@Override public long listWeight(final IntervalList intervalList) { return intervalList.size(); }
@Override public long listWeight(final IntervalList intervalList) { return intervalList.size(); }
public static OverlapDetector<Interval> makeOverlapDetector(final File samFile, final SAMFileHeader header, final File ribosomalIntervalsFile, final Log log) { final OverlapDetector<Interval> ribosomalSequenceOverlapDetector = new OverlapDetector<Interval>(0, 0); if (ribosomalIntervalsFile != null) { final IntervalList ribosomalIntervals = IntervalList.fromFile(ribosomalIntervalsFile); if (ribosomalIntervals.size() == 0) { log.warn("The RIBOSOMAL_INTERVALS file, " + ribosomalIntervalsFile.getAbsolutePath() + " does not contain intervals"); } try { SequenceUtil.assertSequenceDictionariesEqual(header.getSequenceDictionary(), ribosomalIntervals.getHeader().getSequenceDictionary()); } catch (SequenceUtil.SequenceListsDifferException e) { throw new PicardException("Sequence dictionaries differ in " + samFile.getAbsolutePath() + " and " + ribosomalIntervalsFile.getAbsolutePath(), e); } final IntervalList uniquedRibosomalIntervals = ribosomalIntervals.uniqued(); final List<Interval> intervals = uniquedRibosomalIntervals.getIntervals(); ribosomalSequenceOverlapDetector.addAll(intervals, intervals); } return ribosomalSequenceOverlapDetector; }
public static OverlapDetector<Interval> makeOverlapDetector(final File samFile, final SAMFileHeader header, final File ribosomalIntervalsFile, final Log log) { final OverlapDetector<Interval> ribosomalSequenceOverlapDetector = new OverlapDetector<Interval>(0, 0); if (ribosomalIntervalsFile != null) { final IntervalList ribosomalIntervals = IntervalList.fromFile(ribosomalIntervalsFile); if (ribosomalIntervals.size() == 0) { log.warn("The RIBOSOMAL_INTERVALS file, " + ribosomalIntervalsFile.getAbsolutePath() + " does not contain intervals"); } try { SequenceUtil.assertSequenceDictionariesEqual(header.getSequenceDictionary(), ribosomalIntervals.getHeader().getSequenceDictionary()); } catch (SequenceUtil.SequenceListsDifferException e) { throw new PicardException("Sequence dictionaries differ in " + samFile.getAbsolutePath() + " and " + ribosomalIntervalsFile.getAbsolutePath(), e); } final IntervalList uniquedRibosomalIntervals = ribosomalIntervals.uniqued(); final List<Interval> intervals = uniquedRibosomalIntervals.getIntervals(); ribosomalSequenceOverlapDetector.addAll(intervals, intervals); } return ribosomalSequenceOverlapDetector; }
/** Calculates a few statistics about the bait design that can then be output. */ void calculateStatistics(final IntervalList targets, final IntervalList baits) { this.TARGET_TERRITORY = (int) targets.getUniqueBaseCount(); this.TARGET_COUNT = targets.size(); this.BAIT_TERRITORY = (int) baits.getUniqueBaseCount(); this.BAIT_COUNT = baits.size(); this.DESIGN_EFFICIENCY = this.TARGET_TERRITORY / (double) this.BAIT_TERRITORY; // Figure out the intersection between all targets and all baits final IntervalList tmp = new IntervalList(targets.getHeader()); final OverlapDetector<Interval> detector = new OverlapDetector<Interval>(0, 0); detector.addAll(baits.getIntervals(), baits.getIntervals()); for (final Interval target : targets) { final Collection<Interval> overlaps = detector.getOverlaps(target); if (overlaps.isEmpty()) { this.ZERO_BAIT_TARGETS++; } else { for (final Interval i : overlaps) tmp.add(target.intersect(i)); } } tmp.uniqued(); this.BAIT_TARGET_TERRITORY_INTERSECTION = (int) tmp.getBaseCount(); }
/** Calculates a few statistics about the bait design that can then be output. */ void calculateStatistics(final IntervalList targets, final IntervalList baits) { this.TARGET_TERRITORY = (int) targets.getUniqueBaseCount(); this.TARGET_COUNT = targets.size(); this.BAIT_TERRITORY = (int) baits.getUniqueBaseCount(); this.BAIT_COUNT = baits.size(); this.DESIGN_EFFICIENCY = this.TARGET_TERRITORY / (double) this.BAIT_TERRITORY; // Figure out the intersection between all targets and all baits final IntervalList tmp = new IntervalList(targets.getHeader()); final OverlapDetector<Interval> detector = new OverlapDetector<Interval>(0, 0); detector.addAll(baits.getIntervals(), baits.getIntervals()); for (final Interval target : targets) { final Collection<Interval> overlaps = detector.getOverlaps(target); if (overlaps.isEmpty()) { this.ZERO_BAIT_TARGETS++; } else { for (final Interval i : overlaps) tmp.add(target.intersect(i)); } } tmp.uniqued(); this.BAIT_TARGET_TERRITORY_INTERSECTION = (int) tmp.getBaseCount(); }
@Test public void uniqueIntervalsWithoutNames() { final IntervalList test = new IntervalList(this.fileHeader); test.add(new Interval("1", 100, 200)); test.add(new Interval("1", 500, 600)); test.add(new Interval("1", 550, 700)); for (final boolean concat : new boolean[]{true, false}) { final IntervalList unique = test.uniqued(concat); Assert.assertEquals(unique.size(), 2); } }
for (final IntervalList finalInterval : resultIntervals) { totalBaseCount += finalInterval.getBaseCount(); intervalCount += finalInterval.size();
for (final IntervalList finalInterval : resultIntervals) { totalBaseCount += finalInterval.getBaseCount(); intervalCount += finalInterval.size();
log.info("Starting with " + padded.size() + " targets."); padded.uniqued(); log.info("After uniquing " + padded.size() + " targets remain."); log.info("After collapsing nearby targets " + targets.size() + " targets remain."); } else { targets = padded; log.info("Designed and kept " + baits.size() + " baits, discarded " + discardedBaits);
log.info("Starting with " + padded.size() + " targets."); padded.uniqued(); log.info("After uniquing " + padded.size() + " targets remain."); log.info("After collapsing nearby targets " + targets.size() + " targets remain."); } else { targets = padded; log.info("Designed and kept " + baits.size() + " baits, discarded " + discardedBaits);