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Get rid of support for bams without sample information in the read groups. This hidden option wasn't being used anyways because it wasn't hooked up properly in the AlignmentContext.

This commit is contained in:
Eric Banks 2011-11-05 23:54:28 -04:00
parent ad57bcd693
commit a12bc63e5c
6 changed files with 11 additions and 42 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
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@ -131,7 +131,7 @@ public class AlignmentContextUtils {
}
}
public static Map<String, AlignmentContext> splitContextBySampleName(ReadBackedPileup pileup, String assumedSingleSample) {
public static Map<String, AlignmentContext> splitContextBySampleName(ReadBackedPileup pileup) {
return splitContextBySampleName(new AlignmentContext(pileup.getLocation(), pileup));
}

13
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -164,10 +164,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
@Argument(fullName="list", shortName="ls", doc="List the available annotations and exit")
protected Boolean LIST = false;
@Hidden
@Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)
protected String ASSUME_SINGLE_SAMPLE = null;
@Hidden
@Argument(fullName="vcfContainsOnlyIndels", shortName="dels",doc="Use if you are annotating an indel vcf, currently VERY experimental", required = false)
protected boolean indelsOnly = false;
@ -213,11 +209,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
List<String> rodName = Arrays.asList(variantCollection.variants.getName());
Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), rodName);
// if there are no valid samples, warn the user
if ( samples.size() == 0 ) {
logger.warn("There are no samples input at all; use the --sampleName argument to specify one if desired.");
}
if ( USE_ALL_ANNOTATIONS )
engine = new VariantAnnotatorEngine(annotationsToExclude, this, getToolkit());
else
@ -301,9 +292,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
Map<String, AlignmentContext> stratifiedContexts;
if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 ) {
if ( ! context.hasExtendedEventPileup() ) {
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getBasePileup(), ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getBasePileup());
} else {
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getExtendedEventPileup(), ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getExtendedEventPileup());
}
if ( stratifiedContexts != null ) {
annotatedVCs = new ArrayList<VariantContext>(VCs.size());

8
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
View File

@ -39,7 +39,6 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.HashSet;
import java.util.Set;
import java.util.TreeSet;
/**
@ -71,12 +70,7 @@ public class UGCalcLikelihoods extends LocusWalker<VariantCallContext, Integer>
public void initialize() {
// get all of the unique sample names
// if we're supposed to assume a single sample, do so
Set<String> samples = new TreeSet<String>();
if ( UAC.ASSUME_SINGLE_SAMPLE != null )
samples.add(UAC.ASSUME_SINGLE_SAMPLE);
else
samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples);

6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -96,11 +96,6 @@ public class UnifiedArgumentCollection {
@Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype when in GENOTYPE_MODE = GENOTYPE_GIVEN_ALLELES", required=false)
public RodBinding<VariantContext> alleles;
// control the error modes
@Hidden
@Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)
public String ASSUME_SINGLE_SAMPLE = null;
/**
* The minimum confidence needed in a given base for it to be used in variant calling. Note that the base quality of a base
* is capped by the mapping quality so that bases on reads with low mapping quality may get filtered out depending on this value.
@ -170,7 +165,6 @@ public class UnifiedArgumentCollection {
uac.GenotypingMode = GenotypingMode;
uac.OutputMode = OutputMode;
uac.COMPUTE_SLOD = COMPUTE_SLOD;
uac.ASSUME_SINGLE_SAMPLE = ASSUME_SINGLE_SAMPLE;
uac.STANDARD_CONFIDENCE_FOR_CALLING = STANDARD_CONFIDENCE_FOR_CALLING;
uac.STANDARD_CONFIDENCE_FOR_EMITTING = STANDARD_CONFIDENCE_FOR_EMITTING;
uac.MIN_BASE_QUALTY_SCORE = MIN_BASE_QUALTY_SCORE;

7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -206,12 +206,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
**/
public void initialize() {
// get all of the unique sample names
// if we're supposed to assume a single sample, do so
Set<String> samples = new TreeSet<String>();
if ( UAC.ASSUME_SINGLE_SAMPLE != null )
samples.add(UAC.ASSUME_SINGLE_SAMPLE);
else
samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
// initialize the verbose writer
if ( verboseWriter != null )

17
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -106,12 +106,7 @@ public class UnifiedGenotyperEngine {
// ---------------------------------------------------------------------------------------------------------
@Requires({"toolkit != null", "UAC != null"})
public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC) {
this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null,
// get the number of samples
// if we're supposed to assume a single sample, do so
UAC.ASSUME_SINGLE_SAMPLE != null ?
new TreeSet<String>(Arrays.asList(UAC.ASSUME_SINGLE_SAMPLE)) :
SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()));
this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()));
}
@Requires({"toolkit != null", "UAC != null", "logger != null", "samples != null && samples.size() > 0"})
@ -253,7 +248,7 @@ public class UnifiedGenotyperEngine {
pileup = rawContext.getExtendedEventPileup();
else if (rawContext.hasBasePileup())
pileup = rawContext.getBasePileup();
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
vc = annotationEngine.annotateContext(tracker, ref, stratifiedContexts, vc);
}
@ -435,7 +430,7 @@ public class UnifiedGenotyperEngine {
pileup = rawContext.getExtendedEventPileup();
else if (rawContext.hasBasePileup())
pileup = rawContext.getBasePileup();
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
vcCall = annotationEngine.annotateContext(tracker, refContext, stratifiedContexts, vcCall);
}
@ -569,7 +564,7 @@ public class UnifiedGenotyperEngine {
return null;
// stratify the AlignmentContext and cut by sample
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
} else {
@ -586,12 +581,12 @@ public class UnifiedGenotyperEngine {
return null;
// stratify the AlignmentContext and cut by sample
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
}
} else if ( model == GenotypeLikelihoodsCalculationModel.Model.SNP ) {
// stratify the AlignmentContext and cut by sample
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup(), UAC.ASSUME_SINGLE_SAMPLE);
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup());
if( !(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) ) {
int numDeletions = 0;