Examples of uniqued()

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

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                progressLogger.record(sequenceName, start);
            }
            CloserUtil.close(bedReader);

            // Sort and write the output
            intervalList.uniqued().write(OUTPUT);

        } catch (final IOException e) {
            throw new RuntimeException(e);
        }
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Examples of htsjdk.samtools.util.IntervalList.uniqued()

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        final IntervalList possiblySortedResult = SORT ? result.sorted() : result;
        final IntervalList possiblyInvertedResult = INVERT ? IntervalList.invert(possiblySortedResult) : possiblySortedResult;

        //only get unique if this has been asked unless inverting (since the invert will return a unique list)
        final List<Interval> finalIntervals = UNIQUE ? possiblyInvertedResult.uniqued().getIntervals() : possiblyInvertedResult.getIntervals();

        // Decide on a PG ID and make a program group
        final SAMFileHeader header = result.getHeader();
        final Set<String> pgs = new HashSet<String>();
        for (final SAMProgramRecord pg : header.getProgramRecords()) pgs.add(pg.getId());
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Examples of htsjdk.samtools.util.IntervalList.uniqued()

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        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);

        final IntervalList intervalList = VCFFileReader.fromVcf(INPUT);
        // Sort and write the output
        intervalList.uniqued().write(OUTPUT);
        return 0;
    }
}
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