Examples of containsChromosome()

Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder.containsChromosome()

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        if(r[2].equalsIgnoreCase(std)){
            String id= r[0];
            double loc= Double.parseDouble(r[3]);
            String chr= r[1].substring(0,r[1].length()-12).toLowerCase();
            if(ind!=0){
                if(gba.containsChromosome(pc)){
                    if(pc.equals(chr)){
                        GenomicRegion gr= new GenomicRegion(pc, (int)pp, (int)loc-1);
                        ptr.put(pid, gr);
                    }else{
                        double cl= gba.getRegionsForChromosome(pc).get(0).high;
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Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsBuilder.containsChromosome()

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                        ptr.put(pid, gr);
                    }
                }
            }
            if(i==arr.length-1){
                if(gba.containsChromosome(chr)){
                    double cl= gba.getRegionsForChromosome(chr).get(0).high;
                    GenomicRegion gr= new GenomicRegion(chr, (int)loc, (int)cl-1);
                    ptr.put(id, gr);
                }
            }
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Examples of org.broad.igv.sam.reader.FeatureIndex.containsChromosome()

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    public void testIndexSam() throws Exception {
        String samFile = TestUtils.DATA_DIR + "sam/NA12878.muc1.test2.sam";
        String samFileIdx = doStandardIndex(samFile, "sai");

        FeatureIndex idx = SamUtils.getIndexFor(samFile);
        assertTrue(idx.containsChromosome("chr1"));
        assertEquals(1, idx.getIndexedChromosomes().size());
    }

    @Test
    public void testIndexFasta() throws Exception {
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