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| /* | |
| * The MIT License | |
| * | |
| * Copyright (c) 2014 The Broad Institute | |
| * | |
| * Permission is hereby granted, free of charge, to any person obtaining a copy | |
| * of this software and associated documentation files (the "Software"), to deal | |
| * in the Software without restriction, including without limitation the rights | |
| * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| * copies of the Software, and to permit persons to whom the Software is | |
| * furnished to do so, subject to the following conditions: | |
| * | |
| * The above copyright notice and this permission notice shall be included in | |
| * all copies or substantial portions of the Software. | |
| * | |
| * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
| * THE SOFTWARE. | |
| */ | |
| package picard.sam.markduplicates; | |
| import htsjdk.samtools.SAMRecord; | |
| import htsjdk.samtools.SamReader; | |
| import htsjdk.samtools.SamReaderFactory; | |
| import htsjdk.samtools.util.CloseableIterator; | |
| import htsjdk.samtools.util.CloserUtil; | |
| import org.testng.annotations.DataProvider; | |
| import org.testng.annotations.Test; | |
| import java.io.File; | |
| /** | |
| * This class defines the individual test cases to run. The actual running of the test is done | |
| * by AbstractMarkDuplicatesCommandLineProgramTester or children thereof (see getTester). | |
| */ | |
| public abstract class AbstractMarkDuplicatesCommandLineProgramTest { | |
| protected abstract AbstractMarkDuplicatesCommandLineProgramTester getTester(); | |
| protected final static int DEFAULT_BASE_QUALITY = 10; | |
| protected boolean markSecondaryAndSupplementaryRecordsLikeTheCanonical() { return false; } | |
| protected boolean markUnmappedRecordsLikeTheirMates() { return false; } | |
| @Test | |
| public void testSingleUnmappedFragment() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addUnmappedFragment(-1, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoUnmappedFragments() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addUnmappedFragment(-1, DEFAULT_BASE_QUALITY); | |
| tester.addUnmappedFragment(-1, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testSingleUnmappedPair() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addUnmappedPair(-1, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testSingleMappedFragment() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedFragment(1, 1, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedFragments() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedFragment(0, 1, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedFragment(0, 1, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testSingleMappedPair() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(1, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testSingleMappedFragmentAndSingleMappedPair() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedFragment(1, 1, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedPair(1, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedPairs() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(1, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(1, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testThreeMappedPairs() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(1, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(1, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedPair(1, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testSingleMappedFragmentAndTwoMappedPairs() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedFragment(1, 1, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedPair(1, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(1, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedPairsAndTerminalUnmappedFragment() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(1, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(1, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addUnmappedFragment(-1, DEFAULT_BASE_QUALITY); // unmapped fragment at end of file | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedPairsAndTerminalUnmappedPair() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(1, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(1, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addUnmappedPair(-1, DEFAULT_BASE_QUALITY); // unmapped pair at end of file | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testOpticalDuplicateFinding() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| // explicitly creating 1 expected optical duplicate pair | |
| tester.setExpectedOpticalDuplicate(1); | |
| // pass in the read names manually, in order to control duplicates vs optical duplicates | |
| tester.addMatePair("READ0:1:1:1:1", 1, 1, 100, false, false, false, false, "50M", "50M", false, true, false, | |
| false, false, DEFAULT_BASE_QUALITY); // non-duplicate mapped pair to start | |
| tester.addMatePair("READ1:1:1:1:300", 1, 1, 100, false, false, true, true, "50M", "50M", false, true, false, | |
| false, false, DEFAULT_BASE_QUALITY); // duplicate pair, NOT optical duplicate (delta-Y > 100) | |
