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Skip array needs to also be used in the updateDataForRead function of the delocalized BQSR.

This commit is contained in:
Ryan Poplin 2012-09-04 10:33:37 -04:00
parent ff6ebbf3fd
commit c9944d81ef
3 changed files with 40 additions and 38 deletions
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74
protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AdvancedRecalibrationEngine.java
View File

@ -106,47 +106,49 @@ public class AdvancedRecalibrationEngine extends StandardRecalibrationEngine imp
} }
@Override @Override
public synchronized void updateDataForRead(final GATKSAMRecord read, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) { public synchronized void updateDataForRead(final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) {
for( int offset = 0; offset < read.getReadBases().length; offset++ ) { for( int offset = 0; offset < read.getReadBases().length; offset++ ) {
final ReadCovariates readCovariates = covariateKeySetFrom(read); if( !skip[offset] ) {
final ReadCovariates readCovariates = covariateKeySetFrom(read);
tempQualArray[EventType.BASE_SUBSTITUTION.index] = read.getBaseQualities()[offset]; tempQualArray[EventType.BASE_SUBSTITUTION.index] = read.getBaseQualities()[offset];
tempFractionalErrorArray[EventType.BASE_SUBSTITUTION.index] = snpErrors[offset]; tempFractionalErrorArray[EventType.BASE_SUBSTITUTION.index] = snpErrors[offset];
tempQualArray[EventType.BASE_INSERTION.index] = read.getBaseInsertionQualities()[offset]; tempQualArray[EventType.BASE_INSERTION.index] = read.getBaseInsertionQualities()[offset];
tempFractionalErrorArray[EventType.BASE_INSERTION.index] = insertionErrors[offset]; tempFractionalErrorArray[EventType.BASE_INSERTION.index] = insertionErrors[offset];
tempQualArray[EventType.BASE_DELETION.index] = read.getBaseDeletionQualities()[offset]; tempQualArray[EventType.BASE_DELETION.index] = read.getBaseDeletionQualities()[offset];
tempFractionalErrorArray[EventType.BASE_DELETION.index] = deletionErrors[offset]; tempFractionalErrorArray[EventType.BASE_DELETION.index] = deletionErrors[offset];
for (final EventType eventType : EventType.values()) { for (final EventType eventType : EventType.values()) {
final int[] keys = readCovariates.getKeySet(offset, eventType); final int[] keys = readCovariates.getKeySet(offset, eventType);
final int eventIndex = eventType.index; final int eventIndex = eventType.index;
final byte qual = tempQualArray[eventIndex]; final byte qual = tempQualArray[eventIndex];
final double isError = tempFractionalErrorArray[eventIndex]; final double isError = tempFractionalErrorArray[eventIndex];
final NestedIntegerArray<RecalDatum> rgRecalTable = recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE); final NestedIntegerArray<RecalDatum> rgRecalTable = recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE);
final RecalDatum rgPreviousDatum = rgRecalTable.get(keys[0], eventIndex); final RecalDatum rgPreviousDatum = rgRecalTable.get(keys[0], eventIndex);
final RecalDatum rgThisDatum = createDatumObject(qual, isError); final RecalDatum rgThisDatum = createDatumObject(qual, isError);
if (rgPreviousDatum == null) // key doesn't exist yet in the map so make a new bucket and add it if (rgPreviousDatum == null) // key doesn't exist yet in the map so make a new bucket and add it
rgRecalTable.put(rgThisDatum, keys[0], eventIndex); rgRecalTable.put(rgThisDatum, keys[0], eventIndex);
else
rgPreviousDatum.combine(rgThisDatum);
final NestedIntegerArray<RecalDatum> qualRecalTable = recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE);
final RecalDatum qualPreviousDatum = qualRecalTable.get(keys[0], keys[1], eventIndex);
if (qualPreviousDatum == null)
qualRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], eventIndex);
else
qualPreviousDatum.increment(1.0, isError);
for (int i = 2; i < covariates.length; i++) {
if (keys[i] < 0)
continue;
final NestedIntegerArray<RecalDatum> covRecalTable = recalibrationTables.getTable(i);
final RecalDatum covPreviousDatum = covRecalTable.get(keys[0], keys[1], keys[i], eventIndex);
if (covPreviousDatum == null)
covRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], keys[i], eventIndex);
else else
covPreviousDatum.increment(1.0, isError); rgPreviousDatum.combine(rgThisDatum);
final NestedIntegerArray<RecalDatum> qualRecalTable = recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE);
final RecalDatum qualPreviousDatum = qualRecalTable.get(keys[0], keys[1], eventIndex);
if (qualPreviousDatum == null)
qualRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], eventIndex);
else
qualPreviousDatum.increment(1.0, isError);
for (int i = 2; i < covariates.length; i++) {
if (keys[i] < 0)
continue;
final NestedIntegerArray<RecalDatum> covRecalTable = recalibrationTables.getTable(i);
final RecalDatum covPreviousDatum = covRecalTable.get(keys[0], keys[1], keys[i], eventIndex);
if (covPreviousDatum == null)
covRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], keys[i], eventIndex);
else
covPreviousDatum.increment(1.0, isError);
}
} }
} }
} }

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
View File

@ -35,5 +35,5 @@ public interface RecalibrationEngine {
public void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase); public void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase);
public void updateDataForRead(final GATKSAMRecord read, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors); public void updateDataForRead(final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors);
} }

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
View File

@ -93,7 +93,7 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP
} }
@Override @Override
public synchronized void updateDataForRead( final GATKSAMRecord read, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) { public synchronized void updateDataForRead( final GATKSAMRecord read, final boolean[] skip, final double[] snpErrors, final double[] insertionErrors, final double[] deletionErrors ) {
throw new UnsupportedOperationException("Delocalized BQSR is not available in the GATK-lite version"); throw new UnsupportedOperationException("Delocalized BQSR is not available in the GATK-lite version");
} }