| Previous changeset 0:d67642a21a1d (2022-01-28) |
|
Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9" |
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modified:
pharmcat.xml test-data/test_1.pheno.json test-data/test_2.html test-data/test_2.json test-data/test_3.json test-data/test_4.json |
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| diff -r d67642a21a1d -r 891283e0ee89 pharmcat.xml --- a/pharmcat.xml Fri Jan 28 21:18:23 2022 +0000 +++ b/pharmcat.xml Thu May 05 20:27:17 2022 +0000 |
| [ |
| @@ -3,11 +3,11 @@ Pharmacogenomics Clinical Annotation Tool </description> <macros> - <token name="@WRAPPER_VERSION@">1.3.1</token> + <token name="@WRAPPER_VERSION@">1.7.0</token> <token name="@VERSION_SUFFIX@">galaxy0</token> </macros> <requirements> - <container type="docker">pgkb/pharmcat:1.3.1</container> + <container type="docker">pgkb/pharmcat:1.7.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[ ## NAMECALLER FUNCTION @@ -72,14 +72,16 @@ <option value="report">Only reporter</option> </param> <when value="all"> - <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> + <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" + help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> <param name="outside_call" argument="-a" type="data" format="tsv,tabular" label="Gene call TSV file from an outside tool" optional="true"/> <param name="json" argument="-j" type="boolean" truevalue="-j" falsevalue="" label="Output reporter JSON report"/> <param name="phenojson" argument="-pj" type="boolean" truevalue="-pj" falsevalue="" label="Output phenotyper JSON report"/> <!-- <param name="definitions" argument="-na" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> --> </when> <when value="name"> - <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> + <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" + help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> <!-- <param name="definitions" argument="-d" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> --> </when> <when value="pheno"> @@ -89,7 +91,8 @@ <option value="named">Run from the output of the NamedAlleleMatcher</option> </param> <when value="vcf"> - <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> + <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" + help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> </when> <when value="named"> <param name="input" argument="-c" type="data" format="json" label="Input json file" help="JSON output of the NamedAlleleCaller pharmcat function"/> @@ -133,8 +136,8 @@ <!-- ALL FUNCTION --> <test expect_num_outputs="3"> <conditional name="function_select"> - <param name="input" ftype="vcf" value="test.vcf"/> - <param name="outside_call" ftype="tabular" value="test.tsv"/> + <param name="input" value="test.vcf" ftype="vcf" /> + <param name="outside_call" value="test.tsv" ftype="tabular"/> <param name="json" value="-j"/> <param name="phenojson" value="-pj"/> </conditional> @@ -158,10 +161,10 @@ <test expect_num_outputs="2"> <conditional name="function_select"> <param name="function" value="name"/> - <param name="input" ftype="vcf" value="test.vcf"/> + <param name="input" value="test.vcf" ftype="vcf"/> </conditional> - <output name="namer_html" file="test_2.html" lines_diff="2"/> - <output name="namer_json" file="test_2.json" lines_diff="2"/> + <output name="namer_html" file="test_2.html" lines_diff="4" ftype="html" /> + <output name="namer_json" file="test_2.json" lines_diff="2" ftype="json" /> </test> <!-- PHENOTYPER FROM VCF WITH OUTSIDE CALLER--> <test expect_num_outputs="1"> @@ -180,18 +183,18 @@ <conditional name="function_select"> <param name="function" value="pheno"/> <conditional name="method"> - <param name="pheno_function" value="named"/> - <param name="input" value="test_2.json"/> + <param name="pheno_function" value="named" /> + <param name="input" value="test_2.json" ftype="json" /> </conditional> </conditional> - <output name="pheno_json" file="test_4.json" lines_diff="1"/> + <output name="pheno_json" file="test_4.json" lines_diff="34"/> </test> <!-- REPORTER --> <test expect_num_outputs="2"> <conditional name="function_select"> + <param name="input" value="test_3.json" ftype="json"/> <param name="function" value="report"/> - <param name="input" value="test_3.json"/> - <param name="text" value="test text"/> + <param name="text" value="test text"/> </conditional> <output name="report_json"> <assert_contents> @@ -215,4 +218,4 @@ <citations> <citation type="doi" >10.1002/cpt.928</citation> </citations> -</tool> \ No newline at end of file +</tool> |
