[ADAM-1570] Upgrade to bdg-formats 0.11.1.

Resolves #1570.
bigdatagenomics · Jun 22, 2017 · 8cf09f6 · 8cf09f6
1 parent 412d092
commit 8cf09f6
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Showing 6 changed files with 37 additions and 32 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
@@ -255,6 +255,14 @@ class VariantContextConverter(
    */
   private def jFloat(f: Float): java.lang.Float = f
 
+  /**
+   * Converts a Scala double to a Java double.
+   *
+   * @param f Scala double precision floating point value.
+   * @return Java double precision floating point value.
+   */
+  private def jDouble(f: Double): java.lang.Double = f
+
   /**
    * Converts a GATK variant context into one or more ADAM variant context(s).
    *
@@ -818,7 +826,7 @@ class VariantContextConverter(
       val pl = g.getPL
       try {
         val likelihoods = gIndices.map(idx => {
-          jFloat(PhredUtils.phredToLogProbability(pl(idx)).toFloat)
+          jDouble(PhredUtils.phredToLogProbability(pl(idx)))
         }).toList
         gb.setGenotypeLikelihoods(likelihoods)
       } catch {
@@ -838,7 +846,7 @@ class VariantContextConverter(
     if (g.hasPL) {
       val pl = g.getPL
       gb.setNonReferenceLikelihoods(gIndices.map(idx => {
-        jFloat(PhredUtils.phredToLogProbability(pl(idx)).toFloat)
+        jDouble(PhredUtils.phredToLogProbability(pl(idx)))
       }).toList)
     } else {
       gb
@@ -968,8 +976,8 @@ class VariantContextConverter(
     plCalculator(copyNumber)
   }
 
-  private[converters] def nonRefPls(gls: java.util.List[java.lang.Float],
-                                    nls: java.util.List[java.lang.Float]): Array[Int] = {
+  private[converters] def nonRefPls(gls: java.util.List[java.lang.Double],
+                                    nls: java.util.List[java.lang.Double]): Array[Int] = {
     require(gls.length == nls.length,
       "Genotype likelihoods (%s) and non-reference likelihoods (%s) disagree on copy number".format(
         gls.mkString(","), nls.mkString(",")))
@@ -979,12 +987,12 @@ class VariantContextConverter(
     val array = Array.fill(elements) { Int.MinValue }
 
     (0 to copyNumber).foreach(idx => {
-      array(idx) = PhredUtils.logProbabilityToPhred(gls.get(idx).toDouble)
+      array(idx) = PhredUtils.logProbabilityToPhred(gls.get(idx))
     })
 
     var cnIdx = copyNumber + 1
     (1 to copyNumber).foreach(idx => {
-      array(cnIdx + 1) = PhredUtils.logProbabilityToPhred(nls.get(idx).toDouble)
+      array(cnIdx + 1) = PhredUtils.logProbabilityToPhred(nls.get(idx))
       cnIdx += (copyNumber - idx)
     })
 
@@ -1004,11 +1012,11 @@ class VariantContextConverter(
         }
         gb.noPL
       } else {
-        gb.PL(nls.map(l => PhredUtils.logProbabilityToPhred(l.toDouble))
+        gb.PL(nls.map(l => PhredUtils.logProbabilityToPhred(l))
           .toArray)
       }
     } else if (nls.isEmpty) {
-      gb.PL(gls.map(l => PhredUtils.logProbabilityToPhred(l.toDouble))
+      gb.PL(gls.map(l => PhredUtils.logProbabilityToPhred(l))
         .toArray)
     } else {
       gb.PL(nonRefPls(gls, nls))

