Package htsjdk.tribble.bed

Examples of htsjdk.tribble.bed.BEDCodec

53
54
55
56
57
58
59
60
        igvTools = null;
    }

    @Test
    public void testIntervalTest() throws Exception {
        intervalTestFile(new BEDCodec());
        intervalTestFile(new IGVBEDCodec());
    }
View Full Code Here
61
62
63
64
65
66
67
68
69

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

        tstUnigeneBed(bedFile, new IGVBEDCodec());
    }
View Full Code Here
69
70
71
72
73
74
75
76
77
    }

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

        tstUnigeneBed(bedFile, new IGVBEDCodec());
    }
View Full Code Here
77
78
79
80
81
82
83
84
85
    }

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

        tstUnigeneBed(bedFile, new IGVBEDCodec());
    }
View Full Code Here
85
86
87
88
89
90
91
92
93
    }

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

        tstUnigeneBed(bedFile, new IGVBEDCodec());
    }
View Full Code Here
65
66
67
68
69
70
71
72
73
74
75
            /**
             * 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();
View Full Code Here
TOP

Related Classes of htsjdk.tribble.bed.BEDCodec

  • org.broad.igv.tools.parsers.TestBEDCodecs
  • picard.util.BedToIntervalList
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.