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| diff -r d67642a21a1d -r 891283e0ee89 test-data/test_1.pheno.json --- a/test-data/test_1.pheno.json Fri Jan 28 21:18:23 2022 +0000 +++ b/test-data/test_1.pheno.json Thu May 05 20:27:17 2022 +0000 |
| [ |
| b'@@ -1,5 +1,90 @@\n [\n {\n+ "geneSymbol": "ABCG2",\n+ "chr": "chr4",\n+ "phased": true,\n+ "callSource": "MATCHER",\n+ "uncalledHaplotypes": [\n+ "rs2231142 reference (G)",\n+ "rs2231142 variant (T)"\n+ ],\n+ "messages": [],\n+ "relatedDrugs": [\n+ {\n+ "name": "rosuvastatin",\n+ "guidelineId": "RxNorm:301542"\n+ }\n+ ],\n+ "matcherDiplotypes": [\n+ {\n+ "allele1": {\n+ "gene": "ABCG2",\n+ "name": "Unknown",\n+ "function": "Unassigned function",\n+ "reference": false\n+ },\n+ "allele2": {\n+ "gene": "ABCG2",\n+ "name": "Unknown",\n+ "function": "Unassigned function",\n+ "reference": false\n+ },\n+ "gene": "ABCG2",\n+ "phenotypes": [\n+ "No Result"\n+ ],\n+ "variant": null,\n+ "lookupKey": [\n+ "No Result"\n+ ],\n+ "label": "Unknown/Unknown"\n+ }\n+ ],\n+ "diplotypes": [\n+ {\n+ "allele1": {\n+ "gene": "ABCG2",\n+ "name": "Unknown",\n+ "function": "Unassigned function",\n+ "reference": false\n+ },\n+ "allele2": {\n+ "gene": "ABCG2",\n+ "name": "Unknown",\n+ "function": "Unassigned function",\n+ "reference": false\n+ },\n+ "gene": "ABCG2",\n+ "phenotypes": [\n+ "No Result"\n+ ],\n+ "variant": null,\n+ "lookupKey": [\n+ "No Result"\n+ ],\n+ "label": "Unknown/Unknown"\n+ }\n+ ],\n+ "variants": [\n+ {\n+ "gene": "ABCG2",\n+ "chromosome": "chr4",\n+ "position": 88131171,\n+ "dbSnpId": "rs2231142",\n+ "call": null,\n+ "alleles": [\n+ "rs2231142 variant (T)"\n+ ],\n+ "phased": false,\n+ "wildtypeAllele": "G",\n+ "mismatch": false,\n+ "warnings": []\n+ }\n+ ],\n+ "variantsOfInterest": [],\n+ "highlightedVariants": []\n+ },\n+ {\n "geneSymbol": "CACNA1S",\n "chr": "chr1",\n "phased": true,\n@@ -51,9 +136,13 @@\n "reference": true\n },\n "gene": "CACNA1S",\n- "phenotype": "Uncertain Susceptibility",\n+ "phenotypes": [\n+ "Uncertain Susceptibility"\n+ ],\n "variant": null,\n- "lookupKey": "Uncertain Susceptibility",\n+ "lookupKey": [\n+ "Uncertain Susceptibility"\n+ ],\n "label": "Reference/Reference"\n }\n ],\n@@ -72,9 +161,13 @@\n "reference": true\n },\n "gene": "CACNA1S",\n- "phenotype": "Uncertain Susceptibility",\n+ "phenotypes": [\n+ "Uncertain Susceptibility"\n+ ],\n "variant": null,\n- "lookupKey": "Uncertain Susceptibility",\n+ "lookupKey": [\n+ "Uncertain Susceptibility"\n+ ],\n "label": "Reference/Reference"\n }\n ],\n@@ -90,7 +183,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "CACNA1S",\n@@ -103,7 +197,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "G",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n }\n ],\n "variantsOfInterest": [],\n@@ -137,9 +232,13 @@\n "reference": true\n },\n "gene": "CFTR",\n- "phenotype": "ivacaftor non-responsive in CF patients",\n+ "phenotypes": [\n+ "ivacaftor non-responsive in CF patients"\n+ ],\n "variant": null,\n- "lookupKey": "ivacaftor non-responsive in CF patients",\n+ "lookupKey": [\n+ "ivacaftor non-responsive in CF patients"\n+ ],\n "label": "No CPIC variants found"\n }\n ],\n@@ -158,9 +257,13 @@\n "reference": true\n },\n "gene": "CFTR",\n- "phenotype": "ivacaftor non-responsive in CF patients",\n+ "phenotypes": [\n'..b' "gene": "TPMT",\n@@ -6649,7 +7306,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "A",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6662,7 +7320,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "G",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6675,7 +7334,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6688,7 +7348,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6701,7 +7362,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "T",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6714,7 +7376,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "A",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6727,7 +7390,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "T",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n }\n ],\n "variantsOfInterest": [],\n@@ -6777,9 +7441,13 @@\n "reference": true\n },\n "gene": "UGT1A1",\n- "phenotype": "Normal Metabolizer",\n+ "phenotypes": [\n+ "Normal Metabolizer"\n+ ],\n "variant": null,\n- "lookupKey": "Normal Metabolizer",\n+ "lookupKey": [\n+ "Normal Metabolizer"\n+ ],\n "label": "*1/*1"\n }\n ],\n@@ -6798,9 +7466,13 @@\n "reference": true\n },\n "gene": "UGT1A1",\n- "phenotype": "Normal Metabolizer",\n+ "phenotypes": [\n+ "Normal Metabolizer"\n+ ],\n "variant": null,\n- "lookupKey": "Normal Metabolizer",\n+ "lookupKey": [\n+ "Normal Metabolizer"\n+ ],\n "label": "*1/*1"\n }\n ],\n@@ -6818,7 +7490,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "UGT1A1",\n@@ -6835,7 +7508,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "CAT",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "UGT1A1",\n@@ -6848,7 +7522,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "G",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "UGT1A1",\n@@ -6861,7 +7536,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n }\n ],\n "variantsOfInterest": [],\n@@ -6926,9 +7602,9 @@\n "reference": true\n },\n "gene": "VKORC1",\n- "phenotype": null,\n+ "phenotypes": [],\n "variant": null,\n- "lookupKey": null,\n+ "lookupKey": [],\n "label": "rs9923231 reference (C)/rs9923231 reference (C)"\n }\n ],\n@@ -6947,9 +7623,9 @@\n "reference": true\n },\n "gene": "VKORC1",\n- "phenotype": null,\n+ "phenotypes": [],\n "variant": null,\n- "lookupKey": null,\n+ "lookupKey": [],\n "label": "rs9923231 reference (C)/rs9923231 reference (C)"\n }\n ],\n@@ -6965,7 +7641,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n }\n ],\n "variantsOfInterest": [],\n' |
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| diff -r d67642a21a1d -r 891283e0ee89 test-data/test_2.html --- a/test-data/test_2.html Fri Jan 28 21:18:23 2022 +0000 +++ b/test-data/test_2.html Thu May 05 20:27:17 2022 +0000 |
| b |
| b'@@ -50,13 +50,13 @@\n </nav>\n \n <div class="container-fluid">\n- <h3>CACNA1S</h3><ul><li>Reference/Reference (4)</li></ul><table class="table table-striped table-hover table-condensed"><tr><th>Definition Position</th><th>201060815</th><th>201091993</th></tr><tr><th></th><th>rs1800559</th><th>rs772226819</th></tr><tr><th>VCF Position</th><th>201060815</th><th>201091993</th></tr><tr><th>VCF REF,ALTs</th><th>C,T</th><th>G,A</th></tr><tr class="success"><th>VCF Call</th><th>C|C</th><th>G|G</th></tr><tr class="info"><th>Reference</th><td><b>C</b></td><td><b>G</b></td></tr><tr><th></th><td>C</td><td>G</td></tr></table><h3>CFTR</h3><ul><li>ivacaftor non-responsive CFTR sequence/ivacaftor non-responsive CFTR sequence (78)</li></ul><table class="table table-striped table-hover table-condensed"><tr><th>Definition Position</th><th>117509035</th><th>117509069</th><th>117509089</th><th>117530953</th><th>117530955</th><th>117530974</th><th>117530975</th><th>117534318</th><th>117534363</th><th>117534368</th><th>117535285</th><th>117540270</th><th>117540285</th><th>117548795</th><th>117587799</th><th>117587800</th><th>117587801</th><th>117587805</th><th>117587806</th><th>117590409</th><th>117594930</th><th>117602868</th><th>117603708</th><th>117606695</th><th>117611555</th><th>117611595</th><th>117611620</th><th>117611640</th><th>117611646</th><th>117611649</th><th>117611650</th><th>117611663</th><th>117614699</th><th>117639961</th><th>117642451</th><th>117642472</th><th>117