diff --git a/adam-core/src/test/resources/gvcf_multiallelic/multiallelic.vcf b/adam-core/src/test/resources/gvcf_multiallelic/multiallelic.vcf
@@ -136,6 +136,6 @@
 chr22	16157521	.	C	<NON_REF>	.	.	END=16157602	GT:DP:GQ:MIN_DP:PL	0/0:4:9:2:0,0,45
 chr22	16157603	.	G	C,<NON_REF>	.	.	DP=1;MLEAC=1;MLEAF=0.5;MQ=59.0;MQ0=0	GT:AD:DP:GQ:PL	1/1:0,1:1:3:41,3,0,-2147483648,41,41
 chr22	16157604	.	G	<NON_REF>	.	.	END=16157639	GT:DP:GQ:MIN_DP:PL	0/0:2:0:1:0,0,0
-chr22	18030096	.	TAAA	T,<NON_REF>	.	.	BaseQRankSum=-0.133;ClippingRankSum=-1.438;DP=114;MLEAC=0;MLEAF=0.0;MQ=69.72;MQ0=0;MQRankSum=-0.686;ReadPosRankSum=-0.013	GT:AD:DP:GQ:PL	./.:13,3:50:86:2147483647,2147483647,2147483647,-2147483648,2147483647,2147483647
-chr22	18030096	.	TAAA	TA,<NON_REF>	.	.	BaseQRankSum=-0.133;ClippingRankSum=-1.438;DP=114;MLEAC=1;MLEAF=0.5;MQ=69.72;MQ0=0;MQRankSum=-0.686;ReadPosRankSum=-0.013	GT:AD:DP:GQ:PL	1/.:13,17:50:86:2147483647,86,2147483647,-2147483648,2147483647,2147483647
-chr22	18030096	.	TAAA	TAA,<NON_REF>	.	.	BaseQRankSum=-0.133;ClippingRankSum=-1.438;DP=114;MLEAC=1;MLEAF=0.5;MQ=69.72;MQ0=0;MQRankSum=-0.686;ReadPosRankSum=-0.013	GT:AD:DP:GQ:PL	./1:13,17:50:86:2147483647,137,281,-2147483648,2147483647,2147483647
+chr22	18030096	.	TAAA	T,<NON_REF>	.	.	BaseQRankSum=-0.133;ClippingRankSum=-1.438;DP=114;MLEAC=0;MLEAF=0.0;MQ=69.72;MQ0=0;MQRankSum=-0.686;ReadPosRankSum=-0.013	GT:AD:DP:GQ:PL	./.:13,3:50:86:602,508,1628,-2147483648,467,659
+chr22	18030096	.	TAAA	TA,<NON_REF>	.	.	BaseQRankSum=-0.133;ClippingRankSum=-1.438;DP=114;MLEAC=1;MLEAF=0.5;MQ=69.72;MQ0=0;MQRankSum=-0.686;ReadPosRankSum=-0.013	GT:AD:DP:GQ:PL	1/.:13,17:50:86:602,86,553,-2147483648,467,659
+chr22	18030096	.	TAAA	TAA,<NON_REF>	.	.	BaseQRankSum=-0.133;ClippingRankSum=-1.438;DP=114;MLEAC=1;MLEAF=0.5;MQ=69.72;MQ0=0;MQRankSum=-0.686;ReadPosRankSum=-0.013	GT:AD:DP:GQ:PL	./1:13,17:50:86:602,137,281,-2147483648,467,659
diff --git a/adam-core/src/test/resources/sorted.lex.vcf b/adam-core/src/test/resources/sorted.lex.vcf
@@ -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:99:120,0,2147483647	0/1:8,2:10:dp;rd:60:60,0,414	0/0:39,0:39:PASS:99:0,116,2147483647
-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:78:0,78,2147483647
-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:79:0,79,2147483647	0/0:40,0:40:PASS:99:0,117,2147483647	0/1:23,74:97:rd:99:2147483647,0,2147483647
-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:81:2147483647,81,0	1/1:0,19:19:dp:57:2147483647,57,0	1/1:0,22:22:PASS:66:2147483647,66,0
-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:81:2147483647,81,0:0,1,2,3	1/1:0,19:19:dp:57:2147483647,57,0:4,5,6,7	1/1:0,22:22:PASS:66:2147483647,66,0:2,3,4,5
-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:99:353,0,2147483647	0/1:5,15:20:rd:99:2147483647,0,107
+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
diff --git a/adam-core/src/test/resources/sorted.vcf b/adam-core/src/test/resources/sorted.vcf
@@ -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:99:120,0,2147483647	0/1:8,2:10:dp;rd:60:60,0,414	0/0:39,0:39:PASS:99:0,116,2147483647
-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:78:0,78,2147483647
-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:79:0,79,2147483647	0/0:40,0:40:PASS:99:0,117,2147483647	0/1:23,74:97:rd:99:2147483647,0,2147483647
-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:99:353,0,2147483647	0/1:5,15:20:rd:99:2147483647,0,107
-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:81:2147483647,81,0	1/1:0,19:19:dp:57:2147483647,57,0	1/1:0,22:22:PASS:66:2147483647,66,0
-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:81:2147483647,81,0:0,1,2,3	1/1:0,19:19:dp:57:2147483647,57,0:4,5,6,7	1/1:0,22:22:PASS:66:2147483647,66,0:2,3,4,5
+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
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala
@@ -343,16 +343,14 @@ class VariantContextConverterSuite extends ADAMFunSuite {
     assert(adamGT1.getAlleles.sameElements(List(GenotypeAllele.ALT, GenotypeAllele.OTHER_ALT)))
     assert(adamGT1.getAlternateReadDepth === 2)
     assert(adamGT1.getGenotypeLikelihoods
-      .map(f => f: scala.Float)
-      .map(_.toDouble)
+      .map(d => d: scala.Double)
       .map(PhredUtils.logProbabilityToPhred)
       .sameElements(List(59, 0, Int.MaxValue)))
 
