diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index f437db680..07d9892a1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -31,8 +31,6 @@ import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.io.File; - public class UnifiedArgumentCollection { @@ -103,18 +101,13 @@ public class UnifiedArgumentCollection { @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; - // TODO -- delete me - @Hidden - @Argument(fullName = "abort_at_too_much_coverage", doc = "Don't call a site if the downsampled coverage is greater than this value", required = false) - public int COVERAGE_AT_WHICH_TO_ABORT = -1; - - // control the various parameters to be used + /** + * 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. + */ @Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false) public int MIN_BASE_QUALTY_SCORE = 17; - @Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false) - public int MIN_MAPPING_QUALTY_SCORE = 20; - @Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]", required = false) public Double MAX_DELETION_FRACTION = 0.05; @@ -165,14 +158,6 @@ public class UnifiedArgumentCollection { @Argument(fullName = "ignoreSNPAlleles", shortName = "ignoreSNPAlleles", doc = "expt", required = false) public boolean IGNORE_SNP_ALLELES = false; - @Deprecated - @Argument(fullName="output_all_callable_bases", shortName="all_bases", doc="Please use --output_mode EMIT_ALL_SITES instead" ,required=false) - private Boolean ALL_BASES_DEPRECATED = false; - - @Deprecated - @Argument(fullName="genotype", shortName="genotype", doc="Please use --output_mode EMIT_ALL_CONFIDENT_SITES instead" ,required=false) - private Boolean GENOTYPE_DEPRECATED = 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() { @@ -189,7 +174,6 @@ public class UnifiedArgumentCollection { 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.MIN_MAPPING_QUALTY_SCORE = MIN_MAPPING_QUALTY_SCORE; uac.MAX_DELETION_FRACTION = MAX_DELETION_FRACTION; uac.MIN_INDEL_COUNT_FOR_GENOTYPING = MIN_INDEL_COUNT_FOR_GENOTYPING; uac.INDEL_HETEROZYGOSITY = INDEL_HETEROZYGOSITY; @@ -200,7 +184,6 @@ public class UnifiedArgumentCollection { uac.alleles = alleles; // todo- arguments to remove - uac.COVERAGE_AT_WHICH_TO_ABORT = COVERAGE_AT_WHICH_TO_ABORT; uac.IGNORE_SNP_ALLELES = IGNORE_SNP_ALLELES; uac.BANDED_INDEL_COMPUTATION = BANDED_INDEL_COMPUTATION; return uac; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index e99b6af60..993a434ac 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -120,7 +120,6 @@ public class UnifiedGenotyperEngine { this.samples = new TreeSet(samples); // note that, because we cap the base quality by the mapping quality, minMQ cannot be less than minBQ this.UAC = UAC.clone(); - this.UAC.MIN_MAPPING_QUALTY_SCORE = Math.max(UAC.MIN_MAPPING_QUALTY_SCORE, UAC.MIN_BASE_QUALTY_SCORE); this.logger = logger; this.verboseWriter = verboseWriter; @@ -146,9 +145,6 @@ public class UnifiedGenotyperEngine { * @return the VariantCallContext object */ public VariantCallContext calculateLikelihoodsAndGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) { - if ( UAC.COVERAGE_AT_WHICH_TO_ABORT > 0 && rawContext.size() > UAC.COVERAGE_AT_WHICH_TO_ABORT ) - return null; - final GenotypeLikelihoodsCalculationModel.Model model = getCurrentGLModel(tracker, refContext, rawContext ); if( model == null ) { return (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, null, rawContext) : null); @@ -566,7 +562,7 @@ public class UnifiedGenotyperEngine { if (UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) { // regular pileup in this case - ReadBackedPileup pileup = rawContext.getBasePileup() .getMappingFilteredPileup(UAC.MIN_MAPPING_QUALTY_SCORE); + ReadBackedPileup pileup = rawContext.getBasePileup() .getMappingFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE); // don't call when there is no coverage if ( pileup.getNumberOfElements() == 0 && UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES ) @@ -583,7 +579,7 @@ public class UnifiedGenotyperEngine { ReadBackedExtendedEventPileup rawPileup = rawContext.getExtendedEventPileup(); // filter the context based on min mapping quality - ReadBackedExtendedEventPileup pileup = rawPileup.getMappingFilteredPileup(UAC.MIN_MAPPING_QUALTY_SCORE); + ReadBackedExtendedEventPileup pileup = rawPileup.getMappingFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE); // don't call when there is no coverage if ( pileup.getNumberOfElements() == 0 && UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES ) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 7d6cfc7ad..d47c63827 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -18,8 +18,8 @@ import java.util.Map; public class UnifiedGenotyperIntegrationTest extends WalkerTest { private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH --dbsnp " + b36dbSNP129; - private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL --dbsnp " + b36dbSNP129; - private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " -NO_HEADER -glm INDEL --dbsnp " + b37dbSNP132; + private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL -mbq 20 --dbsnp " + b36dbSNP129; + private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " -NO_HEADER -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132; // -------------------------------------------------------------------------------------------------------------- // @@ -114,7 +114,6 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testCallingParameters() { HashMap e = new HashMap(); e.put( "--min_base_quality_score 26", "531966aee1cd5dced61c96c4fedb59a9" ); - e.put( "--min_mapping_quality_score 26", "c71ca370947739cb7d87b59452be7a07" ); e.put( "--computeSLOD", "1a5648f26c18ced27df4be031b44e72d" ); for ( Map.Entry entry : e.entrySet() ) { @@ -241,7 +240,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { 1, Arrays.asList("5fe98ee853586dc9db58f0bc97daea63")); - executeTest(String.format("test indel caller in SLX witn low min allele count"), spec); + executeTest(String.format("test indel caller in SLX with low min allele count"), spec); } @Test