ZoomDataRecord rec = zlIter.next();
protected List<LocusScore> getZoomSummaryScores(String chr, int start, int end, int zoom) { Chromosome c = genome.getChromosome(chr); if (c == null) return null; double nBins = Math.pow(2, zoom); double scale = c.getLength() / (nBins * 700); BBZoomLevelHeader zlHeader = getZoomLevelForScale(scale); if (zlHeader == null) return null; int bbLevel = zlHeader.getZoomLevel(); int reductionLevel = zlHeader.getReductionLevel(); // If we are at the highest precomputed resolution compare to the requested resolution. If they differ // by more than a factor of 2 compute "on the fly" String tmp = chrNameMap.get(chr); String querySeq = tmp == null ? chr : tmp; if (reader.isBigBedFile() || bbLevel > 1 || (bbLevel == 1 && (reductionLevel / scale) < 2)) { ArrayList<LocusScore> scores = new ArrayList(1000); ZoomLevelIterator zlIter = reader.getZoomLevelIterator(bbLevel, querySeq, start, querySeq, end, false); while (zlIter.hasNext()) { ZoomDataRecord rec = zlIter.next(); float v = getValue(rec); BasicScore bs = new BasicScore(rec.getChromStart(), rec.getChromEnd(), v); scores.add(bs); } return scores; } else { // No precomputed scores for this resolution level return null; } }
int length, chunkStart, chunkEnd; while (zoomIterator.hasNext()) { wItem = zoomIterator.next(); chunkStart = (Math.max(region.getStart(), wItem.getChromStart()) - region.getStart()) / windowSize; chunkEnd = (Math.min(region.getEnd(), wItem.getChromEnd()) - region.getStart() - 1) / windowSize;
if (zlIter.hasNext()) { while (zlIter.hasNext()) { ZoomDataRecord rec = zlIter.next(); values[nValues++] = (rec.getMeanVal()); if (nValues >= 10000) {
@Test public void testBigBed() throws IOException { String path = TestUtils.DATA_DIR + "bb/chr21.refseq.bb"; BBFileReader bbReader = new BBFileReader(path); BBFileHeader bbFileHdr = bbReader.getBBFileHeader(); assertTrue(bbFileHdr.isBigBed()); String chr = "chr21"; int start = 26490012; int end = 42182827; for (BBZoomLevelHeader header : bbReader.getZoomLevels().getZoomLevelHeaders()) { assertNotNull(header); ZoomLevelIterator zlIter = bbReader.getZoomLevelIterator(header.getZoomLevel(), chr, start, chr, end, false); while (zlIter.hasNext()) { ZoomDataRecord rec = zlIter.next(); int n = rec.getBasesCovered(); if (n > 0) { assertEquals(chr, rec.getChromName()); assertTrue(rec.getChromEnd() >= start && rec.getChromStart() <= end); } } } }