Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
This commit is contained in:
Ryan Poplin
commit
1ea4e48a27
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@ -66,18 +66,18 @@ public class CycleCovariate implements StandardCovariate {
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// Discrete cycle platforms
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if (DISCRETE_CYCLE_PLATFORMS.contains(ngsPlatform)) {
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final short init;
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final short readOrderFactor = read.getReadPairedFlag() && read.getSecondOfPairFlag() ? (short) -1 : 1;
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final short increment;
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if (!read.getReadNegativeStrandFlag()) {
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init = 1;
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increment = 1;
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short cycle;
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if (read.getReadNegativeStrandFlag()) {
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cycle = (short) (read.getReadLength() * readOrderFactor);
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increment = (short) (-1 * readOrderFactor);
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}
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else {
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init = (short) read.getReadLength();
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increment = -1;
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cycle = readOrderFactor;
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increment = readOrderFactor;
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}
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short cycle = init;
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for (int i = 0; i < read.getReadLength(); i++) {
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cycles[i] = BitSetUtils.bitSetFrom(cycle);
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cycle += increment;
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@ -102,7 +102,7 @@ public class RecalDatum extends Datum {
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@Override
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public String toString() {
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return String.format("%d,%d,%d", numObservations, numMismatches, (byte) Math.floor(getEmpiricalQuality()));
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return String.format("%d,%d,%d,%d", numObservations, numMismatches, (byte) Math.floor(getEmpiricalQuality()), (byte) Math.floor(getEstimatedQReported()));
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}
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@ -143,9 +143,18 @@ public class RecalibrationArgumentCollection {
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@Argument(fullName = "deletions_default_quality", shortName = "ddq", doc = "default quality for the base deletions covariate", required = false)
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public byte DELETIONS_DEFAULT_QUALITY = 45;
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/**
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* Reads with low quality bases on either tail (beginning or end) will not be considered in the context. This parameter defines the quality below which (inclusive) a tail is considered low quality
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*/
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@Argument(fullName = "low_quality_tail", shortName = "lqt", doc = "minimum quality for the bases in the tail of the reads to be considered", required = false)
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public byte LOW_QUAL_TAIL = 2;
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/**
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* BQSR generates a quantization table for quick quantization later by subsequent tools. BQSR does not quantize the base qualities, this is done by the engine with the -qq or -BQSR options.
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* This parameter tells BQSR the number of levels of quantization to use to build the quantization table.
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*/
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@Argument(fullName = "quantizing_levels", shortName = "ql", required = false, doc = "number of distinct quality scores in the quantized output")
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public int QUANTIZING_LEVELS = 16;
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@Hidden
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@ -155,8 +164,11 @@ public class RecalibrationArgumentCollection {
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@Argument(fullName = "force_platform", shortName = "fP", required = false, doc = "If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.")
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public String FORCE_PLATFORM = null;
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@Hidden
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@Argument(fullName = "quantizing_levels", shortName = "ql", required = false, doc = "number of distinct quality scores in the quantized output")
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public int QUANTIZING_LEVELS = 16;
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@Argument(fullName = "keep_intermediate_files", shortName = "k", required = false, doc ="does not remove the temporary csv file created to generate the plots")
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public boolean KEEP_INTERMEDIATE_FILES = false;
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@Hidden
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@Argument(fullName = "no_plots", shortName = "np", required = false, doc = "does not generate any plots -- useful for queue scatter/gathering")
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public boolean NO_PLOTS = false;
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public GATKReportTable generateReportTable() {
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GATKReportTable argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run");
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@ -176,6 +188,8 @@ public class RecalibrationArgumentCollection {
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argumentsTable.set("default_platform", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, DEFAULT_PLATFORM);
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argumentsTable.set("force_platform", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, FORCE_PLATFORM);
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argumentsTable.set("quantizing_levels", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, QUANTIZING_LEVELS);
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argumentsTable.set("keep_intermediate_files", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, KEEP_INTERMEDIATE_FILES);
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argumentsTable.set("no_plots", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, NO_PLOTS);
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return argumentsTable;
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}
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@ -279,6 +279,12 @@ public class RecalibrationReport {
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else if (primaryKey.equals("quantizing_levels"))
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RAC.QUANTIZING_LEVELS = Integer.parseInt((String) value);
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else if (primaryKey.equals("keep_intermediate_files"))
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RAC.KEEP_INTERMEDIATE_FILES = Boolean.parseBoolean((String) value);
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else if (primaryKey.equals("no_plots"))
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RAC.NO_PLOTS = Boolean.parseBoolean((String) value);
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}
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return RAC;
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@ -109,4 +109,10 @@ public class RecalDatum extends RecalDatumOptimized {
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private double qualToErrorProb( final double qual ) {
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return Math.pow(10.0, qual / -10.0);
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}
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@Override
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public String toString() {
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return String.format("%d,%d,%d,%d", numObservations, numMismatches, (byte) Math.floor(getEmpiricalQuality()), (byte) Math.floor(getEstimatedQReported()));
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}
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}
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@ -65,6 +65,19 @@ public class BaseRecalibration {
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quantizationInfo.quantizeQualityScores(quantizationLevels);
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}
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/**
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* This constructor only exists for testing purposes.