| tester.addMatePair("READ2:1:1:1:50", 1, 1, 100, false, false, true, true, "50M", "50M", false, true, false, | |
| false, false, DEFAULT_BASE_QUALITY); // duplicate pair, expected optical duplicate (delta-X and delta-Y < 100) | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testOpticalDuplicateClusterSamePositionNoOpticalDuplicates() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.setExpectedOpticalDuplicate(0); | |
| tester.addMatePair("RUNID:7:1203:2886:82292", 1, 485253, 485253, false, false, true, true, "42M59S", "59S42M", false, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMatePair("RUNID:7:1203:2884:16834", 1, 485253, 485253, false, false, false, false, "59S42M", "42M59S", true, false, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.setExpectedOpticalDuplicate(0); | |
| tester.addMatePair("RUNID:7:1203:2886:16834", 1, 485253, 485253, false, false, true, true, "42M59S", "59S42M", false, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMatePair("RUNID:7:1203:2884:16835", 1, 485253, 485253, false, false, false, false, "59S42M", "42M59S", true, false, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.setExpectedOpticalDuplicate(1); | |
| tester.addMatePair("RUNID:7:1203:2886:16834", 1, 485253, 485253, false, false, true, true, "45M", "45M", false, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMatePair("RUNID:7:1203:2884:16835", 1, 485253, 485253, false, false, false, false, "45M", "45M", false, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testOpticalDuplicateClusterOneEndSamePositionOneCluster() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.setExpectedOpticalDuplicate(1); | |
| tester.addMatePair("RUNID:7:2205:17939:39728", 1, 485328, 485312, false, false, false, false, "55M46S", "30S71M", false, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMatePair("RUNID:7:2205:17949:39745", 1, 485328, 485328, false, false, true, true, "55M46S", "46S55M", false, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test(dataProvider = "secondarySupplementaryData") | |
| public void testManyOpticalDuplicateClusterOneEndSamePositionOneCluster(final Boolean additionalFragSecondary, final Boolean additionalFragSupplementary, final Boolean fragLikeFirst) { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.setExpectedOpticalDuplicate(2); | |
| //canonical | |
| tester.addMatePair("RUNID:7:2205:17939:39728", 1, 485328, 485312, false, false, false, false, "55M46S", "30S71M", false, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| //library | |
| tester.addMatePair("RUNID:7:2205:27949:39745", 1, 485328, 485328, false, false, true, true, "55M46S", "46S55M", false, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| //optical (of canonical) | |
| tester.addMatePair("RUNID:7:2205:17949:39745", 1, 485328, 485328, false, false, true, true, "55M46S", "46S55M", false, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| //non-canonical | |
| tester.addMappedFragment(fragLikeFirst ? "RUNID:7:2205:17939:39728" : "RUNID:7:2205:17949:39745", 1, 400, markSecondaryAndSupplementaryRecordsLikeTheCanonical() && !fragLikeFirst, null, null, additionalFragSecondary, additionalFragSupplementary, DEFAULT_BASE_QUALITY); | |
| //library | |
| tester.addMatePair("RUNID:7:2205:37949:39745", 1, 485328, 485328, false, false, true, true, "55M46S", "46S55M", false, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| //optical of canonical | |
| tester.addMatePair("RUNID:7:2205:17959:39735", 1, 485328, 485328, false, false, true, true, "55M46S", "46S55M", false, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedPairsAndMappedSecondaryFragment() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(1, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(1, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedFragment(1, 200, false, DEFAULT_BASE_QUALITY, true); // mapped non-primary fragment | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testMappedFragmentAndMappedPairFirstOfPairNonPrimary() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedFragment(1, 1, false,DEFAULT_BASE_QUALITY); | |
| tester.addMatePair(1, 200, 0, false, true, false, false, "54M22S", null, false, false, true, true, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedPairsMatesSoftClipped() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(1, 10022, 10051, false, false, "76M", "8S68M", false, true, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(1, 10022, 10063, false, false, "76M", "5S71M", false, true, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedPairsWithSoftClipping() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| // NB: no duplicates | |
| // 5'1: 2, 5'2:46+73M=118 | |
| // 5'1: 2, 5'2:51+68M=118 | |
| tester.addMappedPair(1, 2, 46, false, false, "6S42M28S", "3S73M", false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(1, 2, 51, true, true, "6S42M28S", "8S68M", false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.setNoMateCigars(true); | |
| // NB: no duplicates | |
| // 5'1: 2, 5'2:46+73M=118 | |
| // 5'1: 2, 5'2:51+68M=118 | |
| tester.addMappedPair(1, 12, 46, false, false, "6S42M28S", null, true, DEFAULT_BASE_QUALITY); // only add the first one | |
