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loadGenotypes three time #1480

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xubo245 opened this Issue Apr 9, 2017 · 0 comments

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@xubo245

xubo245 commented Apr 9, 2017

loadGenotypes three time in ADAM

Should it be one time?

in org.bdgenomics.adam.rdd.variant.GenotypeRDDSuite:

code:

  sparkTest("use broadcast join to pull down genotypes mapped to targets") {
    val genotypesPath = testFile("small.vcf")
    val targetsPath = testFile("small.1.bed")

    val genotypes = sc.loadGenotypes(genotypesPath)
    genotypes.rdd.foreach(println)
    val targets = sc.loadFeatures(targetsPath)

    val jRdd = genotypes.broadcastRegionJoin(targets)

    assert(jRdd.rdd.count === 9L)
  }

result:


2017-04-09 16:31:46 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
{"variant": {"contigName": "1", "start": 14396, "end": 14400, "names": [], "referenceAllele": "CTGT", "alternateAllele": "C", "filtersApplied": true, "filtersPassed": false, "filtersFailed": ["IndelQD"], "annotation": {"ancestralAllele": null, "alleleCount": 2, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "referenceReverseReadDepth": null, "alleleFrequency": 0.333, "cigar": null, "dbSnp": null, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attributes": {"MQ0": "0", "ReadPosRankSum": "0.384", "AN": "6", "FS": "7.786", "DP": "69", "ClippingRankSum": "0.138", "BaseQRankSum": "1.8", "MLEAF": "0.333", "MLEAC": "2", "MQ": "26.84", "QD": "1.55", "MQRankSum": "-1.906"}}}, "contigName": "1", "start": 14396, "end": 14400, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": false, "filtersFailed": ["rd"], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 16, "alternateReadDepth": 4, "readDepth": 20, "minReadDepth": null, "genotypeQuality": 99, "genotypeLikelihoods": [-9.999779E-13, "-Infinity", 0.0], "nonReferenceLikelihoods": [], "strandBiasComponents": [], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}
{"variant": {"contigName": "1", "start": 14396, "end": 14400, "names": [], "referenceAllele": "CTGT", "alternateAllele": "C", "filtersApplied": true, "filtersPassed": false, "filtersFailed": ["IndelQD"], "annotation": {"ancestralAllele": null, "alleleCount": 2, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "referenceReverseReadDepth": null, "alleleFrequency": 0.333, "cigar": null, "dbSnp": null, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attributes": {"MQ0": "0", "ReadPosRankSum": "0.384", "AN": "6", "FS": "7.786", "DP": "69", "ClippingRankSum": "0.138", "BaseQRankSum": "1.8", "MLEAF": "0.333", "MLEAC": "2", "MQ": "26.84", "QD": "1.55", "MQRankSum": "-1.906"}}}, "contigName": "1", "start": 14396, "end": 14400, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": false, "filtersFailed": ["dp", "rd"], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12891", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 8, "alternateReadDepth": 2, "readDepth": 10, "minReadDepth": null, "genotypeQuality": 60, "genotypeLikelihoods": [-1.0000005E-6, "-Infinity", 0.0], "nonReferenceLikelihoods": [], "strandBiasComponents": [], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}
{"variant": {"contigName": "1", "start": 14396, "end": 14400, "names": [], "referenceAllele": "CTGT", "alternateAllele": "C", "filtersApplied": true, "filtersPassed": false, "filtersFailed": ["IndelQD"], "annotation": {"ancestralAllele": null, "alleleCount": 2, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "referenceReverseReadDepth": null, "alleleFrequency": 0.333, "cigar": null, "dbSnp": null, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attributes": {"MQ0": "0", "ReadPosRankSum": "0.384", "AN": "6", "FS": "7.786", "DP": "69", "ClippingRankSum": "0.138", "BaseQRankSum": "1.8", "MLEAF": "0.333", "MLEAC": "2", "MQ": "26.84", "QD": "1.55", "MQRankSum": "-1.906"}}}, "contigName": "1", "start": 14396, "end": 14400, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12892", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "REF"], "expectedAlleleDosage": null, "referenceReadDepth": 39, "alternateReadDepth": 0, "readDepth": 39, "minReadDepth": null, "genotypeQuality": 99, "genotypeLikelihoods": ["-Infinity", -2.5118796E-12, 0.0], "nonReferenceLikelihoods": [], "strandBiasComponents": [], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}
