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All definition unit tests fixed.
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@lester-pharmgkb
lester-pharmgkb committed Jan 9, 2017
1 parent b9e2b1f commit c01cdb0
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Showing 15 changed files with 26 additions and 21 deletions.
4 changes: 2 additions & 2 deletions src/test/java/org/pharmgkb/pharmcat/haplotype/NamedAlleleMatcherCyp2c9Test.java
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Expand Up @@ -49,10 +49,10 @@ public void cyp32c9s2s3() throws Exception {

@Test
public void cyp32c9s2s24() throws Exception {
// Test *2/*24, but also matches *1/*24
// Test *2/*24, but also matches *1/*2

Path vcfFile = PathUtils.getPathToResource("org/pharmgkb/pharmcat/haplotype/cyp2c9/s2s24.vcf");
List<String> expectedMatches = Lists.newArrayList("*1/*24", "*2/*24");
List<String> expectedMatches = Lists.newArrayList("*1/*2", "*2/*24");

Result result = testMatchNamedAlleles(m_definitionFile, vcfFile);
assertDiplotypePairs(expectedMatches, result);
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4 changes: 2 additions & 2 deletions src/test/java/org/pharmgkb/pharmcat/haplotype/NamedAlleleMatcherCyp3a5Test.java
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Expand Up @@ -27,7 +27,7 @@ public void before() throws Exception {

@Test
public void cyp3a5s3s9() throws Exception {
// Test *3/*9. Note Y in 99672916 position
// Test *3/*9.

Path vcfFile = PathUtils.getPathToResource("org/pharmgkb/pharmcat/haplotype/cyp3a5/s3s9.vcf");
List<String> expectedMatches = Lists.newArrayList("*3/*9");
Expand All @@ -51,7 +51,7 @@ public void cyp3a5s1s7() throws Exception {
@Test
public void cyp3a5s3s9Homozygous() throws Exception {
Path vcfFile = PathUtils.getPathToResource("org/pharmgkb/pharmcat/haplotype/cyp3a5/s3s9-homozygous.vcf");
List<String> expectedMatches = Lists.newArrayList("*3/*3", "*3/*9", "*9/*9");
List<String> expectedMatches = Lists.newArrayList("*3/*9");

Result result = NamedAlleleMatcherTest.testMatchNamedAlleles(m_definitionFile, vcfFile, true, false, true);
assertDiplotypePairs(expectedMatches, result);
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2 changes: 1 addition & 1 deletion src/test/java/org/pharmgkb/pharmcat/haplotype/NamedAlleleMatcherTest.java
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Expand Up @@ -28,7 +28,7 @@ public class NamedAlleleMatcherTest {


static Result testMatchNamedAlleles(@Nonnull Path tsvFile, @Nonnull Path vcfFile) throws Exception {
return testMatchNamedAlleles(tsvFile, vcfFile, true, false, false);
return testMatchNamedAlleles(tsvFile, vcfFile, true, false, true);
}

