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[ADAM-1682] Add variant quality field. #1684

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merged 3 commits into from Oct 11, 2017
Merged

[ADAM-1682] Add variant quality field. #1684

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100e633
[ADAM-1682] Add variant quality field.
fnothaft Aug 25, 2017
02d6699
Remove info logger in VariantContextConverter that spams the logs.
fnothaft Sep 6, 2017
d97af9e
Bump and pull in split from multiallelic in Variant.
fnothaft Sep 14, 2017
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47 changes: 38 additions & 9 deletions adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
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Expand Up @@ -286,12 +286,10 @@ class VariantContextConverter(
def convert(
vc: HtsjdkVariantContext): Seq[ADAMVariantContext] = {

log.info("Processing %s with alt alleles %s.".format(vc, vc.getAlternateAlleles.toList.mkString(",")))

try {
vc.getAlternateAlleles.toList match {
case List(NON_REF_ALLELE) | List() => {
val variant = variantFormatFn(vc, None, 0)
val variant = variantFormatFn(vc, None, 0, false)
val genotypes = vc.getGenotypes.map(g => {
genotypeFormatFn(g, variant, NON_REF_ALLELE, 0, Some(1), false)
})
Expand All @@ -302,7 +300,7 @@ class VariantContextConverter(
allele.isNonReference,
"Assertion failed when converting: " + vc.toString
)
val variant = variantFormatFn(vc, Some(allele.getDisplayString), 0)
val variant = variantFormatFn(vc, Some(allele.getDisplayString), 0, false)
val genotypes = vc.getGenotypes.map(g => {
genotypeFormatFn(g, variant, allele, 1, None, false)
})
Expand All @@ -313,7 +311,7 @@ class VariantContextConverter(
allele.isNonReference,
"Assertion failed when converting: " + vc.toString
)
val variant = variantFormatFn(vc, Some(allele.getDisplayString), 0)
val variant = variantFormatFn(vc, Some(allele.getDisplayString), 0, false)
val genotypes = vc.getGenotypes.map(g => {
genotypeFormatFn(g, variant, allele, 1, Some(2), false)
})
Expand Down Expand Up @@ -344,7 +342,8 @@ class VariantContextConverter(
val variantIdx = idx - 1
val variant = variantFormatFn(vc,
Some(allele.getDisplayString),
variantIdx)
variantIdx,
true)
val genotypes = vc.getGenotypes.map(g => {
genotypeFormatFn(g, variant, allele, idx, referenceModelIndex, true)
})
Expand Down Expand Up @@ -405,6 +404,17 @@ class VariantContextConverter(
splitIds(vc).fold(vb)(vb.setNames(_))
}

private[converters] def formatQuality(
vc: HtsjdkVariantContext,
vb: Variant.Builder): Variant.Builder = {

if (vc.hasLog10PError) {
vb.setQuality(vc.getPhredScaledQual)
} else {
vb
}
}

private[converters] def formatFilters(
vc: HtsjdkVariantContext,
vb: Variant.Builder): Variant.Builder = {
Expand All @@ -421,6 +431,7 @@ class VariantContextConverter(

private val variantFormatFns: Iterable[(HtsjdkVariantContext, Variant.Builder) => Variant.Builder] = Iterable(
formatNames(_, _),
formatQuality(_, _),
formatFilters(_, _)
)

Expand All @@ -433,6 +444,17 @@ class VariantContextConverter(
joinNames(v).fold(vcb.noID())(vcb.id(_))
}

private[converters] def extractQuality(
v: Variant,
vcb: VariantContextBuilder): VariantContextBuilder = {

if (v.getQuality != null) {
vcb.log10PError(-v.getQuality / 10.0)
} else {
vcb
}
}

private[converters] def extractFilters(
v: Variant,
vcb: VariantContextBuilder): VariantContextBuilder = {
Expand All @@ -457,6 +479,7 @@ class VariantContextConverter(

private val variantExtractFns: Iterable[(Variant, VariantContextBuilder) => VariantContextBuilder] = Iterable(
extractNames(_, _),
extractQuality(_, _),
extractFilters(_, _)
)

