Fixes to BQSR for the --maximum_cycle_value argument.
- It's now written into the recal report so that it can be used in the PrintReads step. - Note that we also now write the --deletions_default_quality value which accidentally wasn't being written before! - Added tests to make sure that the value of the --maximum_cycle_value is being used properly by PR with -BQSR. (This is my last non-branch commit; all future pushes will follow new GATK practices)
This commit is contained in:
Eric Banks
parent
cb2dd470b6
commit
e7c35a907f
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@ -262,8 +262,12 @@ public class RecalibrationArgumentCollection {
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argumentsTable.set("indels_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INDELS_CONTEXT_SIZE);
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argumentsTable.addRowID("mismatches_default_quality", true);
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argumentsTable.set("mismatches_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_DEFAULT_QUALITY);
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argumentsTable.addRowID("deletions_default_quality", true);
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argumentsTable.set("deletions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DELETIONS_DEFAULT_QUALITY);
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argumentsTable.addRowID("insertions_default_quality", true);
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argumentsTable.set("insertions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INSERTIONS_DEFAULT_QUALITY);
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argumentsTable.addRowID("maximum_cycle_value", true);
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argumentsTable.set("maximum_cycle_value", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MAXIMUM_CYCLE_VALUE);
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argumentsTable.addRowID("low_quality_tail", true);
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argumentsTable.set("low_quality_tail", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, LOW_QUAL_TAIL);
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argumentsTable.addRowID("default_platform", true);
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@ -322,6 +322,9 @@ public class RecalibrationReport {
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else if (argument.equals("deletions_default_quality"))
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RAC.DELETIONS_DEFAULT_QUALITY = Byte.parseByte((String) value);
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else if (argument.equals("maximum_cycle_value"))
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RAC.MAXIMUM_CYCLE_VALUE = Integer.parseInt((String) value);
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else if (argument.equals("low_quality_tail"))
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RAC.LOW_QUAL_TAIL = Byte.parseByte((String) value);
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@ -136,9 +136,6 @@ public class CycleCovariate implements StandardCovariate {
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final int MAX_CYCLE_FOR_INDELS = readLength - CUSHION_FOR_INDELS - 1;
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for (int i = 0; i < readLength; i++) {
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if ( cycle > MAXIMUM_CYCLE_VALUE )
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throw new UserException("The maximum allowed value for the cycle is " + MAXIMUM_CYCLE_VALUE + ", but a larger cycle was detected in read " + read.getReadName() + ". Please use the --maximum_cycle_value argument to increase this value (at the expense of requiring more memory to run)");
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final int substitutionKey = keyFromCycle(cycle);
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final int indelKey = (i < CUSHION_FOR_INDELS || i > MAX_CYCLE_FOR_INDELS) ? -1 : substitutionKey;
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values.addCovariate(substitutionKey, indelKey, indelKey, i);
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@ -268,9 +265,12 @@ public class CycleCovariate implements StandardCovariate {
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return (MAXIMUM_CYCLE_VALUE << 1) + 1;
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}
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private static int keyFromCycle(final int cycle) {
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private int keyFromCycle(final int cycle) {
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// no negative values because values must fit into the first few bits of the long
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int result = Math.abs(cycle);
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if ( result > MAXIMUM_CYCLE_VALUE )
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throw new UserException("The maximum allowed value for the cycle is " + MAXIMUM_CYCLE_VALUE + ", but a larger cycle (" + result + ") was detected. Please use the --maximum_cycle_value argument to increase this value (at the expense of requiring more memory to run)");
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result = result << 1; // shift so we can add the "sign" bit
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if ( cycle < 0 )
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result++; // negative cycles get the lower-most bit set
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@ -94,26 +94,27 @@ public class BQSRIntegrationTest extends WalkerTest {
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}
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}
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private static final String HiSeqBam = privateTestDir + "HiSeq.1mb.1RG.bam";
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private static final String HiSeqInterval = "chr1:10,000,000-10,100,000";
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@DataProvider(name = "BQSRTest")
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public Object[][] createBQSRTestData() {
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String HiSeqBam = privateTestDir + "HiSeq.1mb.1RG.bam";
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String HiSeqInterval = "chr1:10,000,000-10,100,000";
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return new Object[][]{
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "6b3f252718f59cf9fd3f7612f73a35bf")},
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "863576ac9ff0b0e02f2e84aef15923a7")},
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "03e28f48201a35c70d1cf48e9f45364f")},
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "6e3c5635d387a1c428a7c9c88ad26488")},
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "6507adcb94bacde4cdee9caa9f14f24b")},
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "399bbb4bf80764dfc644b2f95d824615")},
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "34d70899253c2b3343ca9ae944291c30")},
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{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "e61fa47bfc08433f0cd55558e2081548")},
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{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "5c2622c63225b8b04990baf0ae4de07c")},
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{new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "ee7191d83d7d5bb957dc4595883c32f1")},
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{new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "da92f4730356f479c2c2b71497cfac6d")},
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{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "8075595113b48c0c7ead08ce41bef9fe")},
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{new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "be05834841c5690c66910270521d5c32")},
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{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "e61fa47bfc08433f0cd55558e2081548")},
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{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "8ee0b498dbbc95ce76393a0f089fec92")},
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "61fd466b5e94d2d67e116f6f67c9f939")},
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "e08b5bcdb64f4beea03730e5631a14ca")},
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "448a45dc154c95d1387cb5cdddb67071")},
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "c1e7999e445d51bbe2e775dac5325643")},
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "a57c16918cdfe12d55a89c21bf195279")},
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "836dccacf48ccda6b2843d07e8f1ef4d")},
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{new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "0fb2aedc2f8d66b5821cb570f15a8c4d")},
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{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "c9953f020a65c1603a6d71aeeb1b95f3")},
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{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "85a120b7d86b61597b86b9e93decbdfc")},
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{new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "5248dc49aec0323c74b496bb4928c73c")},
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{new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "cb52f267e0010f849f50b0bf1de474a1")},
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{new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "1425a5063ee757dbfc013df24e65a67a")},
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{new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "c1c3cda8caceed619d3d439c3990cd26")},
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{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "c9953f020a65c1603a6d71aeeb1b95f3")},
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{new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "5bfff0c699345cca12a9b33acf95588f")},
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};
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}
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@ -212,4 +213,33 @@ public class BQSRIntegrationTest extends WalkerTest {
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Arrays.asList(params.md5));
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executeTest("testPrintReads-"+params.args, spec).getFirst();
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}
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@Test
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public void testPRNoFailWithHighMaxCycle() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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" -T PrintReads" +
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" -R " + hg18Reference +
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" -I " + HiSeqBam +
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" -L " + HiSeqInterval +
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" -BQSR " + privateTestDir + "HiSeq.1mb.1RG.highMaxCycle.table" +
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" -o /dev/null",
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0,
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Arrays.<String>asList());
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executeTest("testPRNoFailWithHighMaxCycle", spec);
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}
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@Test
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public void testPRFailWithLowMaxCycle() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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" -T PrintReads" +
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" -R " + hg18Reference +
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" -I " + HiSeqBam +
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" -L " + HiSeqInterval +
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" -BQSR " + privateTestDir + "HiSeq.1mb.1RG.lowMaxCycle.table" +
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" -o /dev/null",
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0,
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UserException.class);
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executeTest("testPRFailWithLowMaxCycle", spec);
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}
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}
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