{"variant": {"contigName": "1", "start": 14521, "end": 14522, "names": [], "referenceAllele": "G", "alternateAllele": "A", "filtersApplied": true, "filtersPassed": false, "filtersFailed": ["VQSRTrancheSNP99.95to100.00"], "annotation": {"ancestralAllele": null, "alleleCount": 2, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "referenceReverseReadDepth": null, "alleleFrequency": 0.333, "cigar": null, "dbSnp": null, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attributes": {"culprit": "MQ", "MQ0": "0", "ReadPosRankSum": "0.952", "AN": "6", "FS": "13.179", "DP": "48", "VQSLOD": "-3.333", "ClippingRankSum": "-2.196", "BaseQRankSum": "2.044", "MLEAF": "0.333", "MLEAC": "2", "MQ": "25.89", "QD": "8.87", "MQRankSum": "-0.063"}}}, "contigName": "1", "start": 14521, "end": 14522, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": false, "filtersFailed": ["dp"], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 10, "alternateReadDepth": 5, "readDepth": 15, "minReadDepth": null, "genotypeQuality": 99, "genotypeLikelihoods": [-1.2589252E-10, "-Infinity", 0.0], "nonReferenceLikelihoods": [], "strandBiasComponents": [], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}
{"variant": {"contigName": "1", "start": 14521, "end": 14522, "names": [], "referenceAllele": "G", "alternateAllele": "A", "filtersApplied": true, "filtersPassed": false, "filtersFailed": ["VQSRTrancheSNP99.95to100.00"], "annotation": {"ancestralAllele": null, "alleleCount": 2, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "referenceReverseReadDepth": null, "alleleFrequency": 0.333, "cigar": null, "dbSnp": null, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attributes": {"culprit": "MQ", "MQ0": "0", "ReadPosRankSum": "0.952", "AN": "6", "FS": "13.179", "DP": "48", "VQSLOD": "-3.333", "ClippingRankSum": "-2.196", "BaseQRankSum": "2.044", "MLEAF": "0.333", "MLEAC": "2", "MQ": "25.89", "QD": "8.87", "MQRankSum": "-0.063"}}}, "contigName": "1", "start": 14521, "end": 14522, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": false, "filtersFailed": ["dp", "rd"], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12891", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 2, "alternateReadDepth": 5, "readDepth": 7, "minReadDepth": null, "genotypeQuality": 34, "genotypeLikelihoods": [-1.5853985E-13, "-Infinity", -3.9818644E-4], "nonReferenceLikelihoods": [], "strandBiasComponents": [], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}
{"variant": {"contigName": "1", "start": 14521, "end": 14522, "names": [], "referenceAllele": "G", "alternateAllele": "A", "filtersApplied": true, "filtersPassed": false, "filtersFailed": ["VQSRTrancheSNP99.95to100.00"], "annotation": {"ancestralAllele": null, "alleleCount": 2, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "referenceReverseReadDepth": null, "alleleFrequency": 0.333, "cigar": null, "dbSnp": null, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attributes": {"culprit": "MQ", "MQ0": "0", "ReadPosRankSum": "0.952", "AN": "6", "FS": "13.179", "DP": "48", "VQSLOD": "-3.333", "ClippingRankSum": "-2.196", "BaseQRankSum": "2.044", "MLEAF": "0.333", "MLEAC": "2", "MQ": "25.89", "QD": "8.87", "MQRankSum": "-0.063"}}}, "contigName": "1", "start": 14521, "end": 14522, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12892", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "REF"], "expectedAlleleDosage": null, "referenceReadDepth": 26, "alternateReadDepth": 0, "readDepth": 26, "minReadDepth": null, "genotypeQuality": 78, "genotypeLikelihoods": ["-Infinity", -1.5848933E-8, 0.0], "nonReferenceLikelihoods": [], "strandBiasComponents": [], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}
{"variant": {"contigName": "1", "start": 19189, "end": 19191, "names": [], "referenceAllele": "GC", "alternateAllele": "G", "filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "annotation": {"ancestralAllele": null, "alleleCount": 3, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "referenceReverseReadDepth": null, "alleleFrequency": 0.5, "cigar": null, "dbSnp": null, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attributes": {"MQ0": "0", "ReadPosRankSum": "-4.072", "AN": "6", "FS": "37.037", "DP": "74", "ClippingRankSum": "3.666", "BaseQRankSum": "4.157", "MLEAF": "0.500", "MLEAC": "3", "MQ": "22.26", "QD": "16.04", "MQRankSum": "0.195"}}}, "contigName": "1", "start": 19189, "end": 19191, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 8, "alternateReadDepth": 14, "readDepth": 22, "minReadDepth": null, "genotypeQuality": 99, "genotypeLikelihoods": [0.0, "-Infinity", 0.0], "nonReferenceLikelihoods": [], "strandBiasComponents": [], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}