     assert(adamGT2.getAlleles.sameElements(List(GenotypeAllele.OTHER_ALT, GenotypeAllele.ALT)))
     assert(adamGT2.getAlternateReadDepth === 3)
     assert(adamGT2.getGenotypeLikelihoods
-      .map(f => f: scala.Float)
-      .map(_.toDouble)
+      .map(d => d: scala.Double)
       .map(PhredUtils.logProbabilityToPhred)
       .sameElements(List(59, 1, 102)))
 
@@ -392,8 +390,7 @@ class VariantContextConverterSuite extends ADAMFunSuite {
     assert(adamGT.getMinReadDepth === 38)
     assert(adamGT.getGenotypeLikelihoods.isEmpty)
     assert(adamGT.getNonReferenceLikelihoods
-      .map(f => f: scala.Float)
-      .map(_.toDouble)
+      .map(d => d: scala.Double)
       .map(PhredUtils.logProbabilityToPhred)
       .sameElements(List(0, 1, 2)))
   }
@@ -925,8 +922,8 @@ class VariantContextConverterSuite extends ADAMFunSuite {
 
   test("extract genotype likelihoods going adam->htsjdk") {
     val g = converter.extractGenotypeLikelihoods(Genotype.newBuilder
-      .setGenotypeLikelihoods(Seq(-0.1f, -0.001f, -0.000001f)
-        .map(f => f: java.lang.Float))
+      .setGenotypeLikelihoods(Seq(-0.1, -0.001, -0.000001)
+        .map(d => d: java.lang.Double))
       .build, newGb)
       .make
 

diff --git a/pom.xml b/pom.xml
@@ -30,7 +30,7 @@
     <hadoop.version>2.7.3</hadoop.version>
     <hadoop-bam.version>7.8.0</hadoop-bam.version>
     <slf4j.version>1.7.22</slf4j.version>
-    <bdg-formats.version>0.11.0</bdg-formats.version>
+    <bdg-formats.version>0.11.1-SNAPSHOT</bdg-formats.version>
     <bdg-utils.version>0.2.13</bdg-utils.version>
     <htsjdk.version>2.9.1</htsjdk.version>
     <scoverage.plugin.version>1.1.1</scoverage.plugin.version>