Expand Down Expand Up @@ -1553,7 +1576,7 @@ class VariantContextConverter(
}

private def makeVariantFormatFn(
headerLines: Seq[VCFHeaderLine]): (HtsjdkVariantContext, Option[String], Int) => Variant = {
headerLines: Seq[VCFHeaderLine]): (HtsjdkVariantContext, Option[String], Int, Boolean) => Variant = {

val attributeFns: Iterable[(HtsjdkVariantContext, Int, Array[Int]) => Option[(String, String)]] = headerLines
.flatMap(hl => hl match {
Expand All @@ -1576,7 +1599,8 @@ class VariantContextConverter(

def convert(vc: HtsjdkVariantContext,
alt: Option[String],
alleleIdx: Int): Variant = {
alleleIdx: Int,
wasSplit: Boolean): Variant = {

// create the builder
val variantBuilder = Variant.newBuilder
Expand All @@ -1585,6 +1609,11 @@ class VariantContextConverter(
.setEnd(vc.getEnd)
.setReferenceAllele(vc.getReference.getBaseString)

// was this split?
if (wasSplit) {
variantBuilder.setSplitFromMultiAllelic(true)
}

alt.foreach(variantBuilder.setAlternateAllele(_))

// bind the conversion functions and fold
Expand Down Expand Up @@ -1651,7 +1680,7 @@ class VariantContextConverter(
variantBuilder.build
}

