Examples of htsjdk.samtools.liftover.LiftOver


    private long successfulIntervals = 0, failedIntervals = 0;


    public void initialize() {
        try {
            liftOver = new LiftOver(CHAIN);
        } catch (RuntimeException e) {
            throw new UserException.BadInput("there is a problem with the chain file you are using: " + e.getMessage());
        }


        liftOver.setLiftOverMinMatch(LiftOver.DEFAULT_LIFTOVER_MINMATCH);

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


        final LiftOver liftOver = new LiftOver(CHAIN);
        liftOver.setLiftOverMinMatch(MIN_LIFTOVER_PCT);


        final IntervalList fromIntervals = IntervalList.fromFile(INPUT);
        final SAMFileHeader toHeader = new SAMFileReader(SEQUENCE_DICTIONARY).getFileHeader();
        liftOver.validateToSequences(toHeader.getSequenceDictionary());
        final IntervalList toIntervals = new IntervalList(toHeader);
        boolean anyFailed = false;
        for (final Interval fromInterval : fromIntervals) {
            final Interval toInterval = liftOver.liftOver(fromInterval);
            if (toInterval != null) {
                toIntervals.add(toInterval);
            } else {
                anyFailed = true;
                LOG.warn("Liftover failed for ", fromInterval, "(len ", fromInterval.length(), ")");
                final List<LiftOver.PartialLiftover> partials = liftOver.diagnosticLiftover(fromInterval);
                for (final LiftOver.PartialLiftover partial : partials) {
                    LOG.info(partial);
                }
            }
        }

Examples of htsjdk.samtools.liftover.LiftOver

Related Classes of htsjdk.samtools.liftover.LiftOver