public Feature next() { BedFeature feat = bedIterator.next(); String[] restOfFields = feat.getRestOfFields(); String[] tokens = new String[restOfFields.length + 3]; tokens[0] = feat.getChromosome(); tokens[1] = String.valueOf(feat.getStartBase()); tokens[2] = String.valueOf(feat.getEndBase()); System.arraycopy(restOfFields, 0, tokens, 3, restOfFields.length); BasicFeature feature = bedCodec.decode(tokens); return feature; }
protected String next() throws IOException{ if(this.tabixIterator != null){ return this.tabixIterator.next(); } else if(this.bigBedIterator != null) { if( ! this.bigBedIterator.hasNext()){ return null; } BedFeature x= this.bigBedIterator.next(); if(x == null){ return null; } StringBuilder sb= new StringBuilder(); sb.append(x.getChromosome()); sb.append("\t"); sb.append(x.getStartBase()); sb.append("\t"); sb.append(x.getEndBase()); for(String field : x.getRestOfFields()){ sb.append("\t"); sb.append(field); } return sb.toString(); } else { throw new RuntimeException(); } }
public MethylScore next() { BedFeature feat = null; while (feat == null && bedIterator.hasNext()) { feat = bedIterator.next(); String[] restOfFields = feat.getRestOfFields(); MethylScore score = type == Type.ZILLER ? createZillerScore(feat, restOfFields) : createUSCScore(feat, restOfFields); return score; } return null; }
@Override protected Variant readNext() { // Get next item BedFeature f = iterator.next(); if (f == null) return null; // Create an ID String id = label + ":" + (f.getStartBase() + 1) + "_" + f.getEndBase(); // Show as one-based coordinates // Get score String restOfFields[] = f.getRestOfFields(); double score = Gpr.parseDoubleSafe(restOfFields[1]); // Create variant Variant variant = new VariantWithScore(getChromosome(f.getChromosome()), f.getStartBase(), f.getEndBase() - 1, id, score); return variant; }