convert(_, _, _)
convert(_, _, _, _)
}

private def makeGenotypeFormatFn(
Expand Down
12 changes: 6 additions & 6 deletions adam-core/src/test/resources/sorted-variants.lex.vcf
View file
Open in desktop
Expand Up @@ -66,9 +66,9 @@
##contig=<ID=2,length=249250621>
##contig=<ID=13,length=249250621>
#CHROM POS ID REF ALT QUAL FILTER INFO
1 14397 . CTGT C . IndelQD AC=2;AF=0.333;AN=6;BaseQRankSum=1.8;ClippingRankSum=0.138;DP=69;FS=7.786;MLEAC=2;MLEAF=0.333;MQ=26.84;MQ0=0;MQRankSum=-1.906;QD=1.55;ReadPosRankSum=0.384
1 14522 . G A . VQSRTrancheSNP99.95to100.00 AC=2;AF=0.333;AN=6;BaseQRankSum=2.044;ClippingRankSum=-2.196;DP=48;FS=13.179;MLEAC=2;MLEAF=0.333;MQ=25.89;MQ0=0;MQRankSum=-0.063;QD=8.87;ReadPosRankSum=0.952;VQSLOD=-3.333;culprit=MQ
1 63735 rs201888535 CCTA C . PASS AC=1;AF=0.167;AN=6;BaseQRankSum=1.138;ClippingRankSum=0.448;DB;DP=176;FS=13.597;MLEAC=1;MLEAF=0.167;MQ=31.06;MQ0=0;MQRankSum=0.636;QD=9.98;ReadPosRankSum=-1.18
13 752721 rs3131972 A G . PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD
13 752791 . A G . PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD
2 19190 . GC G . PASS AC=3;AF=0.5;AN=6;BaseQRankSum=4.157;ClippingRankSum=3.666;DP=74;FS=37.037;MLEAC=3;MLEAF=0.5;MQ=22.26;MQ0=0;MQRankSum=0.195;QD=16.04;ReadPosRankSum=-4.072
1 14397 . CTGT C 139.12 IndelQD AC=2;AF=0.333;AN=6;BaseQRankSum=1.8;ClippingRankSum=0.138;DP=69;FS=7.786;MLEAC=2;MLEAF=0.333;MQ=26.84;MQ0=0;MQRankSum=-1.906;QD=1.55;ReadPosRankSum=0.384
1 14522 . G A 195.16 VQSRTrancheSNP99.95to100.00 AC=2;AF=0.333;AN=6;BaseQRankSum=2.044;ClippingRankSum=-2.196;DP=48;FS=13.179;MLEAC=2;MLEAF=0.333;MQ=25.89;MQ0=0;MQRankSum=-0.063;QD=8.87;ReadPosRankSum=0.952;VQSLOD=-3.333;culprit=MQ
1 63735 rs201888535 CCTA C 2994.09 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=1.138;ClippingRankSum=0.448;DB;DP=176;FS=13.597;MLEAC=1;MLEAF=0.167;MQ=31.06;MQ0=0;MQRankSum=0.636;QD=9.98;ReadPosRankSum=-1.18
13 752721 rs3131972 A G 2486.90 PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD
13 752791 . A G 2486.90 PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD
2 19190 . GC G 1186.88 PASS AC=3;AF=0.5;AN=6;BaseQRankSum=4.157;ClippingRankSum=3.666;DP=74;FS=37.037;MLEAC=3;MLEAF=0.5;MQ=22.26;MQ0=0;MQRankSum=0.195;QD=16.04;ReadPosRankSum=-4.072
12 changes: 6 additions & 6 deletions adam-core/src/test/resources/sorted-variants.vcf
View file
Open in desktop
Expand Up @@ -66,9 +66,9 @@
##contig=<ID=2,length=249250621>
##contig=<ID=13,length=249250621>
#CHROM POS ID REF ALT QUAL FILTER INFO
1 14397 . CTGT C . IndelQD AC=2;AF=0.333;AN=6;BaseQRankSum=1.8;ClippingRankSum=0.138;DP=69;FS=7.786;MLEAC=2;MLEAF=0.333;MQ=26.84;MQ0=0;MQRankSum=-1.906;QD=1.55;ReadPosRankSum=0.384
1 14522 . G A . VQSRTrancheSNP99.95to100.00 AC=2;AF=0.333;AN=6;BaseQRankSum=2.044;ClippingRankSum=-2.196;DP=48;FS=13.179;MLEAC=2;MLEAF=0.333;MQ=25.89;MQ0=0;MQRankSum=-0.063;QD=8.87;ReadPosRankSum=0.952;VQSLOD=-3.333;culprit=MQ
