaderLine("MR") != null && header.getFormatHeaderLine("GB") != null);
List<String> allSamples = new ArrayList(header.getGenotypeSamples());
VariantTrack t = new VariantTrack(locator, src, allSamples, enableMethylationRateSupport);
// VCF tracks handle their own margin
t.setMargin(0);
newTracks.add(t);
}
/**
* Load the input file as a feature, mutation, or maf (multiple alignment) file.
*
* @param locator
* @param newTracks
*/
private void loadTribbleFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException, TribbleIndexNotFoundException {
String typeString = locator.getTypeString();
// Mutation (mut, maf, vcf) files are handled special. Check here, rather than depend on order
// in giant case statement.
if (MutationTrackLoader.isMutationAnnotationFile(locator)) {
loadMutFile(locator, newTracks, genome); // Must be tried before generic "loadIndexed" below
} else if (VariantTrack.isVCF(typeString)) {
loadVCF(locator, newTracks, genome);
} else {
TribbleFeatureSource tribbleFeatureSource =
TribbleFeatureSource.getFeatureSource(locator, genome);
FeatureSource src =
GFFFeatureSource.isGFF(locator.getPath())
? new GFFFeatureSource(tribbleFeatureSource)
: tribbleFeatureSource;
// Create feature source and track
FeatureTrack t = new FeatureTrack(locator, src);
t.setName(locator.getTrackName());
// t.setRendererClass(BasicTribbleRenderer.class);
// Set track properties from header
Object header = tribbleFeatureSource.getHeader();
if (header != null && header instanceof FeatureFileHeader) {
FeatureFileHeader ffh = (FeatureFileHeader) header;
if (ffh.getTrackType() != null) {
t.setTrackType(ffh.getTrackType());
}
if (ffh.getTrackProperties() != null) {
t.setProperties(ffh.getTrackProperties());
}
if (ffh.getTrackType() == TrackType.REPMASK) {
t.setHeight(15);
}
}
if (locator.getPath().contains(".narrowPeak")
|| locator.getPath().contains(".broadPeak")
|| locator.getPath().contains(".gappedPeak")) {
t.setUseScore(true);
}
newTracks.add(t);
}
}
synchronized Iterator<Mutation> getFeatures(String trackKey, String chr, int start, int end)
throws IOException {
if (currentRange == null || !currentRange.contains(chr, start, end)) {
Iterator<Feature> features = tribbleFeatureSource.getFeatures(chr, start, end);
while (features.hasNext()) {
Mutation feat = (Mutation) features.next();
String thisKey = feat.getSampleId();
List<Mutation> keyFeatures = featureMap.get(thisKey);
if (keyFeatures == null) {
keyFeatures = new ArrayList<Mutation>();
featureMap.put(thisKey, keyFeatures);
}
keyFeatures.add(feat);
currentRange = new Range(chr, start, end);
}
}
List<Mutation> featureList = featureMap.get(trackKey);
return featureList == null ? Collections.EMPTY_LIST.iterator() : featureList.iterator();
}
public MutationDataManager(ResourceLocator locator, Genome genome)
throws IOException, TribbleIndexNotFoundException {
this.tribbleFeatureSource = TribbleFeatureSource.getFeatureSource(locator, genome);
this.locator = locator;
}