{"variant": {"contigName": "1", "start": 19189, "end": 19191, "names": [], "referenceAllele": "GC", "alternateAllele": "G", "filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "annotation": {"ancestralAllele": null, "alleleCount": 3, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "referenceReverseReadDepth": null, "alleleFrequency": 0.5, "cigar": null, "dbSnp": null, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attributes": {"MQ0": "0", "ReadPosRankSum": "-4.072", "AN": "6", "FS": "37.037", "DP": "74", "ClippingRankSum": "3.666", "BaseQRankSum": "4.157", "MLEAF": "0.500", "MLEAC": "3", "MQ": "22.26", "QD": "16.04", "MQRankSum": "0.195"}}}, "contigName": "1", "start": 19189, "end": 19191, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12891", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 18, "alternateReadDepth": 13, "readDepth": 31, "minReadDepth": null, "genotypeQuality": 99, "genotypeLikelihoods": [0.0, "-Infinity", 0.0], "nonReferenceLikelihoods": [], "strandBiasComponents": [], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}
{"variant": {"contigName": "1", "start": 19189, "end": 19191, "names": [], "referenceAllele": "GC", "alternateAllele": "G", "filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "annotation": {"ancestralAllele": null, "alleleCount": 3, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "referenceReverseReadDepth": null, "alleleFrequency": 0.5, "cigar": null, "dbSnp": null, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attributes": {"MQ0": "0", "ReadPosRankSum": "-4.072", "AN": "6", "FS": "37.037", "DP": "74", "ClippingRankSum": "3.666", "BaseQRankSum": "4.157", "MLEAF": "0.500", "MLEAC": "3", "MQ": "22.26", "QD": "16.04", "MQRankSum": "0.195"}}}, "contigName": "1", "start": 19189, "end": 19191, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": false, "filtersFailed": ["rd"], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12892", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": 5, "alternateReadDepth": 15, "readDepth": 20, "minReadDepth": null, "genotypeQuality": 99, "genotypeLikelihoods": [0.0, "-Infinity", -1.9952595E-11], "nonReferenceLikelihoods": [], "strandBiasComponents": [], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}
{"variant": {"contigName": "1", "start": 63734, "end": 63738, "names": ["rs201888535"], "referenceAllele": "CCTA", "alternateAllele": "C", "filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "annotation": {"ancestralAllele": null, "alleleCount": 1, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "referenceReverseReadDepth": null, "alleleFrequency": 0.167, "cigar": null, "dbSnp": true, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attributes": {"MQ0": "0", "ReadPosRankSum": "-1.18", "AN": "6", "FS": "13.597", "DP": "176", "ClippingRankSum": "0.448", "BaseQRankSum": "1.138", "MLEAF": "0.167", "MLEAC": "1", "MQ": "31.06", "QD": "9.98", "MQRankSum": "0.636"}}}, "contigName": "1", "start": 63734, "end": 63738, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "REF"], "expectedAlleleDosage": null, "referenceReadDepth": 27, "alternateReadDepth": 0, "readDepth": 27, "minReadDepth": null, "genotypeQuality": 79, "genotypeLikelihoods": ["-Infinity", -1.2589254E-8, 0.0], "nonReferenceLikelihoods": [], "strandBiasComponents": [], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}
{"variant": {"contigName": "1", "start": 63734, "end": 63738, "names": ["rs201888535"], "referenceAllele": "CCTA", "alternateAllele": "C", "filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "annotation": {"ancestralAllele": null, "alleleCount": 1, "readDepth": null, "forwardReadDepth": null, "reverseReadDepth": null, "referenceReadDepth": null, "referenceForwardReadDepth": null, "referenceReverseReadDepth": null, "alleleFrequency": 0.167, "cigar": null, "dbSnp": true, "hapMap2": null, "hapMap3": null, "validated": null, "thousandGenomes": null, "somatic": false, "transcriptEffects": [], "attributes": {"MQ0": "0", "ReadPosRankSum": "-1.18", "AN": "6", "FS": "13.597", "DP": "176", "ClippingRankSum": "0.448", "BaseQRankSum": "1.138", "MLEAF": "0.167", "MLEAC": "1", "MQ": "31.06", "QD": "9.98", "MQRankSum": "0.636"}}}, "contigName": "1", "start": 63734, "end": 63738, "variantCallingAnnotations": {"filtersApplied": true, "filtersPassed": true, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": null, "rmsMapQ": null, "mapq0Reads": null, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12891", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "REF"], "expectedAlleleDosage": null, "referenceReadDepth": 40, "alternateReadDepth": 0, "readDepth": 40, "minReadDepth": null, "genotypeQuality": 99, "genotypeLikelihoods": ["-Infinity", -1.9952928E-12, 0.0], "nonReferenceLikelihoods": [], "strandBiasComponents": [], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}
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@xubo245 xubo245 closed this Apr 9, 2017

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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