1 63735 rs201888535 CCTA C . PASS AC=1;AF=0.167;AN=6;BaseQRankSum=1.138;ClippingRankSum=0.448;DB;DP=176;FS=13.597;MLEAC=1;MLEAF=0.167;MQ=31.06;MQ0=0;MQRankSum=0.636;QD=9.98;ReadPosRankSum=-1.18
2 19190 . GC G . PASS AC=3;AF=0.5;AN=6;BaseQRankSum=4.157;ClippingRankSum=3.666;DP=74;FS=37.037;MLEAC=3;MLEAF=0.5;MQ=22.26;MQ0=0;MQRankSum=0.195;QD=16.04;ReadPosRankSum=-4.072
13 752721 rs3131972 A G . PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD
13 752791 . A G . PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD
1 14397 . CTGT C 139.12 IndelQD AC=2;AF=0.333;AN=6;BaseQRankSum=1.8;ClippingRankSum=0.138;DP=69;FS=7.786;MLEAC=2;MLEAF=0.333;MQ=26.84;MQ0=0;MQRankSum=-1.906;QD=1.55;ReadPosRankSum=0.384
1 14522 . G A 195.16 VQSRTrancheSNP99.95to100.00 AC=2;AF=0.333;AN=6;BaseQRankSum=2.044;ClippingRankSum=-2.196;DP=48;FS=13.179;MLEAC=2;MLEAF=0.333;MQ=25.89;MQ0=0;MQRankSum=-0.063;QD=8.87;ReadPosRankSum=0.952;VQSLOD=-3.333;culprit=MQ
1 63735 rs201888535 CCTA C 2994.09 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=1.138;ClippingRankSum=0.448;DB;DP=176;FS=13.597;MLEAC=1;MLEAF=0.167;MQ=31.06;MQ0=0;MQRankSum=0.636;QD=9.98;ReadPosRankSum=-1.18
2 19190 . GC G 1186.88 PASS AC=3;AF=0.5;AN=6;BaseQRankSum=4.157;ClippingRankSum=3.666;DP=74;FS=37.037;MLEAC=3;MLEAF=0.5;MQ=22.26;MQ0=0;MQRankSum=0.195;QD=16.04;ReadPosRankSum=-4.072
13 752721 rs3131972 A G 2486.90 PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD
13 752791 . A G 2486.90 PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD
12 changes: 6 additions & 6 deletions adam-core/src/test/resources/sorted.lex.vcf
View file
Open in desktop
Expand Up @@ -66,9 +66,9 @@
##contig=<ID=2,length=249250621>
##contig=<ID=13,length=249250621>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12891 NA12892
1 14397 . CTGT C . IndelQD AC=2;AF=0.333;AN=6;BaseQRankSum=1.8;ClippingRankSum=0.138;DP=69;FS=7.786;MLEAC=2;MLEAF=0.333;MQ=26.84;MQ0=0;MQRankSum=-1.906;QD=1.55;ReadPosRankSum=0.384 GT:AD:DP:FT:GQ:PL 0/1:16,4:20:rd:99:120,0,827 0/1:8,2:10:dp;rd:60:60,0,414 0/0:39,0:39:PASS:99:0,116,2114
1 14522 . G A . VQSRTrancheSNP99.95to100.00 AC=2;AF=0.333;AN=6;BaseQRankSum=2.044;ClippingRankSum=-2.196;DP=48;FS=13.179;MLEAC=2;MLEAF=0.333;MQ=25.89;MQ0=0;MQRankSum=-0.063;QD=8.87;ReadPosRankSum=0.952;VQSLOD=-3.333;culprit=MQ GT:AD:DP:FT:GQ:PL 0/1:10,5:15:dp:99:99,0,2147483647 0/1:2,5:7:dp;rd:34:128,0,34 0/0:26,0:26:PASS:78:0,78,783
1 63735 rs201888535 CCTA C . PASS AC=1;AF=0.167;AN=6;BaseQRankSum=1.138;ClippingRankSum=0.448;DB;DP=176;FS=13.597;MLEAC=1;MLEAF=0.167;MQ=31.06;MQ0=0;MQRankSum=0.636;QD=9.98;ReadPosRankSum=-1.18 GT:AD:DP:FT:GQ:PL 0/0:27,0:27:PASS:79:0,79,1425 0/0:40,0:40:PASS:99:0,117,2120 0/1:23,74:97:rd:99:3034,0,942
13 752721 rs3131972 A G . PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD GT:AD:DP:FT:GQ:PL 1/1:0,27:27:PASS:81:1021,81,0 1/1:0,19:19:dp:57:661,57,0 1/1:0,22:22:PASS:66:831,66,0