642483</th><th>117642528</th><th>117664770</th></tr><tr><th></th><th>rs397508256</th><th>rs368505753</th><th>rs115545701</th><th>rs113993958</th><th>rs397508537</th><th>rs77834169</th><th>rs78655421</th><th>rs80282562</th><th>rs397508759</th><th>rs397508761</th><th>rs121908752</th><th>rs77932196</th><th>rs121908753</th><th>rs74551128</th><th>rs121908757</th><th>rs121908755</th><th>rs121909005</th><th>rs121909013</th><th>rs75527207</th><th>rs397508288</th><th>rs397508387</th><th>rs80224560</th><th>rs397508442</th><th>rs141033578</th><th>rs76151804</th><th>rs150212784</th><th>rs397508513</th><th>rs121909020</th><th>rs200321110</th><th>rs202179988</th><th>rs78769542</th><th>rs186045772</th><th>rs75541969</th><th>rs75039782</th><th>rs267606723</th><th>rs74503330</th><th>rs121909041</th><th>rs11971167</th><th>rs193922525</th></tr><tr><th>VCF Position</th><th>117509035</th><th>117509069</th><th>117509089</th><th>117530953</th><th>117530955</th><th>117530974</th><th>117530975</th><th>117534318</th><th>117534363</th><th>117534368</th><th>117535285</th><th>117540270</th><th>117540285</th><th>117548795</th><th>117587799</th><th>117587800</th><th>117587801</th><th>117587805</th><th>117587806</th><th>117590409</th><th>117594930</th><th>117602868</th><th>117603708</th><th>117606695</th><th>117611555</th><th>117611595</th><th>117611620</th><th>117611640</th><th>117611646</th><th>117611649</th><th>117611650</th><th>117611663</th><th>117614699</th><th>117639961</th><th>117642451</th><th>117642472</th><th>117642483</th><th>117642528</th><th>117664770</th></tr><tr><th>VCF REF,ALTs</th><th>G,A</th><th>C,T</th><th>C,T</th><th>G,C</th><th>C,A</th><th>C,T</th><th>G,A</th><th>G,A</th><th>G,A</th><th>A,G</th><th>T,G</th><th>G,A</th><th>G,A</th><th>C,A</th><th>A,C</th><th>G,A</th><th>T,G</th><th>G,A</th><th>G,A</th><th>A,G</th><th>G,T</th><th>G,A</th><th>C,T</th><th>C,T</th><th>A,G</th><th>T,G</th><th>A,C</th><th>G,A</th><th>G,A</th><th>C,T</th><th>G,A</th><th>T,A</th><th>G,C</th><th>C,T</th><th>G,A</th><th>G,A</th><th>T,C</th><th>G,A</th><th>G,A</th></tr><tr class="success"><th>VCF Call</th><th>G|G</th><th>C|C</th><th>C|C</th><th>G|G</th><th>C|C</th><th>C|C</th><th>G|G</th><th>G|G</th><th>G|G</th><th>A|A</th><th>T|T</th><th>G|G</th><th>G|G</th><th>C|C</th><th>A|A</th><th>G|G</th><th>T|T</th><th>G|G</th><th>G|G</th><th>A|A</th><th>G|G</th><th>G|G</th><th>C|C</th><th>C|C</th><th>A|A</th><th>T|T</th><th>A|A</th><th>G|G</th><th>G|G</th><th>C|C</th><th>G|G</th><th>T|T</th><th>G|G</th><th>C|C</th><th>G'..b'43724</th><th>18143728</th><th>18147838</th><th>18147845</th><th>18147851</th><th>18147856</th><th>18147910</th><th>18149004</th><th>18149022</th><th>18149032</th><th>18149045</th><th>18149126</th><th>18149127</th></tr><tr><th>VCF REF,ALTs</th><th>T,C,G</th><th>T,C</th><th>A,C</th><th>C,T</th><th>A,T</th><th>C,T</th><th>A,G</th><th>C,T</th><th>A,G</th><th>A,G</th><th>C,T</th><th>T,A</th><th>C,A</th><th>A,G</th><th>G,C</th><th>T,C</th><th>C,T</th><th>C,G,T</th><th>G,A</th><th>C,T</th><th>C,G</th><th>C,T</th><th>G,A</th><th>T,G</th><th>T,G</th><th>C,G</th><th>C,T</th><th>A,C</th><th>C,T</th><th>G,A</th><th>C,G</th><th>C,A</th><th>G,A</th><th>C,T</th><th>G,C</th><th>A,G</th><th>A,G</th><th>G,C</th><th>C,T</th><th>C,CT</th><th>T,A</th><th>A,G</th><th>T,C</th></tr><tr class="success"><th>VCF Call</th><th>T|T</th><th>T|T</th><th>A|A</th><th>C|C</th><th>A|A</th><th>C|C</th><th>A|A</th><th>C|C</th><th>A|A</th><th>A|A</th><th>C|C</th><th>T|T</th><th>C|C</th><th>A|A</th><th>G|G</th><th>T|T</th><th>C|C</th><th>C|C</th><th>G|G</th><th>C|C</th><th>C|C</th><th>C|C</th><th>G|G</th><th>T|T</th><th>T|T</th><th>C|C</th><th>C|C</th><th>A|A</th><th>C|C</th><th>G|G</th><th>C|C</th><th>C|C</th><th>G|G</th><th>C|C</th><th>G|G</th><th>A|A</th><th>A|A</th><th>G|G</th><th>C|C</th><th>C|C</th><th>T|T</th><th>A|A</th><th>T|T</th></tr><tr