Java Code Examples for htsjdk.samtools.util.StringUtil#charsToBytes()
The following examples show how to use
htsjdk.samtools.util.StringUtil#charsToBytes() .
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Example 1
Source File: SNPUMIBasePileupTest.java From Drop-seq with MIT License | 6 votes |
@Test(enabled=true) /** * Add an uneven number of bases and quals to trip the exception throw. */ public void testAddBaseQualsError () { int snpPos=76227022; Interval snpInterval = new Interval("HUMAN_1", snpPos, snpPos, true, "test"); SNPUMIBasePileup p = new SNPUMIBasePileup(snpInterval, "ACADM", "fake_cell", "AAAAA"); char [] bases = {'A', 'A'}; byte [] quals = {27,17,55}; byte [] bases2 = new byte [bases.length]; StringUtil.charsToBytes(bases, 0, bases.length, bases2, 0); boolean passes=false; try { p.setBasesAndQualities(bases2, quals); } catch (IllegalArgumentException e) { Assert.assertNotNull(e); passes=true; } Assert.assertTrue(passes); }
Example 2
Source File: SNPUMIBasePileupTest.java From Drop-seq with MIT License | 6 votes |
@Test(enabled=true) public void testAddBaseQuals () { int snpPos=76227022; Interval snpInterval = new Interval("HUMAN_1", snpPos, snpPos, true, "test"); SNPUMIBasePileup p = new SNPUMIBasePileup(snpInterval, "ACADM", "fake_cell", "AAAAA"); char [] bases = {'A', 'A'}; byte [] quals = {27,55}; byte [] bases2 = new byte [bases.length]; StringUtil.charsToBytes(bases, 0, bases.length, bases2, 0); boolean passes=true; try { p.setBasesAndQualities(bases2, quals); } catch (IllegalArgumentException e) { passes=false; } Assert.assertTrue(passes); }
Example 3
Source File: DigitalAlleleCountsTest.java From Drop-seq with MIT License | 5 votes |
private SNPUMIBasePileup buildPileUp (final DigitalAlleleCounts dac, final String molecularBarcode, final char [] bases, final byte [] qualities) { SNPUMIBasePileup p = new SNPUMIBasePileup(dac.getSnpInterval(), dac.getGene(), dac.getCell(), molecularBarcode); byte [] bases2 = new byte [bases.length]; StringUtil.charsToBytes(bases, 0, bases.length, bases2, 0); p.setBasesAndQualities(bases2, qualities); return (p); }
Example 4
Source File: SummarizeUMIBaseQualitiesTest.java From Drop-seq with MIT License | 4 votes |
private byte [] getBases (final char [] bases) { byte [] result = new byte [bases.length]; StringUtil.charsToBytes(bases, 0, bases.length, result, 0); return (result); }