13 752791 . A G . PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD GT:AD:DP:FT:GQ:PL:SB 1/1:0,27:27:PASS:81:1021,81,0:0,1,2,3 1/1:0,19:19:dp:57:661,57,0:4,5,6,7 1/1:0,22:22:PASS:66:831,66,0:2,3,4,5
2 19190 . GC G . PASS AC=3;AF=0.5;AN=6;BaseQRankSum=4.157;ClippingRankSum=3.666;DP=74;FS=37.037;MLEAC=3;MLEAF=0.5;MQ=22.26;MQ0=0;MQRankSum=0.195;QD=16.04;ReadPosRankSum=-4.072 GT:AD:DP:FT:GQ:PL 0/1:8,14:22:PASS:99:416,0,2147483647 0/1:18,13:31:PASS:99:353,0,503 0/1:5,15:20:rd:99:457,0,107
1 14397 . CTGT C 139.12 IndelQD AC=2;AF=0.333;AN=6;BaseQRankSum=1.8;ClippingRankSum=0.138;DP=69;FS=7.786;MLEAC=2;MLEAF=0.333;MQ=26.84;MQ0=0;MQRankSum=-1.906;QD=1.55;ReadPosRankSum=0.384 GT:AD:DP:FT:GQ:PL 0/1:16,4:20:rd:99:120,0,827 0/1:8,2:10:dp;rd:60:60,0,414 0/0:39,0:39:PASS:99:0,116,2114
1 14522 . G A 195.16 VQSRTrancheSNP99.95to100.00 AC=2;AF=0.333;AN=6;BaseQRankSum=2.044;ClippingRankSum=-2.196;DP=48;FS=13.179;MLEAC=2;MLEAF=0.333;MQ=25.89;MQ0=0;MQRankSum=-0.063;QD=8.87;ReadPosRankSum=0.952;VQSLOD=-3.333;culprit=MQ GT:AD:DP:FT:GQ:PL 0/1:10,5:15:dp:99:99,0,2147483647 0/1:2,5:7:dp;rd:34:128,0,34 0/0:26,0:26:PASS:78:0,78,783
1 63735 rs201888535 CCTA C 2994.09 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=1.138;ClippingRankSum=0.448;DB;DP=176;FS=13.597;MLEAC=1;MLEAF=0.167;MQ=31.06;MQ0=0;MQRankSum=0.636;QD=9.98;ReadPosRankSum=-1.18 GT:AD:DP:FT:GQ:PL 0/0:27,0:27:PASS:79:0,79,1425 0/0:40,0:40:PASS:99:0,117,2120 0/1:23,74:97:rd:99:3034,0,942
13 752721 rs3131972 A G 2486.90 PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD GT:AD:DP:FT:GQ:PL 1/1:0,27:27:PASS:81:1021,81,0 1/1:0,19:19:dp:57:661,57,0 1/1:0,22:22:PASS:66:831,66,0
13 752791 . A G 2486.90 PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD GT:AD:DP:FT:GQ:PL:SB 1/1:0,27:27:PASS:81:1021,81,0:0,1,2,3 1/1:0,19:19:dp:57:661,57,0:4,5,6,7 1/1:0,22:22:PASS:66:831,66,0:2,3,4,5
2 19190 . GC G 1186.88 PASS AC=3;AF=0.5;AN=6;BaseQRankSum=4.157;ClippingRankSum=3.666;DP=74;FS=37.037;MLEAC=3;MLEAF=0.5;MQ=22.26;MQ0=0;MQRankSum=0.195;QD=16.04;ReadPosRankSum=-4.072 GT:AD:DP:FT:GQ:PL 0/1:8,14:22:PASS:99:416,0,2147483647 0/1:18,13:31:PASS:99:353,0,503 0/1:5,15:20:rd:99:457,0,107
12 changes: 6 additions & 6 deletions adam-core/src/test/resources/sorted.vcf
View file
Open in desktop
Expand Up @@ -66,9 +66,9 @@
##contig=<ID=2,length=249250621>
##contig=<ID=13,length=249250621>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12891 NA12892
1 14397 . CTGT C . IndelQD AC=2;AF=0.333;AN=6;BaseQRankSum=1.8;ClippingRankSum=0.138;DP=69;FS=7.786;MLEAC=2;MLEAF=0.333;MQ=26.84;MQ0=0;MQRankSum=-1.906;QD=1.55;ReadPosRankSum=0.384 GT:AD:DP:FT:GQ:PL 0/1:16,4:20:rd:99:120,0,827 0/1:8,2:10:dp;rd:60:60,0,414 0/0:39,0:39:PASS:99:0,116,2114
1 14522 . G A . VQSRTrancheSNP99.95to100.00 AC=2;AF=0.333;AN=6;BaseQRankSum=2.044;ClippingRankSum=-2.196;DP=48;FS=13.179;MLEAC=2;MLEAF=0.333;MQ=25.89;MQ0=0;MQRankSum=-0.063;QD=8.87;ReadPosRankSum=0.952;VQSLOD=-3.333;culprit=MQ GT:AD:DP:FT:GQ:PL 0/1:10,5:15:dp:99:99,0,2147483647 0/1:2,5:7:dp;rd:34:128,0,34 0/0:26,0:26:PASS:78:0,78,783