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*
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* @param quantizationInfo
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* @param keysAndTablesMap
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* @param requestedCovariates
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*/
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protected BaseRecalibration(QuantizationInfo quantizationInfo, LinkedHashMap<BQSRKeyManager, Map<BitSet, RecalDatum>> keysAndTablesMap, ArrayList<Covariate> requestedCovariates) {
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this.quantizationInfo = quantizationInfo;
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this.keysAndTablesMap = keysAndTablesMap;
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this.requestedCovariates = requestedCovariates;
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}
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/**
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* Recalibrates the base qualities of a read
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*
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@ -110,7 +123,7 @@ public class BaseRecalibration {
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* @param errorModel the event type
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* @return A recalibrated quality score as a byte
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*/
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private byte performSequentialQualityCalculation(BitSet[] key, EventType errorModel) {
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protected byte performSequentialQualityCalculation(BitSet[] key, EventType errorModel) {
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final String UNRECOGNIZED_REPORT_TABLE_EXCEPTION = "Unrecognized table. Did you add an extra required covariate? This is a hard check that needs propagate through the code";
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final String TOO_MANY_KEYS_EXCEPTION = "There should only be one key for the RG collapsed table, something went wrong here";
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@ -26,8 +26,9 @@ public class CycleCovariateUnitTest {
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@Test(enabled = true)
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public void testSimpleCycles() {
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short readLength = 10;
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short readLength = 10;
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GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
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read.setReadPairedFlag(true);
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read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID"));
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read.getReadGroup().setPlatform("illumina");
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@ -38,6 +39,13 @@ public class CycleCovariateUnitTest {
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values = covariate.getValues(read);
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verifyCovariateArray(values.getMismatches(), readLength, (short) -1);
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read.setSecondOfPairFlag(true);
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values = covariate.getValues(read);
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verifyCovariateArray(values.getMismatches(), (short) -readLength, (short) 1);
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read.setReadNegativeStrandFlag(false);
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values = covariate.getValues(read);
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verifyCovariateArray(values.getMismatches(), (short) -1, (short) -1);
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}
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private void verifyCovariateArray(BitSet[] values, short init, short increment) {
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@ -1,13 +1,17 @@
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package org.broadinstitute.sting.utils.recalibration;
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import net.sf.samtools.SAMReadGroupRecord;
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import org.broadinstitute.sting.utils.NGSPlatform;
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import org.broadinstitute.sting.gatk.walkers.bqsr.*;
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import org.broadinstitute.sting.utils.QualityUtils;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.collections.NestedHashMap;
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import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import org.broadinstitute.sting.utils.sam.ReadUtils;
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import org.testng.Assert;
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import org.testng.annotations.BeforeClass;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.util.*;
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/**
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* Unit tests for on-the-fly recalibration.