class="info"><th>*1</th><td><b>T</b></td><td><b>T</b></td><td><b>A</b></td><td><b>C</b></td><td><b>A</b></td><td><b>C</b></td><td><b>A</b></td><td><b>C</b></td><td><b>A</b></td><td><b>A</b></td><td><b>C</b></td><td><b>T</b></td><td><b>C</b></td><td><b>A</b></td><td><b>G</b></td><td><b>T</b></td><td><b>C</b></td><td><b>C</b></td><td><b>G</b></td><td><b>C</b></td><td><b>C</b></td><td><b>C</b></td><td><b>G</b></td><td><b>T</b></td><td><b>T</b></td><td><b>C</b></td><td><b>C</b></td><td><b>A</b></td><td><b>C</b></td><td><b>G</b></td><td><b>C</b></td><td><b>C</b></td><td><b>G</b></td><td><b>C</b></td><td><b>G</b></td><td><b>A</b></td><td><b>A</b></td><td><b>G</b></td><td><b>C</b></td><td><b>C</b></td><td><b>T</b></td><td><b>A</b></td><td><b>T</b></td></tr><tr><th></th><td>T</td><td>T</td><td>A</td><td>C</td><td>A</td><td>C</td><td>A</td><td>C</td><td>A</td><td>A</td><td>C</td><td>T</td><td>C</td><td>A</td><td>G</td><td>T</td><td>C</td><td>C</td><td>G</td><td>C</td><td>C</td><td>C</td><td>G</td><td>T</td><td>T</td><td>C</td><td>C</td><td>A</td><td>C</td><td>G</td><td>C</td><td>C</td><td>G</td><td>C</td><td>G</td><td>A</td><td>A</td><td>G</td><td>C</td><td>C</td><td>T</td><td>A</td><td>T</td></tr></table><h3>UGT1A1</h3><ul><li>*1/*1 (8)</li></ul><table class="table table-striped table-hover table-condensed"><tr><th>Definition Position</th><th>233759924</th><th>233760233</th><th>233760498</th><th>233760973</th></tr><tr><th></th><th>rs887829</th><th>rs3064744</th><th>rs4148323</th><th>rs35350960</th></tr><tr><th>VCF Position</th><th>233759924</th><th>233760233</th><th>233760498</th><th>233760973</th></tr><tr><th>VCF REF,ALTs</th><th>C,T</th><th>CAT,C,CATAT,CATATAT</th><th>G,A</th><th>C,A</th></tr><tr class="success"><th>VCF Call</th><th>C|C</th><th>CAT|CAT</th><th>G|G</th><th>C|C</th></tr><tr class="info"><th>*1</th><td><b>C</b></td><td><b>CAT</b></td><td><b>G</b></td><td><b>C</b></td></tr><tr><th></th><td>C</td><td>CAT</td><td>G</td><td>C</td></tr></table><h3>VKORC1</h3><ul><li>rs9923231 reference (C)/rs9923231 reference (C) (2)</li></ul><table class="table table-striped table-hover table-condensed"><tr><th>Definition Position</th><th>31096368</th></tr><tr><th></th><th>rs9923231</th></tr><tr><th>VCF Position</th><th>31096368</th></tr><tr><th>VCF REF,ALTs</th><th>C,T</th></tr><tr class="success"><th>VCF Call</th><th>C|C</th></tr><tr class="info"><th>rs9923231 reference (C)</th><td><b>C</b></td></tr><tr><th></th><td>C</td></tr></table>\n </div>\n <div class="footer">\n <hr />\n <footer class="container-fluid">\n <small>\n- <p>Generated on 01/27/22.</p>\n+ <p>Generated on 05/04/22.</p>\n </small>\n </footer>\n </div>\n' |
| b |
| diff -r d67642a21a1d -r 891283e0ee89 test-data/test_2.json --- a/test-data/test_2.json Fri Jan 28 21:18:23 2022 +0000 +++ b/test-data/test_2.json Thu May 05 20:27:17 2022 +0000 |
| [ |
| b'@@ -3,11 +3,50 @@\n "namedAlleleMatcherVersion": "1.0.0",\n "genomeBuild": "GRCh38.p13",\n "inputFilename": "input.vcf",\n- "timestamp": "Jan 27, 2022, 11:53:07 PM"\n+ "timestamp": "May 4, 2022, 8:57:03 PM"\n },\n "results": [\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n+ "chromosome": "chr4",\n+ "gene": "ABCG2",\n+ "diplotypes": [],\n+ "haplotypes": [],\n+ "phased": true,\n+ "variants": [],\n+ "variantsOfInterest": [],\n+ "matchData": {\n+ "missingPositions": [\n+ {\n+ "chromosome": "chr4",\n+ "position": 88131171,\n+ "cpicPosition": 88131171,\n+ "rsid": "rs2231142",\n+ "chromosomeHgvsName": "g.88131171G\\u003eT",\n+ "cpicAlleles": [\n+ "G",\n+ "T"\n+ ],\n+ "cpicToVcfAlleleMap": {\n+ "T": "T",\n+ "G": "G"\n+ },\n+ "ref": "G",\n+ "alts": [\n+ "T"\n+ ]\n+ }\n+ ],\n+ "mismatchedAlleles": []\n+ },\n+ "uncallableHaplotypes": [\n+ "rs2231142 variant (T)",\n+ "rs2231142 reference (G)"\n+ ],\n+ "ignoredHaplotypes": []\n+ },\n+ {\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr1",\n "gene": "CACNA1S",\n "diplotypes": [\n@@ -58,7 +97,7 @@\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr7",\n "gene": "CFTR",\n "diplotypes": [\n@@ -294,7 +333,7 @@\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr19",\n "gene": "CYP2B6",\n "diplotypes": [\n@@ -510,7 +549,7 @@\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr10",\n "gene": "CYP2C19",\n "diplotypes": [\n@@ -721,7 +760,7 @@\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr10",\n "gene": "CYP2C9",\n "diplotypes": [\n@@ -1094,6 +1133,101 @@\n "missingPositions": [\n {\n "chromosome": "chr10",\n+ "position": 94938719,\n+ "cpicPosition": 94938719,\n+ "rsid": null,\n+ "chromosomeHgvsName": "g.94938719T\\u003eG",\n+ "cpicAlleles": [\n+ "G",\n+ "T"\n+ ],\n+ "cpicToVcfAlleleMap": {\n+ "T": "T",\n+ "G": "G"\n+ },\n+ "ref": "T",\n+ "alts": [\n+ "G"\n+ ]\n+ },\n+ {\n+ "chromosome": "chr10",\n+ "position": 94938788,\n+ "cpicPosition": 94938788,\n+ "rsid": null,\n+ "chromosomeHgvsName": "g.94938788C\\u003eT",\n+ "cpicAlleles": [\n+ "C",\n+ "T"\n+ ],\n+ "cpicToVcfAlleleMap": {\n+ "C": "C",\n+ "T": "T"\n+ },\n+ "ref": "C",\n+ "alts": [\n+ "T"\n+ ]\n+ },\n+ {\n+ "chromosome": "chr10",\n+ "position": 94938800,\n+ "cpicPosition": 94938800,\n+ "rsid": "rs1364419386",\n+ "chromosomeHgvsName": "g.94938800G\\u003eA",\n+ "cpicAlleles": [\n+ "A",\n+ "G"\n+ ],\n+ "cpicToVcfAlleleMap": {\n+ "A": "A",\n+ "G": "G"\n+ },\n+ "ref": "G",\n+ "alts": [\n+ "A"\n+ ]\n+ },\n+ {\n+ "chromosome": "chr10",\n+ "position": 94941975,\n+ "cpicPosition": 949'..b' "*79"\n ],\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr7",\n "gene": "CYP3A5",\n "diplotypes": [\n@@ -1189,34 +1428,29 @@\n "haplotype1": {\n "name": "*1",\n "sequences": [\n- "99652613:G;99652770:T;99660516:C;99665212:C;99665237:T;99666950:A;99672916:T;99676198:G;"\n+ "99652770:T;99660516:C;99665212:C;99672916:T;99676198:G;"\n ]\n },\n "haplotype2": {\n "name": "*1",\n "sequences": [\n- "99652613:G;99652770:T;99660516:C;99665212:C;99665237:T;99666950:A;99672916:T;99676198:G;"\n+ "99652770:T;99660516:C;99665212:C;99672916:T;99676198:G;"\n ]\n },\n- "score": 16\n+ "score": 10\n }\n ],\n "haplotypes": [\n {\n "name": "*1",\n "sequences": [\n- "99652613:G;99652770:T;99660516:C;99665212:C;99665237:T;99666950:A;99672916:T;99676198:G;"\n+ "99652770:T;99660516:C;99665212:C;99672916:T;99676198:G;"\n ]\n }\n ],\n "phased": true,\n "variants": [\n {\n- "position": 99652613,\n- "rsid": "rs28365083",\n- "vcfCall": "G|G"\n- },\n- {\n "position": 99652770,\n "rsid": "rs41303343",\n "vcfCall": "T|T"\n@@ -1232,16 +1466,6 @@\n "vcfCall": "C|C"\n },\n {\n- "position": 99665237,\n- "rsid": "rs56411402",\n- "vcfCall": "T|T"\n- },\n- {\n- "position": 99666950,\n- "rsid": "rs55965422",\n- "vcfCall": "A|A"\n- },\n- {\n "position": 99672916,\n "rsid": "rs776746",\n "vcfCall": "T|T"\n@@ -1261,7 +1485,7 @@\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr19",\n "gene": "CYP4F2",\n "diplotypes": [\n@@ -1312,7 +1536,7 @@\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr1",\n "gene": "DPYD",\n "diplotypes": [\n@@ -1768,7 +1992,7 @@\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr19",\n "gene": "IFNL3",\n "diplotypes": [\n@@ -1814,7 +2038,7 @@\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr13",\n "gene": "NUDT15",\n "diplotypes": [\n@@ -1940,7 +2164,7 @@\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr19",\n "gene": "RYR1",\n "diplotypes": [\n@@ -2201,7 +2425,7 @@\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr12",\n "gene": "SLCO1B1",\n "diplotypes": [\n@@ -2500,7 +2724,7 @@\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr6",\n "gene": "TPMT",\n "diplotypes": [\n@@ -2756,7 +2980,7 @@\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr2",\n "gene": "UGT1A1",\n "diplotypes": [\n@@ -2817,7 +3041,7 @@\n "ignoredHaplotypes": []\n },\n {\n- "alleleDefinitionVersion": "01/10/22",\n+ "alleleDefinitionVersion": "04/20/22",\n "chromosome": "chr16",\n "gene": "VKORC1",\n "diplotypes": [\n' |
| b |
| diff -r d67642a21a1d -r 891283e0ee89 test-data/test_3.json --- a/test-data/test_3.json Fri Jan 28 21:18:23 2022 +0000 +++ b/test-data/test_3.json Thu May 05 20:27:17 2022 +0000 |
| [ |