/**
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2 changes: 1 addition & 1 deletion src/test/resources/org/pharmgkb/pharmcat/haplotype/UGT1A1/s1s1.vcf
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Expand Up @@ -7,6 +7,6 @@
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr2 233757013 rs4124874 T . . PASS assume-default GT 0/0
chr2 233759924 rs887829 C . . PASS assume-default GT 0/0
chr2 233760234 . ATATATATATATATAA ATATATATATATATATAA,ATATATATATATAA,ATATATATATATATATATAA . PASS s28s36s37-needs-normalization GT 0/0
chr2 233760233 . CAT CATAT,C,CATATAT . PASS PX=UGT1A1:*1[5]isCAT,UGT1A1:*28[1]isCATAT,UGT1A1:*36[1]isC,UGT1A1:*37[1]isCATATAT; GT 0/0
chr2 233760498 rs4148323 G . . PASS assume-default GT 0/0
chr2 233760973 rs35350960 C . . PASS assume-default GT 0/0
2 changes: 1 addition & 1 deletion src/test/resources/org/pharmgkb/pharmcat/haplotype/UGT1A1/s28s37.vcf
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Expand Up @@ -7,6 +7,6 @@
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr2 233757013 rs4124874 T . . PASS assume-default GT 0/0
chr2 233759924 rs887829 C . . PASS assume-default GT 0/0
chr2 233760234 . ATATATATATATATAA ATATATATATATATATAA,ATATATATATATAA,ATATATATATATATATATAA . PASS s28s36s37-needs-normalization GT 1/3
chr2 233760233 . CAT CATAT,C,CATATAT . PASS PX=UGT1A1:*1[5]isCAT,UGT1A1:*28[1]isCATAT,UGT1A1:*36[1]isC,UGT1A1:*37[1]isCATATAT; GT 1/3
chr2 233760498 rs4148323 G . . PASS assume-default GT 0/0
chr2 233760973 rs35350960 C . . PASS assume-default GT 0/0
2 changes: 1 addition & 1 deletion src/test/resources/org/pharmgkb/pharmcat/haplotype/UGT1A1/s28s80.vcf
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Expand Up @@ -7,6 +7,6 @@
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr2 233757013 rs4124874 T . . PASS assume-default GT 0/0
chr2 233759924 rs887829 C T . PASS s80 GT 0/1
chr2 233760234 . ATAA ATATATATATATATAA,ATATATATATATAA,ATATATATATATATATATAA . PASS 8Ns28_6Ns36_8Ns37 GT 0/2
chr2 233760233 . CAT CATAT,C,CATATAT . PASS PX=UGT1A1:*1[5]isCAT,UGT1A1:*28[1]isCATAT,UGT1A1:*36[1]isC,UGT1A1:*37[1]isCATATAT; GT 0/2
chr2 233760498 rs4148323 G . . PASS assume-default GT 0/0
chr2 233760973 rs35350960 C . . PASS assume-default GT 0/0
2 changes: 1 addition & 1 deletion src/test/resources/org/pharmgkb/pharmcat/haplotype/UGT1A1/s6s6.vcf
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Expand Up @@ -7,6 +7,6 @@
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr2 233757013 rs4124874 T . . PASS assume-default GT 0/0
chr2 233759924 rs887829 C . . PASS assume-default GT 0/0
chr2 233760234 . ATATATATATATATAA ATATATATATATATATAA,ATATATATATATAA,ATATATATATATATATATAA . PASS s28s36s37-needs-normalization GT 0/0
chr2 233760233 . CAT CATAT,C,CATATAT . PASS PX=UGT1A1:*1[5]isCAT,UGT1A1:*28[1]isCATAT,UGT1A1:*36[1]isC,UGT1A1:*37[1]isCATATAT; GT 0/0
chr2 233760498 rs4148323 G A . PASS star-6 GT 1/1
chr2 233760973 rs35350960 C . . PASS assume-default GT 0/0
2 changes: 1 addition & 1 deletion src/test/resources/org/pharmgkb/pharmcat/haplotype/cyp2c19/s1s2.vcf
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Expand Up @@ -22,7 +22,7 @@ chr10 94775106 rs145328984 C . . PASS assume-default GT 0/0
chr10 94775121 . C . . PASS assume-default GT 0/0
chr10 94775160 rs118203756 G . . PASS assume-default GT 0/0
chr10 94775185 . A . . PASS assume-default GT 0/0
chr10 94775367 rs12769205 A . . PASS assume-default GT 0/0
chr10 94775367 rs12769205 A G . PASS assume-default GT 0/1
chr10 94775416 rs41291556 T . . PASS assume-default GT 0/0