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@ -17,13 +21,274 @@ import java.io.File;
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*/
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public class BaseRecalibrationUnitTest {
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@Test(enabled=false)
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public void testReadingReport() {
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File csv = new File("public/testdata/exampleGATKREPORT.grp");
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BaseRecalibration baseRecalibration = new BaseRecalibration(csv, -1);
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GATKSAMRecord read = ReadUtils.createRandomRead(1000);
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read.setReadGroup(new GATKSAMReadGroupRecord(new SAMReadGroupRecord("exampleBAM.bam.bam"), NGSPlatform.ILLUMINA));
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baseRecalibration.recalibrateRead(read);
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System.out.println("Success");
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private org.broadinstitute.sting.gatk.walkers.recalibration.RecalDataManager dataManager;
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private LinkedHashMap<BQSRKeyManager, Map<BitSet, RecalDatum>> keysAndTablesMap;
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private BQSRKeyManager rgKeyManager;
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private BQSRKeyManager qsKeyManager;
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private BQSRKeyManager cvKeyManager;
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private ReadGroupCovariate rgCovariate;
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private QualityScoreCovariate qsCovariate;
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private ContextCovariate cxCovariate;
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private CycleCovariate cyCovariate;
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private GATKSAMRecord read = ReadUtils.createRandomRead(10000);
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private BaseRecalibration baseRecalibration;
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private ReadCovariates readCovariates;
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@BeforeClass
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public void init() {
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GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("rg");
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rg.setPlatform("illumina");
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read.setReadGroup(rg);
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byte[] quals = new byte[read.getReadLength()];
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for (int i = 0; i < read.getReadLength(); i++)
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quals[i] = 20;
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read.setBaseQualities(quals);
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RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
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List<Covariate> requiredCovariates = new ArrayList<Covariate>();
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List<Covariate> optionalCovariates = new ArrayList<Covariate>();
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ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>();
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dataManager = new org.broadinstitute.sting.gatk.walkers.recalibration.RecalDataManager(true, 4);
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keysAndTablesMap = new LinkedHashMap<BQSRKeyManager, Map<BitSet, RecalDatum>>();
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rgCovariate = new ReadGroupCovariate();
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rgCovariate.initialize(RAC);
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requiredCovariates.add(rgCovariate);
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rgKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
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keysAndTablesMap.put(rgKeyManager, new HashMap<BitSet, RecalDatum>());
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qsCovariate = new QualityScoreCovariate();
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qsCovariate.initialize(RAC);
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requiredCovariates.add(qsCovariate);
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qsKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
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keysAndTablesMap.put(qsKeyManager, new HashMap<BitSet, RecalDatum>());
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cxCovariate = new ContextCovariate();
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cxCovariate.initialize(RAC);
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optionalCovariates.add(cxCovariate);
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cyCovariate = new CycleCovariate();
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cyCovariate.initialize(RAC);
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optionalCovariates.add(cyCovariate);
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cvKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
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keysAndTablesMap.put(cvKeyManager, new HashMap<BitSet, RecalDatum>());
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for (Covariate cov : requiredCovariates)
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requestedCovariates.add(cov);
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for (Covariate cov : optionalCovariates)
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requestedCovariates.add(cov);
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readCovariates = RecalDataManager.computeCovariates(read, requestedCovariates);
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for (int i=0; i<read.getReadLength(); i++) {
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BitSet[] bitKeys = readCovariates.getMismatchesKeySet(i);
|
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|
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Object[] objKey = buildObjectKey(bitKeys);
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Random random = new Random();
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int nObservations = random.nextInt(10000);
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int nErrors = random.nextInt(10);
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double estimatedQReported = 30;
|
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double empiricalQuality = calcEmpiricalQual(nObservations, nErrors);
|
