Examples of BEDCodec

Examples of htsjdk.tribble.bed.BEDCodec

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        igvTools = null;
    }

    @Test
    public void testIntervalTest() throws Exception {
        intervalTestFile(new BEDCodec());
        intervalTestFile(new IGVBEDCodec());
    }
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Examples of htsjdk.tribble.bed.BEDCodec

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    @Test
    public void testLargeBedNoHeader() throws Exception {
        String bedFile = TestUtils.DATA_DIR + "bed/Unigene.noheader.sorted.bed";
        tstUnigeneBed(bedFile, new BEDCodec());

        tstUnigeneBed(bedFile, new IGVBEDCodec());
    }
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Examples of htsjdk.tribble.bed.BEDCodec

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    }

    @Test
    public void testLargeBedWithHeader() throws Exception {
        String bedFile = TestUtils.DATA_DIR + "bed/Unigene.withheader.sorted.bed";
        tstUnigeneBed(bedFile, new BEDCodec());

        tstUnigeneBed(bedFile, new IGVBEDCodec());
    }
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Examples of htsjdk.tribble.bed.BEDCodec

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    }

    @Test
    public void testLargeBedWeirdHeader() throws Exception {
        String bedFile = TestUtils.DATA_DIR + "bed/Unigene.weirdheader.sorted.bed";
        tstUnigeneBed(bedFile, new BEDCodec());

        tstUnigeneBed(bedFile, new IGVBEDCodec());
    }
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Examples of htsjdk.tribble.bed.BEDCodec

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    }

    @Test
    public void testLargeBedNoTrack() throws Exception {
        String bedFile = TestUtils.DATA_DIR + "bed/Unigene.notrack.sorted.bed";
        tstUnigeneBed(bedFile, new BEDCodec());

        tstUnigeneBed(bedFile, new IGVBEDCodec());
    }
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Examples of htsjdk.tribble.bed.BEDCodec

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            /**
             * NB: BED is zero-based, but a BEDCodec by default (since it is returns tribble Features) has an offset of one,
             * so it returns 1-based starts.  Ugh.  Set to zero.
             */
            final FeatureReader<BEDFeature> bedReader = AbstractFeatureReader.getFeatureReader(INPUT.getAbsolutePath(), new BEDCodec(BEDCodec.StartOffset.ZERO), false);
            final CloseableTribbleIterator<BEDFeature> iterator = bedReader.iterator();
            final ProgressLogger progressLogger = new ProgressLogger(LOG, (int) 1e6);

            while (iterator.hasNext()) {
                final BEDFeature bedFeature = iterator.next();
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