Package htsjdk.samtools.util

Examples of htsjdk.samtools.util.FormatUtil.parseDouble()

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                for (int i = 0; i < parts.length; i++) {
                    Assert.assertEquals(parts, testFile1Data[index]);
                }
            }
            else {
                Assert.assertEquals(testFile1Data[index][0], format.parseDouble(parts[0]));
                Assert.assertEquals(testFile1Data[index][1], format.parseInt(parts[1]));
                Assert.assertEquals(testFile1Data[index][2], format.parseInt(parts[2]));
                Assert.assertEquals(testFile1Data[index][3], format.parseDouble(parts[3]));
            }
            index++;
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            }
            else {
                Assert.assertEquals(testFile1Data[index][0], format.parseDouble(parts[0]));
                Assert.assertEquals(testFile1Data[index][1], format.parseInt(parts[1]));
                Assert.assertEquals(testFile1Data[index][2], format.parseInt(parts[2]));
                Assert.assertEquals(testFile1Data[index][3], format.parseDouble(parts[3]));
            }
            index++;
        }
    }
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                for (int i = 0; i < parts.length; i++) {
                    Assert.assertEquals(parts, testFile1Data[indexIntoTestData]);
                }
            }
            else {
                Assert.assertEquals(testFile1Data[indexIntoTestData][0], format.parseDouble(parts[0]));
                Assert.assertEquals(testFile1Data[indexIntoTestData][1], format.parseInt(parts[1]));
                Assert.assertEquals(testFile1Data[indexIntoTestData][2], format.parseInt(parts[2]));
                Assert.assertEquals(testFile1Data[indexIntoTestData][3], format.parseDouble(parts[3]));
            }
            index++;
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            }
            else {
                Assert.assertEquals(testFile1Data[indexIntoTestData][0], format.parseDouble(parts[0]));
                Assert.assertEquals(testFile1Data[indexIntoTestData][1], format.parseInt(parts[1]));
                Assert.assertEquals(testFile1Data[indexIntoTestData][2], format.parseInt(parts[2]));
                Assert.assertEquals(testFile1Data[indexIntoTestData][3], format.parseDouble(parts[3]));
            }
            index++;
        }
    }
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        expectedMetrics.READ_PAIR_DUPLICATES = expectedMetrics.READ_PAIR_DUPLICATES / 2;
        expectedMetrics.READ_PAIRS_EXAMINED = expectedMetrics.READ_PAIRS_EXAMINED / 2;
        expectedMetrics.calculateDerivedMetrics();

        // Have to run this Double value through the same format/parsing operations as during a file write/read
        expectedMetrics.PERCENT_DUPLICATION = formatter.parseDouble(formatter.format(expectedMetrics.PERCENT_DUPLICATION));
    }

    public void setExpectedOpticalDuplicate(final int expectedOpticalDuplicatePairs) {
        expectedMetrics.READ_PAIR_OPTICAL_DUPLICATES = expectedOpticalDuplicatePairs;
    }
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