chr10 94775453 rs72552267  G . . PASS assume-default GT 0/0
chr10 94775489 rs17884712 G . . PASS assume-default GT 0/0
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2 changes: 1 addition & 1 deletion src/test/resources/org/pharmgkb/pharmcat/haplotype/cyp2c19/s2s2.vcf
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Expand Up @@ -22,7 +22,7 @@ chr10 94775106 rs145328984 C . . PASS assume-default GT 0/0
chr10 94775121 . C . . PASS assume-default GT 0/0
chr10 94775160 rs118203756 G . . PASS assume-default GT 0/0
chr10 94775185 . A . . PASS assume-default GT 0/0
chr10 94775367 rs12769205 A . . PASS assume-default GT 0/0
chr10 94775367 rs12769205 A G . PASS assume-default GT 1/1
chr10 94775416 rs41291556 T . . PASS assume-default GT 0/0
chr10 94775453 rs72552267  G . . PASS assume-default GT 0/0
chr10 94775489 rs17884712 G . . PASS assume-default GT 0/0
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2 changes: 1 addition & 1 deletion src/test/resources/org/pharmgkb/pharmcat/haplotype/cyp2c19/s2s3.vcf
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Expand Up @@ -22,7 +22,7 @@ chr10 94775106 rs145328984 C . . PASS assume-default GT 0/0
chr10 94775121 . C . . PASS assume-default GT 0/0
chr10 94775160 rs118203756 G . . PASS assume-default GT 0/0
chr10 94775185 . A . . PASS assume-default GT 0/0
chr10 94775367 rs12769205 A . . PASS assume-default GT 0/0
chr10 94775367 rs12769205 A G . PASS assume-default GT 0/1
chr10 94775416 rs41291556 T . . PASS assume-default GT 0/0
chr10 94775453 rs72552267  G . . PASS assume-default GT 0/0
chr10 94775489 rs17884712 G . . PASS assume-default GT 0/0
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2 changes: 1 addition & 1 deletion src/test/resources/org/pharmgkb/pharmcat/haplotype/cyp2c9/s24s24.vcf
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Expand Up @@ -25,7 +25,7 @@ chr10 94942234 rs72558189 G A . PASS assume-default GT 0/0
chr10 94942249 rs200965026 C G,T . PASS assume-default GT 0/0
chr10 94942254 rs199523631 C T . PASS assume-default GT 0/0
chr10 94942255 rs200183364 G A . PASS assume-default GT 0/0
chr10 94942290 rs1799853 C T . PASS assume-default GT 0/1
chr10 94942290 rs1799853 C T . PASS assume-default GT 0/0
chr10 94942305 rs754487195 G A . PASS assume-default GT 0/0
chr10 94942309 rs7900194 G A,T . PASS assume-default GT 0/0
chr10 94947782 rs72558190 C A . PASS assume-default GT 0/0
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2 changes: 1 addition & 1 deletion src/test/resources/org/pharmgkb/pharmcat/haplotype/cyp2c9/s2s24.vcf
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Expand Up @@ -25,7 +25,7 @@ chr10 94942234 rs72558189 G A . PASS assume-default GT 0/0
chr10 94942249 rs200965026 C G,T . PASS assume-default GT 0/0
chr10 94942254 rs199523631 C T . PASS assume-default GT 0/0
chr10 94942255 rs200183364 G A . PASS assume-default GT 0/0
chr10 94942290 rs1799853 C T . PASS assume-default GT 0/1
chr10 94942290 rs1799853 C T . PASS assume-default GT 1/0
chr10 94942305 rs754487195 G A . PASS assume-default GT 0/0
chr10 94942309 rs7900194 G A,T . PASS assume-default GT 0/0
chr10 94947782 rs72558190 C A . PASS assume-default GT 0/0
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4 changes: 2 additions & 2 deletions src/test/resources/org/pharmgkb/pharmcat/haplotype/cyp2c9/s2s24only.vcf
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Expand Up @@ -25,7 +25,7 @@ chr10 94942234 rs72558189 G A . PASS assume-default GT 0/0