1 63735 rs201888535 CCTA C . PASS AC=1;AF=0.167;AN=6;BaseQRankSum=1.138;ClippingRankSum=0.448;DB;DP=176;FS=13.597;MLEAC=1;MLEAF=0.167;MQ=31.06;MQ0=0;MQRankSum=0.636;QD=9.98;ReadPosRankSum=-1.18 GT:AD:DP:FT:GQ:PL 0/0:27,0:27:PASS:79:0,79,1425 0/0:40,0:40:PASS:99:0,117,2120 0/1:23,74:97:rd:99:3034,0,942
2 19190 . GC G . PASS AC=3;AF=0.5;AN=6;BaseQRankSum=4.157;ClippingRankSum=3.666;DP=74;FS=37.037;MLEAC=3;MLEAF=0.5;MQ=22.26;MQ0=0;MQRankSum=0.195;QD=16.04;ReadPosRankSum=-4.072 GT:AD:DP:FT:GQ:PL 0/1:8,14:22:PASS:99:416,0,2147483647 0/1:18,13:31:PASS:99:353,0,503 0/1:5,15:20:rd:99:457,0,107
13 752721 rs3131972 A G . PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD GT:AD:DP:FT:GQ:PL 1/1:0,27:27:PASS:81:1021,81,0 1/1:0,19:19:dp:57:661,57,0 1/1:0,22:22:PASS:66:831,66,0
13 752791 . A G . PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD GT:AD:DP:FT:GQ:PL:SB 1/1:0,27:27:PASS:81:1021,81,0:0,1,2,3 1/1:0,19:19:dp:57:661,57,0:4,5,6,7 1/1:0,22:22:PASS:66:831,66,0:2,3,4,5
1 14397 . CTGT C 139.12 IndelQD AC=2;AF=0.333;AN=6;BaseQRankSum=1.8;ClippingRankSum=0.138;DP=69;FS=7.786;MLEAC=2;MLEAF=0.333;MQ=26.84;MQ0=0;MQRankSum=-1.906;QD=1.55;ReadPosRankSum=0.384 GT:AD:DP:FT:GQ:PL 0/1:16,4:20:rd:99:120,0,827 0/1:8,2:10:dp;rd:60:60,0,414 0/0:39,0:39:PASS:99:0,116,2114
1 14522 . G A 195.16 VQSRTrancheSNP99.95to100.00 AC=2;AF=0.333;AN=6;BaseQRankSum=2.044;ClippingRankSum=-2.196;DP=48;FS=13.179;MLEAC=2;MLEAF=0.333;MQ=25.89;MQ0=0;MQRankSum=-0.063;QD=8.87;ReadPosRankSum=0.952;VQSLOD=-3.333;culprit=MQ GT:AD:DP:FT:GQ:PL 0/1:10,5:15:dp:99:99,0,2147483647 0/1:2,5:7:dp;rd:34:128,0,34 0/0:26,0:26:PASS:78:0,78,783
1 63735 rs201888535 CCTA C 2994.09 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=1.138;ClippingRankSum=0.448;DB;DP=176;FS=13.597;MLEAC=1;MLEAF=0.167;MQ=31.06;MQ0=0;MQRankSum=0.636;QD=9.98;ReadPosRankSum=-1.18 GT:AD:DP:FT:GQ:PL 0/0:27,0:27:PASS:79:0,79,1425 0/0:40,0:40:PASS:99:0,117,2120 0/1:23,74:97:rd:99:3034,0,942
2 19190 . GC G 1186.88 PASS AC=3;AF=0.5;AN=6;BaseQRankSum=4.157;ClippingRankSum=3.666;DP=74;FS=37.037;MLEAC=3;MLEAF=0.5;MQ=22.26;MQ0=0;MQRankSum=0.195;QD=16.04;ReadPosRankSum=-4.072 GT:AD:DP:FT:GQ:PL 0/1:8,14:22:PASS:99:416,0,2147483647 0/1:18,13:31:PASS:99:353,0,503 0/1:5,15:20:rd:99:457,0,107
13 752721 rs3131972 A G 2486.90 PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD GT:AD:DP:FT:GQ:PL 1/1:0,27:27:PASS:81:1021,81,0 1/1:0,19:19:dp:57:661,57,0 1/1:0,22:22:PASS:66:831,66,0
13 752791 . A G 2486.90 PASS AC=6;AF=1.0;AN=6;DB;DP=69;FS=0.0;MLEAC=6;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.67;VQSLOD=18.94;culprit=QD GT:AD:DP:FT:GQ:PL:SB 1/1:0,27:27:PASS:81:1021,81,0:0,1,2,3 1/1:0,19:19:dp:57:661,57,0:4,5,6,7 1/1:0,22:22:PASS:66:831,66,0:2,3,4,5
35 changes: 35 additions & 0 deletions adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala
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Expand Up @@ -336,6 +336,7 @@ class VariantContextConverterSuite extends ADAMFunSuite {