| tester.addMappedPair(1, 12, 51, false, false, "6S42M28S", null, true, DEFAULT_BASE_QUALITY); // only add the first one | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedPairsWithSoftClippingBoth() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| // mapped reference length: 73 + 42 = 115 | |
| tester.addMappedPair(1, 10046, 10002, true, true, "3S73M", "6S42M28S", true, false, false, DEFAULT_BASE_QUALITY); | |
| // mapped reference length: 68 + 48 = 116 | |
| tester.addMappedPair(1, 10051, 10002, false, false, "8S68M", "6S48M22S", true, false, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testMatePairSecondUnmapped() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMatePair(1, 10049, 10049, false, true, false, false, "11M2I63M", null, false, false, false, false, false, DEFAULT_BASE_QUALITY); // neither are duplicates | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testMatePairFirstUnmapped() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMatePair(1, 10056, 10056, true, false, false, false, null, "54M22S", false, false, false, false, false, DEFAULT_BASE_QUALITY); // neither are duplicates | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testMappedFragmentAndMatePairSecondUnmapped() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMatePair(1, 10049, 10049, false, true, false, false, "11M2I63M", null, false, false, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedFragment(1, 10049, true, DEFAULT_BASE_QUALITY); // duplicate | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testMappedFragmentAndMatePairFirstUnmapped() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMatePair(1, 10049, 10049, true, false, false, false, null, "11M2I63M", false, false, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedFragment(1, 10049, true, DEFAULT_BASE_QUALITY); // duplicate | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testMappedPairAndMatePairSecondUnmapped() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMatePair(1, 10040, 10040, false, true, true, markUnmappedRecordsLikeTheirMates(), "76M", null, false, false, false, false, false, DEFAULT_BASE_QUALITY); // second a duplicate, | |
| // second end unmapped | |
| tester.addMappedPair(1, 10189, 10040, false, false, "41S35M", "65M11S", true, false, false, DEFAULT_BASE_QUALITY); // mapped OK | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testMappedPairAndMatePairFirstUnmapped() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMatePair(1, 10040, 10040, true, false, markUnmappedRecordsLikeTheirMates(), true, null, "76M", false, false, false, false, false, DEFAULT_BASE_QUALITY); // first a duplicate, | |
| // first end unmapped | |
| tester.addMappedPair(1, 10189, 10040, false, false, "41S35M", "65M11S", true, false, false, DEFAULT_BASE_QUALITY); // mapped OK | |
| tester.runTest(); | |
| } | |
| // TODO: fails on MarkDuplicatesWithMateCigar | |
| @Test | |
| public void testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| // first end mapped OK -, second end unmapped | |
| tester.addMatePair(1, 484071, 484071, false, true, false, false, "66S35M", null, true, false, false, false, false, DEFAULT_BASE_QUALITY); | |
| // mapped OK +/- | |
| tester.addMappedPair(1, 484105, 484075, false, false, "35M66S", "30S71M", false, true, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testMappedPairAndMappedFragmentAndMatePairSecondUnmapped() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMatePair(1, 10040, 10040, false, true, true, markUnmappedRecordsLikeTheirMates(), "76M", null, false, false, false, false, false, DEFAULT_BASE_QUALITY); // first a duplicate, | |
| // second end unmapped | |
| tester.addMappedPair(1, 10189, 10040, false, false, "41S35M", "65M11S", true, false, false, DEFAULT_BASE_QUALITY); // mapped OK | |
| tester.addMappedFragment(1, 10040, true, DEFAULT_BASE_QUALITY); // duplicate | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testMappedPairAndMappedFragmentAndMatePairFirstUnmapped() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMatePair(1, 10040, 10040, true, false, markUnmappedRecordsLikeTheirMates(), true, null, "76M", false, false, false, false, false, DEFAULT_BASE_QUALITY); // first a duplicate, | |
| // first end unmapped | |
| tester.addMappedPair(1, 10189, 10040, false, false, "41S35M", "65M11S", true, false, false, DEFAULT_BASE_QUALITY); // mapped OK | |
| tester.addMappedFragment(1, 10040, true, DEFAULT_BASE_QUALITY); // duplicate | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedPairsWithOppositeOrientations() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(1, 10182, 10038, true, true, "32S44M", "66M10S", true, false, false, DEFAULT_BASE_QUALITY); // -/+ | |
| tester.addMappedPair(1, 10038, 10182, false, false, "70M6S", "32S44M", false, true, false, DEFAULT_BASE_QUALITY); // +/-, both are duplicates | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedPairsWithOppositeOrientationsNumberTwo() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(1, 10038, 10182, false, false, "70M6S", "32S44M", false, true, false, DEFAULT_BASE_QUALITY); // +/-, both are duplicates | |
