zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Changing the commenting style in the BQSR

This commit is contained in:
Ryan Poplin 2012-08-29 11:27:45 -04:00
parent 19cc0b373e
commit e12ae65d33
10 changed files with 105 additions and 102 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
View File

@ -32,13 +32,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -299,6 +297,4 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
return table;
}
}

12
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
View File

@ -216,12 +216,14 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
*/
public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
long countedSites = 0L;
if (tracker.getValues(RAC.knownSites).size() == 0) { // Only analyze sites not present in the provided known sites
// Only analyze sites not present in the provided known sites
if (tracker.getValues(RAC.knownSites).size() == 0) {
for (final PileupElement p : context.getBasePileup()) {
final GATKSAMRecord read = p.getRead();
final int offset = p.getOffset();
if (readHasBeenSkipped(read) || isLowQualityBase(read, offset)) // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases)
// This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases)
if (readHasBeenSkipped(read) || isLowQualityBase(read, offset))
continue;
if (readNotSeen(read)) {
@ -234,10 +236,12 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
read.setTemporaryAttribute(COVARS_ATTRIBUTE, RecalUtils.computeCovariates(read, requestedCovariates));
}
if (!ReadUtils.isSOLiDRead(read) || // SOLID bams have inserted the reference base into the read if the color space in inconsistent with the read base so skip it
// SOLID bams have inserted the reference base into the read if the color space in inconsistent with the read base so skip it
if (!ReadUtils.isSOLiDRead(read) ||
RAC.SOLID_RECAL_MODE == RecalUtils.SOLID_RECAL_MODE.DO_NOTHING ||
RecalUtils.isColorSpaceConsistent(read, offset))
recalibrationEngine.updateDataForPileupElement(p, ref.getBase()); // This base finally passed all the checks for a good base, so add it to the big data hashmap
// This base finally passed all the checks for a good base, so add it to the big data hashmap
recalibrationEngine.updateDataForPileupElement(p, ref.getBase());
}
countedSites++;
}

4
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
View File

@ -103,7 +103,9 @@ public class BaseRecalibration {
}
}
RecalUtils.computeCovariates(read, requestedCovariates, readCovariates); // compute all covariates for the read
// Compute all covariates for the read
RecalUtils.computeCovariates(read, requestedCovariates, readCovariates);
for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings
if (disableIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) {
read.setBaseQualities(null, errorModel);

9
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
View File

@ -116,7 +116,8 @@ public class RecalUtils {
if (!argumentCollection.DO_NOT_USE_STANDARD_COVARIATES)
optionalCovariates = addStandardCovariatesToList(standardClasses); // add the standard covariates if -standard was specified by the user
if (argumentCollection.COVARIATES != null) { // parse the -cov arguments that were provided, skipping over the ones already specified
// parse the -cov arguments that were provided, skipping over the ones already specified
if (argumentCollection.COVARIATES != null) {
for (String requestedCovariateString : argumentCollection.COVARIATES) {
// help the transition from BQSR v1 to BQSR v2
if ( requestedCovariateString.equals("DinucCovariate") )
@ -349,7 +350,6 @@ public class RecalUtils {
return Utils.join(",", names);
}
public static void outputRecalibrationReport(final GATKReportTable argumentTable, final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates, final PrintStream outputFile) {
outputRecalibrationReport(argumentTable, quantizationInfo.generateReportTable(), generateReportTables(recalibrationTables, requestedCovariates), outputFile);
}
@ -542,7 +542,8 @@ public class RecalUtils {
if (!ReadUtils.isSOLiDRead(read)) // If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base
return true;
if (read.getAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG) == null) { // Haven't calculated the inconsistency array yet for this read
// Haven't calculated the inconsistency array yet for this read
if (read.getAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG) == null) {
final Object attr = read.getAttribute(RecalUtils.COLOR_SPACE_ATTRIBUTE_TAG);
if (attr != null) {
byte[] colorSpace;
@ -774,6 +775,4 @@ public class RecalUtils {
return base;
}
}
}

3
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
View File

@ -198,7 +198,8 @@ public class RecalibrationReport {
final long nErrors = (Long) reportTable.get(row, RecalUtils.NUMBER_ERRORS_COLUMN_NAME);
final double empiricalQuality = (Double) reportTable.get(row, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME);
final double estimatedQReported = hasEstimatedQReportedColumn ? // the estimatedQreported column only exists in the ReadGroup table
// the estimatedQreported column only exists in the ReadGroup table
final double estimatedQReported = hasEstimatedQReportedColumn ?
(Double) reportTable.get(row, RecalUtils.ESTIMATED_Q_REPORTED_COLUMN_NAME) : // we get it if we are in the read group table
Byte.parseByte((String) reportTable.get(row, RecalUtils.QUALITY_SCORE_COLUMN_NAME)); // or we use the reported quality if we are in any other table

3
public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
View File

@ -87,7 +87,8 @@ public class ContextCovariate implements StandardCovariate {
// store the original bases and then write Ns over low quality ones
final byte[] originalBases = read.getReadBases().clone();
final GATKSAMRecord clippedRead = ReadClipper.clipLowQualEnds(read, LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS); // Write N's over the low quality tail of the reads to avoid adding them into the context
// Write N's over the low quality tail of the reads to avoid adding them into the context
final GATKSAMRecord clippedRead = ReadClipper.clipLowQualEnds(read, LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS);
final boolean negativeStrand = clippedRead.getReadNegativeStrandFlag();
byte[] bases = clippedRead.getReadBases();