From 82f213177730123def312b6a5b64878f7f665769 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 2 Sep 2011 12:27:11 -0400 Subject: [PATCH] Simplied getAttributeAsX interfaces -- Removed versions getAttribriteAsX(key) that except on not having the value. -- Removed version that getAttributeAsXNoException(key) -- The only available assessors are now getAttributeAsX(key, default). -- This single accessors properly handle their argument types, so if the value is a double it is returned directly for getAttributeAsDouble(), or if it's a string it's converted to a double. If the key isn't found, default is returned. --- .../gatk/walkers/annotator/SBByDepth.java | 2 +- .../indels/HaplotypeIndelErrorModel.java | 2 +- .../gatk/walkers/phasing/PhasingRead.java | 2 +- .../walkers/phasing/RefSeqDataParser.java | 10 ++-- .../varianteval/evaluators/CountVariants.java | 6 +-- .../evaluators/GenotypePhasingEvaluator.java | 3 +- .../evaluators/SimpleMetricsByAC.java | 2 +- .../evaluators/TiTvVariantEvaluator.java | 2 +- .../evaluators/ValidationReport.java | 2 +- .../stratifications/AlleleCount.java | 2 +- .../stratifications/AlleleFrequency.java | 2 +- .../stratifications/Degeneracy.java | 10 ++-- .../stratifications/FunctionalClass.java | 4 +- .../VQSRCalibrationCurve.java | 4 +- .../walkers/variantutils/SelectVariants.java | 2 +- .../walkers/variantutils/VariantsToTable.java | 2 +- .../sting/utils/codecs/vcf/VCFCodec.java | 14 +++-- .../sting/utils/variantcontext/Genotype.java | 9 ---- .../InferredGeneticContext.java | 53 ++++++++++++------- .../utils/variantcontext/VariantContext.java | 10 ---- .../variantcontext/VariantContextUtils.java | 16 +++--- 21 files changed, 79 insertions(+), 80 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java index 180bed24d..d2c4d24ab 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java @@ -26,7 +26,7 @@ public class SBByDepth extends AnnotationByDepth { if (!vc.hasAttribute(VCFConstants.STRAND_BIAS_KEY)) return null; - double sBias = Double.valueOf(vc.getAttributeAsString(VCFConstants.STRAND_BIAS_KEY)); + double sBias = vc.getAttributeAsDouble(VCFConstants.STRAND_BIAS_KEY, -1); final Map genotypes = vc.getGenotypes(); if ( genotypes == null || genotypes.size() == 0 ) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java index e68aa31e0..232e468f9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java @@ -73,7 +73,7 @@ public class HaplotypeIndelErrorModel { baseMatchArray = new double[MAX_CACHED_QUAL+1]; baseMismatchArray = new double[MAX_CACHED_QUAL+1]; for (int k=1; k <= MAX_CACHED_QUAL; k++) { - double baseProb = QualityUtils.qualToProb(k); + double baseProb = QualityUtils.qualToProb((byte)k); baseMatchArray[k] = probToQual(baseProb); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java index a56c9e21e..63fb33295 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java @@ -37,7 +37,7 @@ public class PhasingRead extends BaseArray { public PhasingRead(int length, int mappingQual) { super(length); - this.mappingProb = new PreciseNonNegativeDouble(QualityUtils.qualToProb(mappingQual)); + this.mappingProb = new PreciseNonNegativeDouble(QualityUtils.qualToProb((byte)mappingQual)); this.baseProbs = new PreciseNonNegativeDouble[length]; Arrays.fill(this.baseProbs, null); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java index 55da1c152..f94140814 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java @@ -44,12 +44,12 @@ public class RefSeqDataParser { String nameKeyToUseMultiplePrefix = nameKeyToUse + "_"; Map entriesToNames = new HashMap(); - Integer numRecords = vc.getAttributeAsIntegerNoException(NUM_RECORDS_KEY); - if (numRecords != null) { + int numRecords = vc.getAttributeAsInt(NUM_RECORDS_KEY, -1); + if (numRecords != -1) { boolean done = false; if (numRecords == 1) { // Check if perhaps the single record doesn't end with "_1": - String name = vc.getAttributeAsStringNoException(nameKeyToUse); + String name = vc.getAttributeAsString(nameKeyToUse, null); if (name != null) { entriesToNames.put(nameKeyToUse, name); done = true; @@ -59,14 +59,14 @@ public class RefSeqDataParser { if (!done) { for (int i = 1; i <= numRecords; i++) { String key = nameKeyToUseMultiplePrefix + i; - String name = vc.getAttributeAsStringNoException(key); + String name = vc.getAttributeAsString(key, null); if (name != null) entriesToNames.put(key, name); } } } else { // no entry with the # of records: - String name = vc.getAttributeAsStringNoException(nameKeyToUse); + String name = vc.getAttributeAsString(nameKeyToUse, null); if (name != null) { entriesToNames.put(nameKeyToUse, name); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java index 59ef3d992..fd379dfda 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java @@ -109,12 +109,12 @@ public class CountVariants extends VariantEvaluator implements StandardEval { case SNP: nVariantLoci++; nSNPs++; - if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++; + if (vc1.getAttributeAsBoolean("ISSINGLETON", false)) nSingletons++; break; case MNP: nVariantLoci++; nMNPs++; - if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++; + if (vc1.getAttributeAsBoolean("ISSINGLETON", false)) nSingletons++; break; case INDEL: nVariantLoci++; @@ -136,7 +136,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval { String refStr = vc1.getReference().getBaseString().toUpperCase(); - String aaStr = vc1.hasAttribute("ANCESTRALALLELE") ? vc1.getAttributeAsString("ANCESTRALALLELE").toUpperCase() : null; + String aaStr = vc1.hasAttribute("ANCESTRALALLELE") ? vc1.getAttributeAsString("ANCESTRALALLELE", null).toUpperCase() : null; // if (aaStr.equals(".")) { // aaStr = refStr; // } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java index a476a2680..e69dbfb28 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java @@ -219,7 +219,8 @@ public class GenotypePhasingEvaluator extends VariantEvaluator { } public static Double getPQ(Genotype gt) { - return gt.getAttributeAsDoubleNoException(ReadBackedPhasingWalker.PQ_KEY); + Double d = gt.getAttributeAsDouble(ReadBackedPhasingWalker.PQ_KEY, -1); + return d == -1 ? null : d; } public static boolean topMatchesTop(AllelePair b1, AllelePair b2) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java index d466645ea..38cbf1c45 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java @@ -120,7 +120,7 @@ public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval if ( eval.hasGenotypes() ) ac = eval.getChromosomeCount(eval.getAlternateAllele(0)); else if ( eval.hasAttribute("AC") ) { - ac = Integer.valueOf(eval.getAttributeAsString("AC")); + ac = eval.getAttributeAsInt("AC", -1); } if ( ac != -1 ) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java index be957abd7..ee58012a0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java @@ -50,7 +50,7 @@ public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEv } String refStr = vc.getReference().getBaseString().toUpperCase(); - String aaStr = vc.getAttributeAsString("ANCESTRALALLELE").toUpperCase(); + String aaStr = vc.getAttributeAsString("ANCESTRALALLELE", null).toUpperCase(); if (aaStr != null && !aaStr.equalsIgnoreCase("null") && !aaStr.equals(".")) { BaseUtils.BaseSubstitutionType aaSubType = BaseUtils.SNPSubstitutionType(aaStr.getBytes()[0], vc.getAlternateAllele(0).getBases()[0]); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java index 9c331b577..7fa56785b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java @@ -130,7 +130,7 @@ public class ValidationReport extends VariantEvaluator implements StandardEval { //// System.out.printf(" ac = %d%n", ac); } else - ac = vc.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY); + ac = vc.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0); return ac > 0 ? SiteStatus.POLY : SiteStatus.MONO; } else if ( vc.hasGenotypes() ) { return vc.isPolymorphic() ? SiteStatus.POLY : SiteStatus.MONO; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java index 5cdea4e00..56b06d032 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java @@ -45,7 +45,7 @@ public class AlleleCount extends VariantStratifier { if (eval != null) { int AC = -1; if ( eval.hasAttribute("AC") && eval.getAttribute("AC") instanceof Integer ) { - AC = eval.getAttributeAsInt("AC"); + AC = eval.getAttributeAsInt("AC", 0); } else if ( eval.isVariant() ) { for (Allele allele : eval.getAlternateAlleles()) AC = Math.max(AC, eval.getChromosomeCount(allele)); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java index 96d9f30ec..ac1ee9e0e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java @@ -28,7 +28,7 @@ public class AlleleFrequency extends VariantStratifier { if (eval != null) { try { - relevantStates.add(String.format("%.3f", (5.0 * MathUtils.round(eval.getAttributeAsDouble("AF") / 5.0, 3)))); + relevantStates.add(String.format("%.3f", (5.0 * MathUtils.round(eval.getAttributeAsDouble("AF", 0.0) / 5.0, 3)))); } catch (Exception e) { return relevantStates; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java index cc878e975..06ac05ec8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java @@ -92,8 +92,8 @@ public class Degeneracy extends VariantStratifier { Integer frame = null; if (eval.hasAttribute("refseq.functionalClass")) { - aa = eval.getAttributeAsString("refseq.variantAA"); - frame = eval.getAttributeAsInt("refseq.frame"); + aa = eval.getAttributeAsString("refseq.variantAA", null); + frame = eval.getAttributeAsInt("refseq.frame", 0); } else if (eval.hasAttribute("refseq.functionalClass_1")) { int annotationId = 1; String key; @@ -101,7 +101,7 @@ public class Degeneracy extends VariantStratifier { do { key = String.format("refseq.functionalClass_%d", annotationId); - String newtype = eval.getAttributeAsString(key); + String newtype = eval.getAttributeAsString(key, null); if ( newtype != null && ( type == null || @@ -111,13 +111,13 @@ public class Degeneracy extends VariantStratifier { type = newtype; String aakey = String.format("refseq.variantAA_%d", annotationId); - aa = eval.getAttributeAsString(aakey); + aa = eval.getAttributeAsString(aakey, null); if (aa != null) { String framekey = String.format("refseq.frame_%d", annotationId); if (eval.hasAttribute(framekey)) { - frame = eval.getAttributeAsInt(framekey); + frame = eval.getAttributeAsInt(framekey, 0); } } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java index 0de871fe6..4af12fbd1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java @@ -32,7 +32,7 @@ public class FunctionalClass extends VariantStratifier { String type = null; if (eval.hasAttribute("refseq.functionalClass")) { - type = eval.getAttributeAsString("refseq.functionalClass"); + type = eval.getAttributeAsString("refseq.functionalClass", null); } else if (eval.hasAttribute("refseq.functionalClass_1")) { int annotationId = 1; String key; @@ -40,7 +40,7 @@ public class FunctionalClass extends VariantStratifier { do { key = String.format("refseq.functionalClass_%d", annotationId); - String newtype = eval.getAttributeAsString(key); + String newtype = eval.getAttributeAsString(key, null); if ( newtype != null && !newtype.equalsIgnoreCase("null") && ( type == null || diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java index bc7252ec2..04ba3ff14 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java @@ -115,7 +115,7 @@ public class VQSRCalibrationCurve { if ( vc.isFiltered() ) return 0.0; else if ( vc.hasAttribute(VQSRQualKey) ) { - double qual = vc.getAttributeAsDouble(VQSRQualKey); + double qual = vc.getAttributeAsDouble(VQSRQualKey, 0.0); return probTrueVariant(qual); } else { throw new UserException.VariantContextMissingRequiredField(VQSRQualKey, vc); @@ -143,7 +143,7 @@ public class VQSRCalibrationCurve { for ( int i = 0; i < log10Likelihoods.length; i++) { double p = Math.pow(10, log10Likelihoods[i]); double q = alpha * p + (1-alpha) * noInfoPr; - if ( DEBUG ) System.out.printf(" vqslod = %.2f, p = %.2e, alpha = %.2e, q = %.2e%n", vc.getAttributeAsDouble(VQSRQualKey), p, alpha, q); + if ( DEBUG ) System.out.printf(" vqslod = %.2f, p = %.2e, alpha = %.2e, q = %.2e%n", vc.getAttributeAsDouble(VQSRQualKey, 0.0), p, alpha, q); updated[i] = Math.log10(q); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index bb3cd82a1..ceafb0cf5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -575,7 +575,7 @@ public class SelectVariants extends RodWalker { // ok we have a comp VC and we need to match the AF spectrum of inputAFRodName. // We then pick a variant with probablity AF*desiredFraction if ( sub.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) ) { - String afo = sub.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY); + String afo = sub.