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Added a --no_indel_quals argument that when used with -BQSR inhibits the writing of base insertion and base deletion quality tags.

This commit is contained in:
Eric Banks 2012-07-04 01:22:20 -04:00
parent 33306d2e20
commit dd571d9aa0
5 changed files with 28 additions and 8 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -197,7 +197,7 @@ public class GenomeAnalysisEngine {
private BaseRecalibration baseRecalibration = null;
public BaseRecalibration getBaseRecalibration() { return baseRecalibration; }
public boolean hasBaseRecalibration() { return baseRecalibration != null; }
public void setBaseRecalibration(File recalFile, int quantizationLevels) { baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels); }
public void setBaseRecalibration(final File recalFile, final int quantizationLevels, final boolean noIndelQuals) { baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels, noIndelQuals); }
/**
* Actually run the GATK with the specified walker.
@ -227,7 +227,7 @@ public class GenomeAnalysisEngine {
// if the use specified an input BQSR recalibration table then enable on the fly recalibration
if (this.getArguments().BQSR_RECAL_FILE != null)
setBaseRecalibration(this.getArguments().BQSR_RECAL_FILE, this.getArguments().quantizationLevels);
setBaseRecalibration(this.getArguments().BQSR_RECAL_FILE, this.getArguments().quantizationLevels, this.getArguments().noIndelQuals);
// 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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@ -209,6 +209,12 @@ public class GATKArgumentCollection {
@Argument(fullName="quantize_quals", shortName = "qq", doc = "Quantize quality scores to a given number of levels.", required=false)
public int quantizationLevels = -1;
/**
* Turns off printing of the base insertion and base deletion tags when using the -BQSR argument. Only the base substitution qualities will be produced.
*/
@Argument(fullName="no_indel_quals", shortName = "NIQ", doc = "If true, inhibits printing of base insertion and base deletion tags.", required=false)
public boolean noIndelQuals = false;
@Argument(fullName="defaultBaseQualities", shortName = "DBQ", doc = "If reads are missing some or all base quality scores, this value will be used for all base quality scores", required=false)
public byte defaultBaseQualities = -1;

8
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
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@ -664,8 +664,12 @@ public class SAMDataSource {
IndexedFastaSequenceFile refReader,
BaseRecalibration bqsrApplier,
byte defaultBaseQualities) {
// **** NOTE: ALL FILTERING SHOULD BE DONE BEFORE ANY ITERATORS THAT MODIFY THE READS! ****
// (otherwise we will process something that we may end up throwing away)
// *********************************************************************************** //
// * NOTE: ALL FILTERING SHOULD BE DONE BEFORE ANY ITERATORS THAT MODIFY THE READS! * //
// * (otherwise we will process something that we may end up throwing away) * //
// *********************************************************************************** //
if (downsamplingFraction != null)
wrappedIterator = new DownsampleIterator(wrappedIterator, downsamplingFraction);

14
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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@ -49,6 +49,8 @@ public class BaseRecalibration {
private final RecalibrationTables recalibrationTables;
private final Covariate[] requestedCovariates; // list of all covariates to be used in this calculation
private final boolean noIndelQuals;
private static final NestedHashMap[] qualityScoreByFullCovariateKey = new NestedHashMap[EventType.values().length]; // Caches the result of performSequentialQualityCalculation(..) for all sets of covariate values.
static {
for (int i = 0; i < EventType.values().length; i++)
@ -58,10 +60,11 @@ public class BaseRecalibration {
/**
* Constructor using a GATK Report file
*
* @param RECAL_FILE a GATK Report file containing the recalibration information
* @param RECAL_FILE a GATK Report file containing the recalibration information
* @param quantizationLevels number of bins to quantize the quality scores
* @param noIndelQuals if true, do not emit base indel qualities
*/
public BaseRecalibration(final File RECAL_FILE, int quantizationLevels) {
public BaseRecalibration(final File RECAL_FILE, final int quantizationLevels, final boolean noIndelQuals) {
RecalibrationReport recalibrationReport = new RecalibrationReport(RECAL_FILE);
recalibrationTables = recalibrationReport.getRecalibrationTables();
@ -73,6 +76,7 @@ public class BaseRecalibration {
quantizationInfo.quantizeQualityScores(quantizationLevels);
readCovariates = new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length);
this.noIndelQuals = noIndelQuals;
}
/**
@ -87,6 +91,7 @@ public class BaseRecalibration {
this.recalibrationTables = recalibrationTables;
this.requestedCovariates = requestedCovariates;
readCovariates = new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length);
noIndelQuals = false;
}
/**
@ -99,6 +104,11 @@ public class BaseRecalibration {
public void recalibrateRead(final GATKSAMRecord read) {
RecalDataManager.computeCovariates(read, requestedCovariates, readCovariates); // compute all covariates for the read
for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings
if (noIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) {
read.setBaseQualities(null, errorModel);
continue;
}
final byte[] quals = read.getBaseQualities(errorModel);
final int[][] fullReadKeySet = readCovariates.getKeySet(errorModel); // get the keyset for this base using the error model

4
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -173,10 +173,10 @@ public class GATKSAMRecord extends BAMRecord {
setBaseQualities(quals);
break;
case BASE_INSERTION:
setAttribute( GATKSAMRecord.BQSR_BASE_INSERTION_QUALITIES, SAMUtils.phredToFastq(quals) );
setAttribute( GATKSAMRecord.BQSR_BASE_INSERTION_QUALITIES, quals == null ? null : SAMUtils.phredToFastq(quals) );
break;
case BASE_DELETION:
setAttribute( GATKSAMRecord.BQSR_BASE_DELETION_QUALITIES, SAMUtils.phredToFastq(quals) );
setAttribute( GATKSAMRecord.BQSR_BASE_DELETION_QUALITIES, quals == null ? null : SAMUtils.phredToFastq(quals) );
break;
default:
throw new ReviewedStingException("Unrecognized Base Recalibration type: " + errorModel );