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org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum oldDatum = new org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum(nObservations, nErrors, estimatedQReported, empiricalQuality);
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dataManager.addToAllTables(objKey, oldDatum, QualityUtils.MIN_USABLE_Q_SCORE);
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RecalDatum newDatum = new RecalDatum(nObservations, nErrors, estimatedQReported, empiricalQuality);
|
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for (Map.Entry<BQSRKeyManager, Map<BitSet, RecalDatum>> mapEntry : keysAndTablesMap.entrySet()) {
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List<BitSet> keys = mapEntry.getKey().bitSetsFromAllKeys(bitKeys, EventType.BASE_SUBSTITUTION);
|
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for (BitSet key : keys)
|
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updateCovariateWithKeySet(mapEntry.getValue(), key, newDatum);
|
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}
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}
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dataManager.generateEmpiricalQualities(1, QualityUtils.MAX_QUAL_SCORE);
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|
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List<Byte> quantizedQuals = new ArrayList<Byte>();
|
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List<Long> qualCounts = new ArrayList<Long>();
|
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for (byte i = 0; i <= QualityUtils.MAX_QUAL_SCORE; i++) {
|
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quantizedQuals.add(i);
|
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qualCounts.add(1L);
|
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}
|
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QuantizationInfo quantizationInfo = new QuantizationInfo(quantizedQuals, qualCounts);
|
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quantizationInfo.noQuantization();
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baseRecalibration = new BaseRecalibration(quantizationInfo, keysAndTablesMap, requestedCovariates);
|
||||
|
||||
}
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||||
|
||||
|
||||
@Test(enabled=true)
|
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public void testGoldStandardComparison() {
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debugTables();
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for (int i = 0; i < read.getReadLength(); i++) {
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BitSet [] bitKey = readCovariates.getKeySet(i, EventType.BASE_SUBSTITUTION);
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Object [] objKey = buildObjectKey(bitKey);
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byte v2 = baseRecalibration.performSequentialQualityCalculation(bitKey, EventType.BASE_SUBSTITUTION);
|
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byte v1 = goldStandardSequentialCalculation(objKey);
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Assert.assertEquals(v2, v1);
|
||||
}
|
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}
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private Object[] buildObjectKey(BitSet[] bitKey) {
|
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Object[] key = new Object[bitKey.length];
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key[0] = rgCovariate.keyFromBitSet(bitKey[0]);
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key[1] = qsCovariate.keyFromBitSet(bitKey[1]);
|
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key[2] = cxCovariate.keyFromBitSet(bitKey[2]);
|
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key[3] = cyCovariate.keyFromBitSet(bitKey[3]);
|
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return key;
|
||||
}
|
||||
|
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private void debugTables() {
|
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System.out.println("\nV1 Table\n");
|
||||
System.out.println("ReadGroup Table:");
|
||||
NestedHashMap nestedTable = dataManager.getCollapsedTable(0);
|
||||
printNestedHashMap(nestedTable.data, "");
|
||||
System.out.println("\nQualityScore Table:");
|
||||
nestedTable = dataManager.getCollapsedTable(1);
|
||||
printNestedHashMap(nestedTable.data, "");
|
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System.out.println("\nCovariates Table:");
|
||||
nestedTable = dataManager.getCollapsedTable(2);
|
||||
printNestedHashMap(nestedTable.data, "");
|
||||
nestedTable = dataManager.getCollapsedTable(3);
|
||||
printNestedHashMap(nestedTable.data, "");
|
||||
|
||||
|
||||
int i = 0;
|
||||
System.out.println("\nV2 Table\n");
|
||||
for (Map.Entry<BQSRKeyManager, Map<BitSet, RecalDatum>> mapEntry : keysAndTablesMap.entrySet()) {
|
||||
BQSRKeyManager keyManager = mapEntry.getKey();
|
||||
Map<BitSet, RecalDatum> table = mapEntry.getValue();
|
||||
switch(i++) {
|
||||
case 0 :
|
||||
System.out.println("ReadGroup Table:");
|
||||
break;
|
||||
case 1 :
|
||||
System.out.println("QualityScore Table:");
|
||||
break;
|
||||
case 2 :
|
||||
System.out.println("Covariates Table:");
|
||||
break;
|
||||
}
|
||||
for (Map.Entry<BitSet, RecalDatum> entry : table.entrySet()) {
|
||||
BitSet key = entry.getKey();
|
||||
RecalDatum datum = entry.getValue();
|
||||
List<Object> keySet = keyManager.keySetFrom(key);
|
||||
System.out.println(String.format("%s => %s", Utils.join(",", keySet), datum));
|
||||
}
|
||||
System.out.println();
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
private static void printNestedHashMap(Map<Object,Object> table, String output) {
|
||||
for (Object key : table.keySet()) {
|
||||
String ret = "";
|
||||
if (output.isEmpty())
|
||||
ret = "" + key;
|
||||
else
|
||||
ret = output + "," + key;
|
||||
|
||||
Object next = table.get(key);
|
||||
if (next instanceof org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum)
|
||||
System.out.println(ret + " => " + next);
|
||||
else
|
||||
printNestedHashMap((Map<Object, Object>) next, "" + ret);
|
||||
}
|
||||
}
|
||||
|
||||
private void updateCovariateWithKeySet(final Map<BitSet, RecalDatum> recalTable, final BitSet hashKey, final RecalDatum datum) {
|
||||
RecalDatum previousDatum = recalTable.get(hashKey); // using the list of covariate values as a key, pick out the RecalDatum from the data HashMap
|
||||
if (previousDatum == null) // key doesn't exist yet in the map so make a new bucket and add it
|
||||
recalTable.put(hashKey, datum.copy());
|
||||
else
|
||||
previousDatum.combine(datum); // add one to the number of observations and potentially one to the number of mismatches
|
||||
}
|
||||
|
||||
/**
|
||||
* Implements a serial recalibration of the reads using the combinational table.
|
||||
* First, we perform a positional recalibration, and then a subsequent dinuc correction.
