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

Refactoring the Unified (and Standard) Argument Collections because it was really ugly that the subclass had to do all the cloning for the super class. The clone() method is really not recommended best practice in Java anyways, so I changed it so that we use standard overloaded constructors. Confirmed that the Haplotype Caller --help docs do not include UG-specific arguments.

This commit is contained in:
Eric Banks 2012-10-20 20:35:54 -04:00
parent a647f1e076
commit 2c624f76c8
3 changed files with 62 additions and 58 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -241,14 +241,14 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
samplesList.addAll( samples );
// initialize the UnifiedGenotyper Engine which is used to call into the exact model
final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection( SCAC ); // this adapter is used so that the full set of unused UG arguments aren't exposed to the HC user
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC.clone(), logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY; // low values used for isActive determination only, default/user-specified values used for actual calling
UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY; // low values used for isActive determination only, default/user-specified values used for actual calling
UAC.STANDARD_CONFIDENCE_FOR_CALLING = Math.max( 4.0, UAC.STANDARD_CONFIDENCE_FOR_CALLING );
UAC.STANDARD_CONFIDENCE_FOR_EMITTING = Math.max( 4.0, UAC.STANDARD_CONFIDENCE_FOR_EMITTING );
// create a UAC but with the exactCallsLog = null, so we only output the log for the HC caller itself, if requested
UnifiedArgumentCollection simpleUAC = UAC.clone();
UnifiedArgumentCollection simpleUAC = new UnifiedArgumentCollection(UAC);
simpleUAC.exactCallsLog = null;
UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);

26
public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
View File

@ -69,7 +69,33 @@ public class StandardCallerArgumentCollection {
@Argument(fullName = "max_alternate_alleles_for_indels", shortName = "maxAltAllelesForIndels", doc = "Maximum number of alternate alleles to genotype for indels only", required = false)
public int MAX_ALTERNATE_ALLELES_FOR_INDELS = 2;
/**
* If this fraction is greater is than zero, the caller will aggressively attempt to remove contamination through biased down-sampling of reads.
* Basically, it will ignore the contamination fraction of reads for each alternate allele. So if the pileup contains N total bases, then we
* will try to remove (N * contamination fraction) bases for each alternate allele.
*/
@Hidden
@Argument(fullName = "contamination_percentage_to_filter", shortName = "contamination", doc = "Fraction of contamination in sequencing data (for all samples) to aggressively remove", required = false)
public double CONTAMINATION_PERCENTAGE = 0.0;
@Hidden
@Argument(shortName = "logExactCalls", doc="x", required=false)
public File exactCallsLog = null;
public StandardCallerArgumentCollection() { }
// Developers must remember to add any newly added arguments to the list here as well otherwise they won't get changed from their default value!
public StandardCallerArgumentCollection(final StandardCallerArgumentCollection SCAC) {
this.alleles = SCAC.alleles;
this.GenotypingMode = SCAC.GenotypingMode;
this.heterozygosity = SCAC.heterozygosity;
this.MAX_ALTERNATE_ALLELES = SCAC.MAX_ALTERNATE_ALLELES;
this.MAX_ALTERNATE_ALLELES_FOR_INDELS = SCAC.MAX_ALTERNATE_ALLELES_FOR_INDELS;
this.OutputMode = SCAC.OutputMode;
this.STANDARD_CONFIDENCE_FOR_CALLING = SCAC.STANDARD_CONFIDENCE_FOR_CALLING;
this.STANDARD_CONFIDENCE_FOR_EMITTING = SCAC.STANDARD_CONFIDENCE_FOR_EMITTING;
this.CONTAMINATION_PERCENTAGE = SCAC.CONTAMINATION_PERCENTAGE;
this.exactCallsLog = SCAC.exactCallsLog;
}
}