chr10 94942249 rs200965026 C G,T . PASS assume-default GT 0/0
chr10 94942254 rs199523631 C T . PASS assume-default GT 0/0
chr10 94942255 rs200183364 G A . PASS assume-default GT 0/0
chr10 94942290 rs1799853 C T . PASS assume-default GT 1/1
chr10 94942290 rs1799853 C T . PASS assume-default GT 0/1
chr10 94942305 rs754487195 G A . PASS assume-default GT 0/0
chr10 94942309 rs7900194 G A,T . PASS assume-default GT 0/0
chr10 94947782 rs72558190 C A . PASS assume-default GT 0/0
Expand All @@ -48,7 +48,7 @@ chr10 94981201 rs57505750 T C . PASS assume-default GT 0/0
chr10 94981224 rs28371685 C T . PASS assume-default GT 0/0
chr10 94981225 rs367826293 G A . PASS assume-default GT 0/0
chr10 94981250 rs750820937 C A . PASS assume-default GT 0/0
chr10 94981281 rs749060448 G A . PASS assume-default GT 0/1
chr10 94981281 rs749060448 G A . PASS assume-default GT 1/1
chr10 94981296 rs1057910 A C . PASS assume-default GT 0/0
chr10 94981297 rs56165452 T C . PASS assume-default GT 0/0
chr10 94981301 rs28371686 C G . PASS assume-default GT 0/0
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11 changes: 8 additions & 3 deletions src/test/resources/org/pharmgkb/pharmcat/haplotype/cyp3a5/s3s9-homozygous.vcf
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Expand Up @@ -5,6 +5,11 @@
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FILTER=<ID=PASS,Description="All filters passed">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr7 99652770 rs41303343 T TA 487.65 . AC=0;AF=0.006579;AN=2;BaseQRankSum=-1.045;ClippingRankSum=2.457;DB;DP=2794;FS=0;MLEAC=1;MLEAF=0.006579;MQ=59.34;MQRankSum=-0.16;QD=15.24;ReadPosRankSum=-0.626;SOR=0.659 GT:AD:DP:GQ:PL 0/0:32,0:32:96:0,96,1199
chr7 99665212 rs10264272 C T 1185.93 . AC=0;AF=0.013;AN=2;BaseQRankSum=-0.815;ClippingRankSum=-0.51;DB;DP=3172;FS=0;MLEAC=2;MLEAF=0.013;MQ=59.08;MQRankSum=-1.012;QD=19.13;ReadPosRankSum=2.173;SOR=0.68 GT:AD:DP:GQ:PL 0/0:31,0:31:93:0,93,1260
chr7 99672916 rs776746 C T 17718.5 . AC=0;AF=0.191;AN=2;BaseQRankSum=0.956;ClippingRankSum=1.14;DB;DP=2428;FS=1.439;MLEAC=29;MLEAF=0.191;MQ=59.04;MQRankSum=1.377;QD=27.39;ReadPosRankSum=-0.127;SOR=0.537 GT:AD:DP:GQ:PL 0/0:30,0:30:90:0,90,1256
chr7 99676198 rs55817950 G . . PASS assume-default GT 0/0
chr7 99672916 rs776746 T C . PASS star-3-star-9 GT 0/1
chr7 99666950 rs55965422 A . . PASS assume-default GT 0/0
chr7 99665237 rs56411402 T . . PASS assume-default GT 0/0
chr7 99665212 rs10264272 C . . PASS assume-default GT 0/0
chr7 99660516 rs28383479 C T . PASS star-9 GT 1/1
chr7 99652770 rs41303343 T . . PASS assume-default GT 0/0
chr7 99652613 rs28365083 G . . PASS assume-default GT 0/0
4 changes: 2 additions & 2 deletions src/test/resources/org/pharmgkb/pharmcat/haplotype/cyp3a5/s3s9.vcf
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Expand Up @@ -6,10 +6,10 @@
##FILTER=<ID=PASS,Description="All filters passed">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr7 99676198 rs55817950 G . . PASS assume-default GT 0/0
chr7 99672916 rs776746 T C . PASS star-3-star-9 GT 1/1
chr7 99672916 rs776746 T C . PASS star-3-star-9 GT 1|0
chr7 99666950 rs55965422 A . . PASS assume-default GT 0/0
chr7 99665237 rs56411402 T . . PASS assume-default GT 0/0
chr7 99665212 rs10264272 C . . PASS assume-default GT 0/0
chr7 99660516 rs28383479 C T . PASS star-9 GT 0/1
chr7 99660516 rs28383479 C T . PASS star-9 GT 0|1
chr7 99652770 rs41303343 T . . PASS assume-default GT 0/0
chr7 99652613 rs28365083 G . . PASS assume-default GT 0/0

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