for (adamVC <- adamVCs) {
assert(adamVC.genotypes.size === 1)
assert(adamVC.variant.variant.getSplitFromMultiAllelic)
val adamGT = adamVC.genotypes.head
assert(adamGT.getSplitFromMultiAllelic)
assert(adamGT.getReferenceReadDepth === 4)
Expand Down Expand Up @@ -1206,6 +1207,22 @@ class VariantContextConverterSuite extends ADAMFunSuite {
assert(v.getNames.get(1) === "secondName")
}

test("no quality going htsjdk->adam") {
val v = buildVariant(Map.empty,
converter.formatQuality)
assert(v.getQuality === null)
}

test("quality set going htsjdk->adam") {
val v = buildVariant(Map.empty,
converter.formatQuality,
fns = Iterable((vcb: VariantContextBuilder) => {
vcb.log10PError(-10.0)
}))
assert(v.getQuality > 99.9)
assert(v.getQuality < 100.1)
}

test("no filters applied going htsjdk->adam") {
val v = buildVariant(Map.empty,
converter.formatFilters,
Expand Down Expand Up @@ -1283,6 +1300,24 @@ class VariantContextConverterSuite extends ADAMFunSuite {
assert(vc.getID === "name1;name2")
}

test("no qual set adam->htsjdk") {
val vc = converter.extractQuality(emptyV, htsjdkSNVBuilder)
.make

assert(!vc.hasLog10PError)
}

test("qual is set adam->htsjdk") {
val vc = converter.extractQuality(Variant.newBuilder
.setQuality(100.0)
.build, htsjdkSNVBuilder)
.make

assert(vc.hasLog10PError)
assert(vc.getPhredScaledQual > 99.9)
assert(vc.getPhredScaledQual < 100.1)
}

test("no filters applied adam->htsjdk") {
val vc = converter.extractFilters(Variant.newBuilder
.setFiltersApplied(false)
Expand Down
2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -27,7 +27,7 @@
<hadoop.version>2.7.3</hadoop.version>
<hadoop-bam.version>7.9.0</hadoop-bam.version>
<slf4j.version>1.7.25</slf4j.version>
<bdg-formats.version>0.11.1</bdg-formats.version>
<bdg-formats.version>0.11.3</bdg-formats.version>
<bdg-utils.version>0.2.13</bdg-utils.version>
<htsjdk.version>2.11.0</htsjdk.version>
<scoverage.plugin.version>1.1.1</scoverage.plugin.version>
Expand Down