|
||||
*
|
||||
* Given the full recalibration table, we perform the following preprocessing steps:
|
||||
*
|
||||
* - calculate the global quality score shift across all data [DeltaQ]
|
||||
* - calculate for each of cycle and dinuc the shift of the quality scores relative to the global shift
|
||||
* -- i.e., DeltaQ(dinuc) = Sum(pos) Sum(Qual) Qempirical(pos, qual, dinuc) - Qreported(pos, qual, dinuc) / Npos * Nqual
|
||||
* - The final shift equation is:
|
||||
*
|
||||
* Qrecal = Qreported + DeltaQ + DeltaQ(pos) + DeltaQ(dinuc) + DeltaQ( ... any other covariate ... )
|
||||
*
|
||||
* @param key The list of Comparables that were calculated from the covariates
|
||||
* @return A recalibrated quality score as a byte
|
||||
*/
|
||||
private byte goldStandardSequentialCalculation(final Object... key) {
|
||||
|
||||
final byte qualFromRead = (byte) Integer.parseInt(key[1].toString());
|
||||
final Object[] readGroupCollapsedKey = new Object[1];
|
||||
final Object[] qualityScoreCollapsedKey = new Object[2];
|
||||
final Object[] covariateCollapsedKey = new Object[3];
|
||||
|
||||
// The global quality shift (over the read group only)
|
||||
readGroupCollapsedKey[0] = key[0];
|
||||
final org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum globalRecalDatum = ((org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum) dataManager.getCollapsedTable(0).get(readGroupCollapsedKey));
|
||||
double globalDeltaQ = 0.0;
|
||||
if (globalRecalDatum != null) {
|
||||
final double globalDeltaQEmpirical = globalRecalDatum.getEmpiricalQuality();
|
||||
final double aggregrateQReported = globalRecalDatum.getEstimatedQReported();
|
||||
globalDeltaQ = globalDeltaQEmpirical - aggregrateQReported;
|
||||
}
|
||||
|
||||
// The shift in quality between reported and empirical
|
||||
qualityScoreCollapsedKey[0] = key[0];
|
||||
qualityScoreCollapsedKey[1] = key[1];
|
||||
final org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum qReportedRecalDatum = ((org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum) dataManager.getCollapsedTable(1).get(qualityScoreCollapsedKey));
|
||||
double deltaQReported = 0.0;
|
||||
if (qReportedRecalDatum != null) {
|
||||
final double deltaQReportedEmpirical = qReportedRecalDatum.getEmpiricalQuality();
|
||||
deltaQReported = deltaQReportedEmpirical - qualFromRead - globalDeltaQ;
|
||||
}
|
||||
|
||||
// The shift in quality due to each covariate by itself in turn
|
||||
double deltaQCovariates = 0.0;
|
||||
double deltaQCovariateEmpirical;
|
||||
covariateCollapsedKey[0] = key[0];
|
||||
covariateCollapsedKey[1] = key[1];
|
||||
for (int iii = 2; iii < key.length; iii++) {
|
||||
covariateCollapsedKey[2] = key[iii]; // The given covariate
|
||||
final org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum covariateRecalDatum = ((org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum) dataManager.getCollapsedTable(iii).get(covariateCollapsedKey));
|
||||
if (covariateRecalDatum != null) {
|
||||
deltaQCovariateEmpirical = covariateRecalDatum.getEmpiricalQuality();
|
||||
deltaQCovariates += (deltaQCovariateEmpirical - qualFromRead - (globalDeltaQ + deltaQReported));
|
||||
}
|
||||
}
|
||||
|
||||
final double newQuality = qualFromRead + globalDeltaQ + deltaQReported + deltaQCovariates;
|
||||
return QualityUtils.boundQual((int) Math.round(newQuality), QualityUtils.MAX_QUAL_SCORE);
|
||||
|
||||
// Verbose printouts used to validate with old recalibrator
|
||||
//if(key.contains(null)) {
|
||||
// System.out.println( key + String.format(" => %d + %.2f + %.2f + %.2f + %.2f = %d",
|
||||
// qualFromRead, globalDeltaQ, deltaQReported, deltaQPos, deltaQDinuc, newQualityByte));
|
||||
//}
|
||||
//else {
|
||||
// System.out.println( String.format("%s %s %s %s => %d + %.2f + %.2f + %.2f + %.2f = %d",
|
||||
// key.get(0).toString(), key.get(3).toString(), key.get(2).toString(), key.get(1).toString(), qualFromRead, globalDeltaQ, deltaQReported, deltaQPos, deltaQDinuc, newQualityByte) );
|
||||
//}
|
||||
|
||||
//return newQualityByte;
|
||||
}
|
||||
|
||||
public static double calcEmpiricalQual(final int observations, final int errors) {
|
||||
final int smoothing = 1;
|
||||
final double doubleMismatches = (double) (errors + smoothing);
|
||||
final double doubleObservations = (double) ( observations + smoothing );
|
||||
double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations);
|
||||
return Math.min(QualityUtils.MAX_QUAL_SCORE, empiricalQual);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue