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Add the ability to emit the original quals in the OQ tag

This commit is contained in:
Eric Banks 2012-07-17 15:52:56 -04:00
parent 4e3780fd4f
commit 8dbc9cb29c
4 changed files with 25 additions and 5 deletions
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3
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
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@ -107,7 +107,8 @@ public class BQSRIntegrationTest extends WalkerTest {
{new PRTest("", "d2d6ed8667cdba7e56f5db97d6262676")},
{new PRTest(" -qq -1", "b7053d3d67aba6d8892f0a60f0ded338")},
{new PRTest(" -qq 6", "bfbf0855185b2b70aa35237fb71e4487")},
{new PRTest(" -DIQ", "66aa65223f192ee39c1773aa187fd493")}
{new PRTest(" -DIQ", "66aa65223f192ee39c1773aa187fd493")},
{new PRTest(" -EOQ", "")}
};
}

6
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -198,8 +198,8 @@ public class GenomeAnalysisEngine {
private BaseRecalibration baseRecalibration = null;
public BaseRecalibration getBaseRecalibration() { return baseRecalibration; }
public boolean hasBaseRecalibration() { return baseRecalibration != null; }
public void setBaseRecalibration(final File recalFile, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan) {
baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels, disableIndelQuals, preserveQLessThan);
public void setBaseRecalibration(final File recalFile, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan, final boolean emitOriginalQuals) {
baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels, disableIndelQuals, preserveQLessThan, emitOriginalQuals);
}
/**
@ -239,7 +239,7 @@ public class GenomeAnalysisEngine {
// if the use specified an input BQSR recalibration table then enable on the fly recalibration
if (args.BQSR_RECAL_FILE != null)
setBaseRecalibration(args.BQSR_RECAL_FILE, args.quantizationLevels, args.disableIndelQuals, args.PRESERVE_QSCORES_LESS_THAN);
setBaseRecalibration(args.BQSR_RECAL_FILE, args.quantizationLevels, args.disableIndelQuals, args.PRESERVE_QSCORES_LESS_THAN, args.emitOriginalQuals);
// Determine how the threads should be divided between CPU vs. IO.
determineThreadAllocation();

6
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -220,6 +220,12 @@ public class GATKArgumentCollection {
@Argument(fullName="disable_indel_quals", shortName = "DIQ", doc = "If true, disables printing of base insertion and base deletion tags (with -BQSR)", required=false)
public boolean disableIndelQuals = false;
/**
* By default, the OQ tag in not emitted when using the -BQSR argument.
*/
@Argument(fullName="emit_original_quals", shortName = "EOQ", doc = "If true, enables printing of the OQ tag with the original base qualities (with -BQSR)", required=false)
public boolean emitOriginalQuals = false;
/**
* Do not modify quality scores less than this value but rather just write them out unmodified in the recalibrated BAM file.
* In general it's unsafe to change qualities scores below < 6, since base callers use these values to indicate random or bad bases.

15
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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@ -25,11 +25,14 @@
package org.broadinstitute.sting.utils.recalibration;
import net.sf.samtools.SAMTag;
import net.sf.samtools.SAMUtils;
import org.broadinstitute.sting.gatk.walkers.bqsr.*;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.collections.NestedIntegerArray;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.File;
@ -51,6 +54,7 @@ public class BaseRecalibration {
private final boolean disableIndelQuals;
private final int preserveQLessThan;
private final boolean emitOriginalQuals;
private static final NestedHashMap[] qualityScoreByFullCovariateKey = new NestedHashMap[EventType.values().length]; // Caches the result of performSequentialQualityCalculation(..) for all sets of covariate values.
static {
@ -66,7 +70,7 @@ public class BaseRecalibration {
* @param disableIndelQuals if true, do not emit base indel qualities
* @param preserveQLessThan preserve quality scores less than this value
*/
public BaseRecalibration(final File RECAL_FILE, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan) {
public BaseRecalibration(final File RECAL_FILE, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan, final boolean emitOriginalQuals) {
RecalibrationReport recalibrationReport = new RecalibrationReport(RECAL_FILE);
recalibrationTables = recalibrationReport.getRecalibrationTables();
@ -80,6 +84,7 @@ public class BaseRecalibration {
readCovariates = new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length);
this.disableIndelQuals = disableIndelQuals;
this.preserveQLessThan = preserveQLessThan;
this.emitOriginalQuals = emitOriginalQuals;
}
/**
@ -90,6 +95,14 @@ public class BaseRecalibration {
* @param read the read to recalibrate
*/
public void recalibrateRead(final GATKSAMRecord read) {
if (emitOriginalQuals && read.getAttribute(SAMTag.OQ.name()) == null) { // Save the old qualities if the tag isn't already taken in the read
try {
read.setAttribute(SAMTag.OQ.name(), SAMUtils.phredToFastq(read.getBaseQualities()));
} catch (IllegalArgumentException e) {
throw new UserException.MalformedBAM(read, "illegal base quality encountered; " + e.getMessage());
}
}
RecalDataManager.computeCovariates(read, requestedCovariates, readCovariates); // compute all covariates for the read
for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings
if (disableIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) {