Removing the min mapping quality argument since it wasn't being used in the normal processing of the pileups in UG - only for indel pileups. Instead, we apply the min base quality to the reads in the pileup for indels and define it to be the min 'confidence' of the base. Docs are updated but I didn't rename the argument as I don't want people to complain.
This commit is contained in:
Eric Banks
parent
967ff647b8
commit
e1edd6bd12
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@ -31,8 +31,6 @@ import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.RodBinding;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.io.File;
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public class UnifiedArgumentCollection {
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@ -103,18 +101,13 @@ public class UnifiedArgumentCollection {
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@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)
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public String ASSUME_SINGLE_SAMPLE = null;
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// TODO -- delete me
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@Hidden
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@Argument(fullName = "abort_at_too_much_coverage", doc = "Don't call a site if the downsampled coverage is greater than this value", required = false)
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public int COVERAGE_AT_WHICH_TO_ABORT = -1;
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// control the various parameters to be used
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/**
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* The minimum confidence needed in a given base for it to be used in variant calling. Note that the base quality of a base
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* is capped by the mapping quality so that bases on reads with low mapping quality may get filtered out depending on this value.
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*/
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@Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
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public int MIN_BASE_QUALTY_SCORE = 17;
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@Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false)
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public int MIN_MAPPING_QUALTY_SCORE = 20;
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@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)
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public Double MAX_DELETION_FRACTION = 0.05;
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@ -165,14 +158,6 @@ public class UnifiedArgumentCollection {
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@Argument(fullName = "ignoreSNPAlleles", shortName = "ignoreSNPAlleles", doc = "expt", required = false)
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public boolean IGNORE_SNP_ALLELES = false;
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@Deprecated
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@Argument(fullName="output_all_callable_bases", shortName="all_bases", doc="Please use --output_mode EMIT_ALL_SITES instead" ,required=false)
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private Boolean ALL_BASES_DEPRECATED = false;
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@Deprecated
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@Argument(fullName="genotype", shortName="genotype", doc="Please use --output_mode EMIT_ALL_CONFIDENT_SITES instead" ,required=false)
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private Boolean GENOTYPE_DEPRECATED = false;
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// 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!
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public UnifiedArgumentCollection clone() {
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@ -189,7 +174,6 @@ public class UnifiedArgumentCollection {
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uac.STANDARD_CONFIDENCE_FOR_CALLING = STANDARD_CONFIDENCE_FOR_CALLING;
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uac.STANDARD_CONFIDENCE_FOR_EMITTING = STANDARD_CONFIDENCE_FOR_EMITTING;
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uac.MIN_BASE_QUALTY_SCORE = MIN_BASE_QUALTY_SCORE;
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uac.MIN_MAPPING_QUALTY_SCORE = MIN_MAPPING_QUALTY_SCORE;
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uac.MAX_DELETION_FRACTION = MAX_DELETION_FRACTION;
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uac.MIN_INDEL_COUNT_FOR_GENOTYPING = MIN_INDEL_COUNT_FOR_GENOTYPING;
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uac.INDEL_HETEROZYGOSITY = INDEL_HETEROZYGOSITY;
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@ -200,7 +184,6 @@ public class UnifiedArgumentCollection {
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uac.alleles = alleles;
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// todo- arguments to remove
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uac.COVERAGE_AT_WHICH_TO_ABORT = COVERAGE_AT_WHICH_TO_ABORT;
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uac.IGNORE_SNP_ALLELES = IGNORE_SNP_ALLELES;
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uac.BANDED_INDEL_COMPUTATION = BANDED_INDEL_COMPUTATION;
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return uac;
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@ -120,7 +120,6 @@ public class UnifiedGenotyperEngine {
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this.samples = new TreeSet<String>(samples);
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// note that, because we cap the base quality by the mapping quality, minMQ cannot be less than minBQ
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this.UAC = UAC.clone();
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this.UAC.MIN_MAPPING_QUALTY_SCORE = Math.max(UAC.MIN_MAPPING_QUALTY_SCORE, UAC.MIN_BASE_QUALTY_SCORE);
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this.logger = logger;
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this.verboseWriter = verboseWriter;
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@ -146,9 +145,6 @@ public class UnifiedGenotyperEngine {
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* @return the VariantCallContext object
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*/
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public VariantCallContext calculateLikelihoodsAndGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
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if ( UAC.COVERAGE_AT_WHICH_TO_ABORT > 0 && rawContext.size() > UAC.COVERAGE_AT_WHICH_TO_ABORT )
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return null;
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final GenotypeLikelihoodsCalculationModel.Model model = getCurrentGLModel(tracker, refContext, rawContext );
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if( model == null ) {
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return (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, null, rawContext) : null);
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@ -566,7 +562,7 @@ public class UnifiedGenotyperEngine {
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if (UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
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// regular pileup in this case
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ReadBackedPileup pileup = rawContext.getBasePileup() .getMappingFilteredPileup(UAC.MIN_MAPPING_QUALTY_SCORE);
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ReadBackedPileup pileup = rawContext.getBasePileup() .getMappingFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE);
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// don't call when there is no coverage
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if ( pileup.getNumberOfElements() == 0 && UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES )
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@ -583,7 +579,7 @@ public class UnifiedGenotyperEngine {
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ReadBackedExtendedEventPileup rawPileup = rawContext.getExtendedEventPileup();
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// filter the context based on min mapping quality
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ReadBackedExtendedEventPileup pileup = rawPileup.getMappingFilteredPileup(UAC.MIN_MAPPING_QUALTY_SCORE);
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ReadBackedExtendedEventPileup pileup = rawPileup.getMappingFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE);
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// don't call when there is no coverage
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if ( pileup.getNumberOfElements() == 0 && UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES )
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@ -18,8 +18,8 @@ import java.util.Map;
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public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH --dbsnp " + b36dbSNP129;
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private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL --dbsnp " + b36dbSNP129;
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private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " -NO_HEADER -glm INDEL --dbsnp " + b37dbSNP132;
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private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL -mbq 20 --dbsnp " + b36dbSNP129;
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private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " -NO_HEADER -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132;
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// --------------------------------------------------------------------------------------------------------------
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//
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@ -114,7 +114,6 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testCallingParameters() {
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HashMap<String, String> e = new HashMap<String, String>();
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e.put( "--min_base_quality_score 26", "531966aee1cd5dced61c96c4fedb59a9" );
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e.put( "--min_mapping_quality_score 26", "c71ca370947739cb7d87b59452be7a07" );
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e.put( "--computeSLOD", "1a5648f26c18ced27df4be031b44e72d" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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@ -241,7 +240,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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1,
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Arrays.asList("5fe98ee853586dc9db58f0bc97daea63"));
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executeTest(String.format("test indel caller in SLX witn low min allele count"), spec);
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executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
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}
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@Test
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