Package htsjdk.samtools.util

Examples of htsjdk.samtools.util.IntervalList.unique()

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                        i.isNegativeStrand(),
                        i.getName()));
            }

            log.info("Starting with " + padded.size() + " targets.");
            padded.unique();
            log.info("After uniquing " + padded.size() + " targets remain.");

            if (MERGE_NEARBY_TARGETS) {
                final ListIterator<Interval> iterator = padded.getIntervals().listIterator();
                Interval previous = iterator.next();
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            else {
                for (final Interval i : overlaps) tmp.add(target.intersect(i));
            }
        }

        tmp.unique();
        this.BAIT_TARGET_TERRITORY_INTERSECTION = (int) tmp.getBaseCount();
    }

    /** Method that writes out all the parameter values that were used in the design using reflection. */
    void writeParametersFile(final File file) {
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                SequenceUtil.assertSequenceDictionariesEqual(header.getSequenceDictionary(), ribosomalIntervals.getHeader().getSequenceDictionary());
            } catch (SequenceUtil.SequenceListsDifferException e) {
                throw new PicardException("Sequence dictionaries differ in " + samFile.getAbsolutePath() + " and " + ribosomalIntervalsFile.getAbsolutePath(),
                        e);
            }
            ribosomalIntervals.unique();
            final List<Interval> intervals = ribosomalIntervals.getIntervals();
            ribosomalSequenceOverlapDetector.addAll(intervals, intervals);
        }
        return ribosomalSequenceOverlapDetector;
    }
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        // Make an iterator that will filter out funny looking things
        final SamLocusIterator iterator;
        if (INTERVALS != null) {
            final IntervalList intervals = IntervalList.fromFile(INTERVALS);
            intervals.unique();
            iterator = new SamLocusIterator(in, intervals, false);
        }
        else {
            iterator = new SamLocusIterator(in);
        }
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