90
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
View File

@ -186,63 +186,41 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
@Argument(shortName="ef", fullName="exclude_filtered_reference_sites", doc="Don't include in the analysis sites where the reference sample VCF is filtered. Default: false.", required=false)
boolean EXCLUDE_FILTERED_REFERENCE_SITES = false;
// Developers must remember to add any newly added arguments to the list here as well otherwise they won't get changed from their default value!
public UnifiedArgumentCollection clone() {
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
uac.GLmodel = GLmodel;
uac.AFmodel = AFmodel;
uac.heterozygosity = heterozygosity;
uac.PCR_error = PCR_error;
uac.GenotypingMode = GenotypingMode;
uac.OutputMode = OutputMode;
uac.NO_SLOD = NO_SLOD;
uac.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED = ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED;
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;
uac.MAX_DELETION_FRACTION = MAX_DELETION_FRACTION;
uac.MIN_INDEL_COUNT_FOR_GENOTYPING = MIN_INDEL_COUNT_FOR_GENOTYPING;
uac.MIN_INDEL_FRACTION_PER_SAMPLE = MIN_INDEL_FRACTION_PER_SAMPLE;
uac.INDEL_HETEROZYGOSITY = INDEL_HETEROZYGOSITY;
uac.INDEL_GAP_OPEN_PENALTY = INDEL_GAP_OPEN_PENALTY;
uac.INDEL_GAP_CONTINUATION_PENALTY = INDEL_GAP_CONTINUATION_PENALTY;
uac.OUTPUT_DEBUG_INDEL_INFO = OUTPUT_DEBUG_INDEL_INFO;
uac.INDEL_HAPLOTYPE_SIZE = INDEL_HAPLOTYPE_SIZE;
uac.alleles = alleles;
uac.MAX_ALTERNATE_ALLELES = MAX_ALTERNATE_ALLELES;
uac.MAX_ALTERNATE_ALLELES_FOR_INDELS = MAX_ALTERNATE_ALLELES_FOR_INDELS;
uac.GLmodel = GLmodel;
uac.TREAT_ALL_READS_AS_SINGLE_POOL = TREAT_ALL_READS_AS_SINGLE_POOL;
uac.referenceSampleRod = referenceSampleRod;
uac.referenceSampleName = referenceSampleName;
uac.samplePloidy = samplePloidy;
uac.maxQualityScore = minQualityScore;
uac.phredScaledPrior = phredScaledPrior;
uac.minPower = minPower;
uac.minReferenceDepth = minReferenceDepth;
uac.EXCLUDE_FILTERED_REFERENCE_SITES = EXCLUDE_FILTERED_REFERENCE_SITES;
uac.IGNORE_LANE_INFO = IGNORE_LANE_INFO;
uac.exactCallsLog = exactCallsLog;
uac.pairHMM = pairHMM;
// todo- arguments to remove
uac.IGNORE_SNP_ALLELES = IGNORE_SNP_ALLELES;
return uac;
}
public UnifiedArgumentCollection() { }
public UnifiedArgumentCollection( final StandardCallerArgumentCollection SCAC ) {
super();
this.alleles = SCAC.alleles;
this.GenotypingMode = SCAC.GenotypingMode;
this.heterozygosity = SCAC.heterozygosity;
this.MAX_ALTERNATE_ALLELES = SCAC.MAX_ALTERNATE_ALLELES;
this.MAX_ALTERNATE_ALLELES_FOR_INDELS = SCAC.MAX_ALTERNATE_ALLELES_FOR_INDELS;
this.OutputMode = SCAC.OutputMode;
this.STANDARD_CONFIDENCE_FOR_CALLING = SCAC.STANDARD_CONFIDENCE_FOR_CALLING;
this.STANDARD_CONFIDENCE_FOR_EMITTING = SCAC.STANDARD_CONFIDENCE_FOR_EMITTING;
this.exactCallsLog = SCAC.exactCallsLog;
public UnifiedArgumentCollection(final StandardCallerArgumentCollection SCAC) {
super(SCAC);
}
// Developers must remember to add any newly added arguments to the list here as well otherwise they won't get changed from their default value!
public UnifiedArgumentCollection(final UnifiedArgumentCollection uac) {
this.GLmodel = uac.GLmodel;
this.AFmodel = uac.AFmodel;
this.PCR_error = uac.PCR_error;
this.NO_SLOD = uac.NO_SLOD;
this.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED = uac.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED;
this.MIN_BASE_QUALTY_SCORE = uac.MIN_BASE_QUALTY_SCORE;
this.MAX_DELETION_FRACTION = uac.MAX_DELETION_FRACTION;
this.MIN_INDEL_COUNT_FOR_GENOTYPING = uac.MIN_INDEL_COUNT_FOR_GENOTYPING;
this.MIN_INDEL_FRACTION_PER_SAMPLE = uac.MIN_INDEL_FRACTION_PER_SAMPLE;
this.INDEL_HETEROZYGOSITY = uac.INDEL_HETEROZYGOSITY;
this.INDEL_GAP_OPEN_PENALTY = uac.INDEL_GAP_OPEN_PENALTY;
this.INDEL_GAP_CONTINUATION_PENALTY = uac.INDEL_GAP_CONTINUATION_PENALTY;
this.OUTPUT_DEBUG_INDEL_INFO = uac.OUTPUT_DEBUG_INDEL_INFO;
this.INDEL_HAPLOTYPE_SIZE = uac.INDEL_HAPLOTYPE_SIZE;
this.TREAT_ALL_READS_AS_SINGLE_POOL = uac.TREAT_ALL_READS_AS_SINGLE_POOL;
this.referenceSampleRod = uac.referenceSampleRod;
this.referenceSampleName = uac.referenceSampleName;
this.samplePloidy = uac.samplePloidy;
this.maxQualityScore = uac.minQualityScore;
this.phredScaledPrior = uac.phredScaledPrior;
this.minPower = uac.minPower;
this.minReferenceDepth = uac.minReferenceDepth;
this.EXCLUDE_FILTERED_REFERENCE_SITES = uac.EXCLUDE_FILTERED_REFERENCE_SITES;
this.IGNORE_LANE_INFO = uac.IGNORE_LANE_INFO;
this.pairHMM = uac.pairHMM;
// todo- arguments to remove
this.IGNORE_SNP_ALLELES = uac.IGNORE_SNP_ALLELES;
}
}