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY, null); double af; double afBoost = 1.0; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 2a877fb09..aafbe4db4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -192,7 +192,7 @@ public class VariantsToTable extends RodWalker { if ( getters.containsKey(field) ) { val = getters.get(field).get(vc); } else if ( vc.hasAttribute(field) ) { - val = vc.getAttributeAsString(field); + val = vc.getAttributeAsString(field, null); } else if ( isWildCard(field) ) { Set wildVals = new HashSet(); for ( Map.Entry elt : vc.getAttributes().entrySet()) { diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java index cd320b332..94e40fc98 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java @@ -105,7 +105,10 @@ public class VCFCodec extends AbstractVCFCodec { * @return a set of the filters applied or null if filters were not applied to the record (e.g. as per the missing value in a VCF) */ protected Set parseFilters(String filterString) { + return parseFilters(filterHash, lineNo, filterString); + } + public static Set parseFilters(final Map> cache, final int lineNo, final String filterString) { // null for unfiltered if ( filterString.equals(VCFConstants.UNFILTERED) ) return null; @@ -113,13 +116,13 @@ public class VCFCodec extends AbstractVCFCodec { if ( filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) return Collections.emptySet(); if ( filterString.equals(VCFConstants.PASSES_FILTERS_v3) ) - generateException(VCFConstants.PASSES_FILTERS_v3 + " is an invalid filter name in vcf4"); + generateException(VCFConstants.PASSES_FILTERS_v3 + " is an invalid filter name in vcf4", lineNo); if ( filterString.length() == 0 ) - generateException("The VCF specification requires a valid filter status"); + generateException("The VCF specification requires a valid filter status", lineNo); // do we have the filter string cached? - if ( filterHash.containsKey(filterString) ) - return filterHash.get(filterString); + if ( cache != null && cache.containsKey(filterString) ) + return Collections.unmodifiableSet(cache.get(filterString)); // empty set for passes filters LinkedHashSet fFields = new LinkedHashSet(); @@ -129,7 +132,8 @@ public class VCFCodec extends AbstractVCFCodec { else fFields.addAll(Arrays.asList(filterString.split(VCFConstants.FILTER_CODE_SEPARATOR))); - filterHash.put(filterString, fFields); + fFields = fFields; + if ( cache != null ) cache.put(filterString, fFields); return Collections.unmodifiableSet(fFields); } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java index fdf3d97db..85d752003 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java @@ -293,17 +293,8 @@ public class Genotype { return commonInfo.getAttribute(key, defaultValue); } - public String getAttributeAsString(String key) { return commonInfo.getAttributeAsString(key); } public String getAttributeAsString(String key, String defaultValue) { return commonInfo.getAttributeAsString(key, defaultValue); } - public int getAttributeAsInt(String key) { return commonInfo.getAttributeAsInt(key); } public int getAttributeAsInt(String key, int defaultValue) { return commonInfo.getAttributeAsInt(key, defaultValue); } - public double getAttributeAsDouble(String key) { return commonInfo.getAttributeAsDouble(key); } public double getAttributeAsDouble(String key, double defaultValue) { return commonInfo.getAttributeAsDouble(key, defaultValue); } - public boolean getAttributeAsBoolean(String key) { return commonInfo.getAttributeAsBoolean(key); } public boolean getAttributeAsBoolean(String key, boolean defaultValue) { return commonInfo.getAttributeAsBoolean(key, defaultValue); } - - public Integer getAttributeAsIntegerNoException(String key) { return commonInfo.getAttributeAsIntegerNoException(key); } - public Double getAttributeAsDoubleNoException(String key) { return commonInfo.getAttributeAsDoubleNoException(key); } - public String getAttributeAsStringNoException(String key) { return commonInfo.getAttributeAsStringNoException(key); } - public Boolean getAttributeAsBooleanNoException(String key) { return commonInfo.getAttributeAsBooleanNoException(key); } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java