| tester.addMappedPair(1, 10182, 10038, true, true, "32S44M", "66M10S", true, false, false, DEFAULT_BASE_QUALITY); // -/+ | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testThreeMappedPairsWithMatchingSecondMate() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| // Read0 and Read2 are duplicates | |
| // 10181+41=10220, 10058 | |
| tester.addMappedPair(1, 10181, 10058, false, false, "41S35M", "47M29S", true, false, false, DEFAULT_BASE_QUALITY); // -/+ | |
| // 10181+37=10216, 10058 | |
| tester.addMappedPair(1, 10181, 10058, true, true, "37S39M", "44M32S", true, false, false, DEFAULT_BASE_QUALITY); // -/+ | |
| // 10180+36=10216, 10058 | |
| tester.addMappedPair(1, 10180, 10058, false, false, "36S40M", "50M26S", true, false, false, DEFAULT_BASE_QUALITY); // -/+, both are duplicates | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testMappedPairWithSamePosition() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(1, 4914, 4914, false, false, "37M39S", "73M3S", false, false, false, DEFAULT_BASE_QUALITY); // +/+ | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testMappedPairWithSamePositionSameCigar() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(1, 4914, 4914, false, false, "37M39S", "37M39S", false, false, false, DEFAULT_BASE_QUALITY); // +/+ | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedPairWithSamePosition() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(0, 5604914, 5604914, false, false, "37M39S", "73M3S", false, false, false, DEFAULT_BASE_QUALITY); // +/+ | |
| tester.addMappedPair(0, 5604914, 5604914, true, true, "37M39S", "73M3S", false, false, false, DEFAULT_BASE_QUALITY); // +/+ | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedPairWithSamePositionDifferentStrands() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(0, 5604914, 5604914, false, false, "50M", "50M", true, false, false, DEFAULT_BASE_QUALITY); // +/- | |
| tester.addMappedPair(0, 5604914, 5604914, true, true, "50M", "50M", false, true, false, DEFAULT_BASE_QUALITY); // -/+ | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoMappedPairWithSamePositionDifferentStrands2() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(0, 5604914, 5604915, false, false, "50M", "50M", true, false, false, DEFAULT_BASE_QUALITY); // +/- | |
| tester.addMappedPair(0, 5604915, 5604914, true, true, "50M", "50M", false, true, false, DEFAULT_BASE_QUALITY); // -/+ | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testMappedPairWithFirstEndSamePositionAndOther() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(0, 5604914, 5605914, false, false, "37M39S", "73M3S", false, false, false, DEFAULT_BASE_QUALITY); // +/+ | |
| tester.addMappedPair(0, 5604914, 5604914, false, false, "37M39S", "73M3S", false, false, false, DEFAULT_BASE_QUALITY); // +/+ | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoGroupsOnDifferentChromosomesOfTwoFragments() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedFragment(0, 1, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedFragment(0, 1, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedFragment(1, 1, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedFragment(1, 1, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(0, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(0, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedPair(1, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(1, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(0, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(0, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedPair(0, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedPair(1, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(1, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedPair(1, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(0, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(0, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedPair(0, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedPair(1, 1, 100, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(1, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedPair(1, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedPair(2, 1, 100, false, false , DEFAULT_BASE_QUALITY); | |
| tester.addMappedPair(2, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.addMappedPair(2, 1, 100, true, true, DEFAULT_BASE_QUALITY); // duplicate!!! | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testBulkFragmentsNoDuplicates() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| for(int position = 1; position <= 10000; position += 1) { | |
| tester.addMappedFragment(0, position, false, "100M", DEFAULT_BASE_QUALITY); | |
| } | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testBulkFragmentsWithDuplicates() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| for(int position = 1; position <= 10000; position += 1) { | |
| tester.addMappedFragment(0, position, false, "100M", DEFAULT_BASE_QUALITY); | |
| tester.addMappedFragment(0, position, true, "100M", DEFAULT_BASE_QUALITY); | |
| tester.addMappedFragment(0, position, true, "100M", DEFAULT_BASE_QUALITY); | |
| tester.addMappedFragment(0, position, true, "100M", DEFAULT_BASE_QUALITY); | |
| tester.addMappedFragment(0, position, true, "100M", DEFAULT_BASE_QUALITY); | |
| } | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testStackOverFlowPairSetSwap() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| final File input = new File("testdata/picard/sam/MarkDuplicates/markDuplicatesWithMateCigar.pairSet.swap.sam"); | |
| final SamReader reader = SamReaderFactory.makeDefault().open(input); | |
| tester.setHeader(reader.getFileHeader()); | |
| for (final SAMRecord record : reader) { | |
| tester.addRecord(record); | |
| } | |
| CloserUtil.close(reader); | |
| tester.setExpectedOpticalDuplicate(1); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testSecondEndIsBeforeFirstInCoordinate() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.addMappedPair(0, 108855339, 108855323, false, false, "33S35M", "17S51M", true, true, false, DEFAULT_BASE_QUALITY); // +/- | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testPathologicalOrderingAtTheSamePosition() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.setExpectedOpticalDuplicate(1); | |
| tester.addMatePair("RUNID:3:1:15013:113051", 0, 129384554, 129384554, false, false, false, false, "68M", "68M", false, false, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMatePair("RUNID:3:1:15029:113060", 0, 129384554, 129384554, false, false, true, true, "68M", "68M", false, false, false, false, false, DEFAULT_BASE_QUALITY); | |
| // Create the pathology | |
| final CloseableIterator<SAMRecord> iterator = tester.getRecordIterator(); | |
| final int[] qualityOffset = {20, 30, 10, 40}; // creates an interesting pathological ordering | |
| int index = 0; | |
| while (iterator.hasNext()) { | |
| final SAMRecord record = iterator.next(); | |
| final byte[] quals = new byte[record.getReadLength()]; | |
| for (int i = 0; i < record.getReadLength(); i++) { | |
| quals[i] = (byte)(qualityOffset[index] + 10); | |
| } | |
| record.setBaseQualities(quals); | |
| index++; | |
| } | |
| iterator.close(); | |
| // Run the test | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testDifferentChromosomesInOppositeOrder() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.setExpectedOpticalDuplicate(1); | |
| tester.addMatePair("RUNID:6:101:17642:6835", 0, 1, 123989, 18281, false, false, true, true, "37S64M", "52M49S", false, false, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMatePair("RUNID:6:101:17616:6888", 1, 0, 18281, 123989, false, false, false, false, "52M49S", "37S64M", false, false, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test | |
| public void testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate() { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.setExpectedOpticalDuplicate(1); | |
| tester.addMatePair("RUNID:1:1:15993:13361", 2, 41212324, 41212310, false, false, false, false, "33S35M", "19S49M", true, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMatePair("RUNID:1:1:16020:13352", 2, 41212324, 41212319, false, false, true, true, "33S35M", "28S40M", true, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @DataProvider(name = "secondarySupplementaryData") | |
| public Object[][] secondarySupplementaryData() { | |
| return new Object[][] { | |
| { true, true , true}, | |
| { true, false, true}, | |
| { false, true , true}, | |
| { true, true , false}, | |
| { true, false, false}, | |
| { false, true , false} | |
| }; | |
| } | |
| @Test(dataProvider = "secondarySupplementaryData") | |
| public void testTwoMappedPairsWithSupplementaryReads(final Boolean additionalFragSecondary, final Boolean additionalFragSupplementary, final Boolean fragLikeFirst) { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.setExpectedOpticalDuplicate(1); | |
| tester.addMatePair("RUNID:1:1:15993:13361", 2, 41212324, 41212310, false, false, false, false, "33S35M", "19S49M", true, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMatePair("RUNID:1:1:16020:13352", 2, 41212324, 41212319, false, false, true, true, "33S35M", "28S40M", true, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedFragment(fragLikeFirst ? "RUNID:1:1:15993:13361" : "RUNID:1:1:16020:13352", 1, 400, markSecondaryAndSupplementaryRecordsLikeTheCanonical() && !fragLikeFirst, null, null, additionalFragSecondary, additionalFragSupplementary, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| @Test(dataProvider = "secondarySupplementaryData") | |
| public void testTwoMappedPairsWithSupplementaryReadsAfterCanonical(final Boolean additionalFragSecondary, final Boolean additionalFragSupplementary, final Boolean fragLikeFirst) { | |
| final AbstractMarkDuplicatesCommandLineProgramTester tester = getTester(); | |
| tester.setExpectedOpticalDuplicate(1); | |
| tester.addMatePair("RUNID:1:1:15993:13361", 2, 41212324, 41212310, false, false, false, false, "33S35M", "19S49M", true, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMatePair("RUNID:1:1:16020:13352", 2, 41212324, 41212319, false, false, true, true, "33S35M", "28S40M", true, true, false, false, false, DEFAULT_BASE_QUALITY); | |
| tester.addMappedFragment(fragLikeFirst ? "RUNID:1:1:15993:13361" : "RUNID:1:1:16020:13352", 1, 400, markSecondaryAndSupplementaryRecordsLikeTheCanonical() && !fragLikeFirst, null, null, additionalFragSecondary, additionalFragSupplementary, DEFAULT_BASE_QUALITY); | |
| tester.runTest(); | |
| } | |
| } |