Examples of GATKBAMFileSpan

htsjdk.samtools.GATKBAMFileSpan
A temporary solution to work around Java access rights issues: override BAMFileSpan and make it public. TODO: Eliminate once we determine the final fate of the BAM index reading code.

Examples of htsjdk.samtools.GATKBAMFileSpan

    }


    @Test
    public void testFilePointerCombineDisjoint() {
        FilePointer one = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",1,5));
        one.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,1)));
        FilePointer two = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",6,10));
        two.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(1,2)));


        FilePointer result = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",1,10));
        result.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,2)));


        Assert.assertEquals(one.combine(genomeLocParser,two),result,"Combination of two file pointers is incorrect");
        Assert.assertEquals(two.combine(genomeLocParser,one),result,"Combination of two file pointers is incorrect");


        //Now test that adjacent (but disjoint) intervals are properly handled with OVERLAPPING_ONLY
        one = new FilePointer(IntervalMergingRule.OVERLAPPING_ONLY, genomeLocParser.createGenomeLoc("chr1",1,5));
        one.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,1)));
        two = new FilePointer(IntervalMergingRule.OVERLAPPING_ONLY, genomeLocParser.createGenomeLoc("chr1",6,10));
        two.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(1,2)));


        result = new FilePointer(IntervalMergingRule.OVERLAPPING_ONLY,
                genomeLocParser.createGenomeLoc("chr1",1,5),
                genomeLocParser.createGenomeLoc("chr1",6,10));
        result.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,2)));


        Assert.assertEquals(one.combine(genomeLocParser,two),result,"Combination of two file pointers is incorrect");
        Assert.assertEquals(two.combine(genomeLocParser,one),result,"Combination of two file pointers is incorrect");
    }

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Examples of htsjdk.samtools.GATKBAMFileSpan

    }


    @Test
    public void testFilePointerCombineJoint() {
        FilePointer one = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",1,5));
        one.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,2)));
        FilePointer two = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",2,6));
        two.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(1,3)));


        FilePointer result = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",1,6));
        result.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,3)));        


        Assert.assertEquals(one.combine(genomeLocParser,two),result,"Combination of two file pointers is incorrect");
        Assert.assertEquals(two.combine(genomeLocParser,one),result,"Combination of two file pointers is incorrect");


        //Repeat the tests for OVERLAPPING_ONLY
        one = new FilePointer(IntervalMergingRule.OVERLAPPING_ONLY, genomeLocParser.createGenomeLoc("chr1",1,5));
        one.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,2)));
        two = new FilePointer(IntervalMergingRule.OVERLAPPING_ONLY, genomeLocParser.createGenomeLoc("chr1",2,6));
        two.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(1,3)));


        result = new FilePointer(IntervalMergingRule.OVERLAPPING_ONLY, genomeLocParser.createGenomeLoc("chr1",1,6));
        result.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,3)));


        Assert.assertEquals(one.combine(genomeLocParser,two),result,"Combination of two file pointers is incorrect");
        Assert.assertEquals(two.combine(genomeLocParser,one),result,"Combination of two file pointers is incorrect");
    }

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Examples of htsjdk.samtools.GATKBAMFileSpan

    }


    @Test
    public void testFilePointerCombineOneSided() {
        FilePointer filePointer = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",1,5));
        filePointer.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,1)));
        FilePointer empty = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",6,10));
        // Do not add file spans to empty result


        FilePointer result = new FilePointer(IntervalMergingRule.ALL, genomeLocParser.createGenomeLoc("chr1",1,10));
        result.addFileSpans(readerID,new GATKBAMFileSpan(new GATKChunk(0,1)));
        Assert.assertEquals(filePointer.combine(genomeLocParser,empty),result,"Combination of two file pointers is incorrect");
        Assert.assertEquals(empty.combine(genomeLocParser,filePointer),result,"Combination of two file pointers is incorrect");
    }

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