index 3d162adb0..4266fb4b5 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java @@ -204,27 +204,40 @@ public final class InferredGeneticContext { return defaultValue; } -// public AttributedObject getAttributes(Collection keys) { -// AttributedObject selected = new AttributedObject(); -// -// for ( Object key : keys ) -// selected.putAttribute(key, this.getAttribute(key)); -// -// return selected; -// } + public String getAttributeAsString(String key, String defaultValue) { + Object x = getAttribute(key); + if ( x == null ) return defaultValue; + if ( x instanceof String ) return (String)x; + return String.valueOf(x); // throws an exception if this isn't a string + } - public String getAttributeAsString(String key) { return (String.valueOf(getAttribute(key))); } // **NOTE**: will turn a null Object into the String "null" - public int getAttributeAsInt(String key) { Object x = getAttribute(key); return x instanceof Integer ? (Integer)x : Integer.valueOf((String)x); } - public double getAttributeAsDouble(String key) { Object x = getAttribute(key); return x instanceof Double ? (Double)x : Double.valueOf((String)x); } - public boolean getAttributeAsBoolean(String key) { Object x = getAttribute(key); return x instanceof Boolean ? (Boolean)x : Boolean.valueOf((String)x); } + public int getAttributeAsInt(String key, int defaultValue) { + Object x = getAttribute(key); + if ( x == null ) return defaultValue; + if ( x instanceof Integer ) return (Integer)x; + return Integer.valueOf((String)x); // throws an exception if this isn't a string + } - public String getAttributeAsString(String key, String defaultValue) { return (String)getAttribute(key, defaultValue); } - public int getAttributeAsInt(String key, int defaultValue) { return (Integer)getAttribute(key, defaultValue); } - public double getAttributeAsDouble(String key, double defaultValue) { return (Double)getAttribute(key, defaultValue); } - public boolean getAttributeAsBoolean(String key, boolean defaultValue){ return (Boolean)getAttribute(key, defaultValue); } + public double getAttributeAsDouble(String key, double defaultValue) { + Object x = getAttribute(key); + if ( x == null ) return defaultValue; + if ( x instanceof Double ) return (Double)x; + return Double.valueOf((String)x); // throws an exception if this isn't a string + } - public Integer getAttributeAsIntegerNoException(String key) { try {return getAttributeAsInt(key);} catch (Exception e) {return null;} } - public Double getAttributeAsDoubleNoException(String key) { try {return getAttributeAsDouble(key);} catch (Exception e) {return null;} } - public String getAttributeAsStringNoException(String key) { if (getAttribute(key) == null) return null; return getAttributeAsString(key); } - public Boolean getAttributeAsBooleanNoException(String key) { try {return getAttributeAsBoolean(key);} catch (Exception e) {return null;} } + public boolean getAttributeAsBoolean(String key, boolean defaultValue) { + Object x = getAttribute(key); + if ( x == null ) return defaultValue; + if ( x instanceof Boolean ) return (Boolean)x; + return Boolean.valueOf((String)x); // throws an exception if this isn't a string + } + +// public String getAttributeAsString(String key) { return (String.valueOf(getAttribute(key))); } // **NOTE**: will turn a null Object into the String "null" +// public int getAttributeAsInt(String key) { Object x = getAttribute(key); return x instanceof Integer ? (Integer)x : Integer.valueOf((String)x); } +// public double getAttributeAsDouble(String key) { Object x = getAttribute(key); return x instanceof Double ? (Double)x : Double.valueOf((String)x); } +// public boolean getAttributeAsBoolean(String key) { Object x = getAttribute(key); return x instanceof Boolean ? (Boolean)x : Boolean.valueOf((String)x); } +// public Integer getAttributeAsIntegerNoException(String key) { try {return getAttributeAsInt(key);} catch (Exception e) {return null;} } +// public Double getAttributeAsDoubleNoException(String key) { try {return getAttributeAsDouble(key);} catch (Exception e) {return null;} } +// public String getAttributeAsStringNoException(String key) { if (getAttribute(key) == null) return null; return getAttributeAsString(key); } +// public Boolean getAttributeAsBooleanNoException(String key) { try {return getAttributeAsBoolean(key);} catch (Exception e) {return null;} } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java index 673fe4529..e6637a5d9 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -666,21 +666,11 @@ public class VariantContext implements Feature { // to enable tribble intergrati return commonInfo.getAttribute(key, defaultValue); } - public String getAttributeAsString(String key) { return commonInfo.getAttributeAsString(key); } public String getAttributeAsString(String key, String defaultValue) { return commonInfo.getAttributeAsString(key, defaultValue); } - public int getAttributeAsInt(String key) { return commonInfo.getAttributeAsInt(key); } public int getAttributeAsInt(String key, int defaultValue) { return commonInfo.getAttributeAsInt(key, defaultValue); } - public double getAttributeAsDouble(String key) { return commonInfo.getAttributeAsDouble(key); } public double getAttributeAsDouble(String key, double defaultValue) { return commonInfo.getAttributeAsDouble(key, defaultValue); } - public boolean getAttributeAsBoolean(String key) { return commonInfo.getAttributeAsBoolean(key); } public boolean getAttributeAsBoolean(String key, boolean defaultValue) { return commonInfo.getAttributeAsBoolean(key, defaultValue); } - public Integer getAttributeAsIntegerNoException(String key) { return commonInfo.getAttributeAsIntegerNoException(key); } - public Double getAttributeAsDoubleNoException(String key) { return commonInfo.getAttributeAsDoubleNoException(key); } - public String getAttributeAsStringNoException(String key) { return commonInfo.getAttributeAsStringNoException(key); } - public Boolean getAttributeAsBooleanNoException(String key) { return commonInfo.getAttributeAsBooleanNoException(key); } - - // --------------------------------------------------------------------------------------------------------- // // Working with alleles diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index 986d6305c..d5c541b19 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -565,11 +565,11 @@ public class VariantContextUtils { // special case DP (add it up) and ID (just preserve it) // if (vc.hasAttribute(VCFConstants.DEPTH_KEY)) - depth += Integer.valueOf(vc.getAttributeAsString(VCFConstants.DEPTH_KEY)); + depth += vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0); if (rsID == null && vc.hasID()) rsID = vc.getID(); if (mergeInfoWithMaxAC && vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) { - String rawAlleleCounts = vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY); + String rawAlleleCounts = vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY, null); // lets see if the string contains a , separator if (rawAlleleCounts.contains(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)) { List alleleCountArray = Arrays.asList(rawAlleleCounts.substring(1, rawAlleleCounts.length() - 1).split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)); @@ -1147,9 +1147,7 @@ public class VariantContextUtils { for (String orAttrib : MERGE_OR_ATTRIBS) { boolean attribVal = false; for (VariantContext vc : vcList) { - Boolean val = vc.getAttributeAsBooleanNoException(orAttrib); - if (val != null) - attribVal = (attribVal || val); + attribVal = vc.getAttributeAsBoolean(orAttrib, false); if (attribVal) // already true, so no reason to continue: break; } @@ -1159,7 +1157,7 @@ public class VariantContextUtils { // Merge ID fields: String iDVal = null; for (VariantContext vc : vcList) { - String val = vc.getAttributeAsStringNoException(VariantContext.ID_KEY); + String val = vc.getAttributeAsString(VariantContext.ID_KEY, null); if (val != null && !val.equals(VCFConstants.EMPTY_ID_FIELD)) { if (iDVal == null) iDVal = val; @@ -1239,8 +1237,10 @@ public class VariantContextUtils { public PhaseAndQuality(Genotype gt) { this.isPhased = gt.isPhased(); - if (this.isPhased) - this.PQ = gt.getAttributeAsDoubleNoException(ReadBackedPhasingWalker.PQ_KEY); + if (this.isPhased) { + this.PQ = gt.getAttributeAsDouble(ReadBackedPhasingWalker.PQ_KEY, -1); + if ( this.PQ == -1 ) this.PQ = null; + } } }