| b'@@ -1,5 +1,85 @@\n [\n {\n+ "geneSymbol": "ABCG2",\n+ "chr": "chr4",\n+ "phased": true,\n+ "callSource": "MATCHER",\n+ "uncalledHaplotypes": [\n+ "rs2231142 reference (G)",\n+ "rs2231142 variant (T)"\n+ ],\n+ "messages": [],\n+ "relatedDrugs": [],\n+ "matcherDiplotypes": [\n+ {\n+ "allele1": {\n+ "gene": "ABCG2",\n+ "name": "Unknown",\n+ "function": "Unassigned function",\n+ "reference": false\n+ },\n+ "allele2": {\n+ "gene": "ABCG2",\n+ "name": "Unknown",\n+ "function": "Unassigned function",\n+ "reference": false\n+ },\n+ "gene": "ABCG2",\n+ "phenotypes": [\n+ "No Result"\n+ ],\n+ "variant": null,\n+ "lookupKey": [\n+ "No Result"\n+ ],\n+ "label": "Unknown/Unknown"\n+ }\n+ ],\n+ "diplotypes": [\n+ {\n+ "allele1": {\n+ "gene": "ABCG2",\n+ "name": "Unknown",\n+ "function": "Unassigned function",\n+ "reference": false\n+ },\n+ "allele2": {\n+ "gene": "ABCG2",\n+ "name": "Unknown",\n+ "function": "Unassigned function",\n+ "reference": false\n+ },\n+ "gene": "ABCG2",\n+ "phenotypes": [\n+ "No Result"\n+ ],\n+ "variant": null,\n+ "lookupKey": [\n+ "No Result"\n+ ],\n+ "label": "Unknown/Unknown"\n+ }\n+ ],\n+ "variants": [\n+ {\n+ "gene": "ABCG2",\n+ "chromosome": "chr4",\n+ "position": 88131171,\n+ "dbSnpId": "rs2231142",\n+ "call": null,\n+ "alleles": [\n+ "rs2231142 variant (T)"\n+ ],\n+ "phased": false,\n+ "wildtypeAllele": "G",\n+ "mismatch": false,\n+ "warnings": []\n+ }\n+ ],\n+ "variantsOfInterest": [],\n+ "highlightedVariants": []\n+ },\n+ {\n "geneSymbol": "CACNA1S",\n "chr": "chr1",\n "phased": true,\n@@ -22,9 +102,13 @@\n "reference": true\n },\n "gene": "CACNA1S",\n- "phenotype": "Uncertain Susceptibility",\n+ "phenotypes": [\n+ "Uncertain Susceptibility"\n+ ],\n "variant": null,\n- "lookupKey": "Uncertain Susceptibility",\n+ "lookupKey": [\n+ "Uncertain Susceptibility"\n+ ],\n "label": "Reference/Reference"\n }\n ],\n@@ -43,9 +127,13 @@\n "reference": true\n },\n "gene": "CACNA1S",\n- "phenotype": "Uncertain Susceptibility",\n+ "phenotypes": [\n+ "Uncertain Susceptibility"\n+ ],\n "variant": null,\n- "lookupKey": "Uncertain Susceptibility",\n+ "lookupKey": [\n+ "Uncertain Susceptibility"\n+ ],\n "label": "Reference/Reference"\n }\n ],\n@@ -61,7 +149,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "CACNA1S",\n@@ -74,7 +163,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "G",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n }\n ],\n "variantsOfInterest": [],\n@@ -103,9 +193,13 @@\n "reference": true\n },\n "gene": "CFTR",\n- "phenotype": "ivacaftor non-responsive in CF patients",\n+ "phenotypes": [\n+ "ivacaftor non-responsive in CF patients"\n+ ],\n "variant": null,\n- "lookupKey": "ivacaftor non-responsive in CF patients",\n+ "lookupKey": [\n+ "ivacaftor non-responsive in CF patients"\n+ ],\n "label": "No CPIC variants found"\n }\n ],\n@@ -124,9 +218,13 @@\n "reference": true\n },\n "gene": "CFTR",\n- "phenotype": "ivacaftor non-responsive in CF patients",\n+ "phenotypes": [\n+ "ivacaftor non-responsive in CF patients"\n+ ],\n "variant": null,\n- '..b' "gene": "TPMT",\n@@ -6333,7 +6949,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "A",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6346,7 +6963,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "G",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6359,7 +6977,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6372,7 +6991,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6385,7 +7005,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "T",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6398,7 +7019,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "A",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6411,7 +7033,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "T",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n }\n ],\n "variantsOfInterest": [],\n@@ -6456,9 +7079,13 @@\n "reference": true\n },\n "gene": "UGT1A1",\n- "phenotype": "Normal Metabolizer",\n+ "phenotypes": [\n+ "Normal Metabolizer"\n+ ],\n "variant": null,\n- "lookupKey": "Normal Metabolizer",\n+ "lookupKey": [\n+ "Normal Metabolizer"\n+ ],\n "label": "*1/*1"\n }\n ],\n@@ -6477,9 +7104,13 @@\n "reference": true\n },\n "gene": "UGT1A1",\n- "phenotype": "Normal Metabolizer",\n+ "phenotypes": [\n+ "Normal Metabolizer"\n+ ],\n "variant": null,\n- "lookupKey": "Normal Metabolizer",\n+ "lookupKey": [\n+ "Normal Metabolizer"\n+ ],\n "label": "*1/*1"\n }\n ],\n@@ -6497,7 +7128,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "UGT1A1",\n@@ -6514,7 +7146,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "CAT",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "UGT1A1",\n@@ -6527,7 +7160,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "G",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "UGT1A1",\n@@ -6540,7 +7174,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n }\n ],\n "variantsOfInterest": [],\n@@ -6600,9 +7235,9 @@\n "reference": true\n },\n "gene": "VKORC1",\n- "phenotype": null,\n+ "phenotypes": [],\n "variant": null,\n- "lookupKey": null,\n+ "lookupKey": [],\n "label": "rs9923231 reference (C)/rs9923231 reference (C)"\n }\n ],\n@@ -6621,9 +7256,9 @@\n "reference": true\n },\n "gene": "VKORC1",\n- "phenotype": null,\n+ "phenotypes": [],\n "variant": null,\n- "lookupKey": null,\n+ "lookupKey": [],\n "label": "rs9923231 reference (C)/rs9923231 reference (C)"\n }\n ],\n@@ -6639,7 +7274,8 @@\n ],\n "phased": true,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n }\n ],\n "variantsOfInterest": [],\n' |
| b |
| diff -r d67642a21a1d -r 891283e0ee89 test-data/test_4.json --- a/test-data/test_4.json Fri Jan 28 21:18:23 2022 +0000 +++ b/test-data/test_4.json Thu May 05 20:27:17 2022 +0000 |
| [ |
| b'@@ -1,5 +1,85 @@\n [\n {\n+ "geneSymbol": "ABCG2",\n+ "chr": "chr4",\n+ "phased": true,\n+ "callSource": "MATCHER",\n+ "uncalledHaplotypes": [\n+ "rs2231142 reference (G)",\n+ "rs2231142 variant (T)"\n+ ],\n+ "messages": [],\n+ "relatedDrugs": [],\n+ "matcherDiplotypes": [\n+ {\n+ "allele1": {\n+ "gene": "ABCG2",\n+ "name": "Unknown",\n+ "function": "Unassigned function",\n+ "reference": false\n+ },\n+ "allele2": {\n+ "gene": "ABCG2",\n+ "name": "Unknown",\n+ "function": "Unassigned function",\n+ "reference": false\n+ },\n+ "gene": "ABCG2",\n+ "phenotypes": [\n+ "No Result"\n+ ],\n+ "variant": null,\n+ "lookupKey": [\n+ "No Result"\n+ ],\n+ "label": "Unknown/Unknown"\n+ }\n+ ],\n+ "diplotypes": [\n+ {\n+ "allele1": {\n+ "gene": "ABCG2",\n+ "name": "Unknown",\n+ "function": "Unassigned function",\n+ "reference": false\n+ },\n+ "allele2": {\n+ "gene": "ABCG2",\n+ "name": "Unknown",\n+ "function": "Unassigned function",\n+ "reference": false\n+ },\n+ "gene": "ABCG2",\n+ "phenotypes": [\n+ "No Result"\n+ ],\n+ "variant": null,\n+ "lookupKey": [\n+ "No Result"\n+ ],\n+ "label": "Unknown/Unknown"\n+ }\n+ ],\n+ "variants": [\n+ {\n+ "gene": "ABCG2",\n+ "chromosome": "chr4",\n+ "position": 88131171,\n+ "dbSnpId": "rs2231142",\n+ "call": null,\n+ "alleles": [\n+ "rs2231142 variant (T)"\n+ ],\n+ "phased": false,\n+ "wildtypeAllele": "G",\n+ "mismatch": false,\n+ "warnings": []\n+ }\n+ ],\n+ "variantsOfInterest": [],\n+ "highlightedVariants": []\n+ },\n+ {\n "geneSymbol": "CACNA1S",\n "chr": "chr1",\n "phased": true,\n@@ -22,9 +102,13 @@\n "reference": true\n },\n "gene": "CACNA1S",\n- "phenotype": "Uncertain Susceptibility",\n+ "phenotypes": [\n+ "Uncertain Susceptibility"\n+ ],\n "variant": null,\n- "lookupKey": "Uncertain Susceptibility",\n+ "lookupKey": [\n+ "Uncertain Susceptibility"\n+ ],\n "label": "Reference/Reference"\n }\n ],\n@@ -43,9 +127,13 @@\n "reference": true\n },\n "gene": "CACNA1S",\n- "phenotype": "Uncertain Susceptibility",\n+ "phenotypes": [\n+ "Uncertain Susceptibility"\n+ ],\n "variant": null,\n- "lookupKey": "Uncertain Susceptibility",\n+ "lookupKey": [\n+ "Uncertain Susceptibility"\n+ ],\n "label": "Reference/Reference"\n }\n ],\n@@ -61,7 +149,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "CACNA1S",\n@@ -74,7 +163,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "G",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n }\n ],\n "variantsOfInterest": [],\n@@ -103,9 +193,13 @@\n "reference": true\n },\n "gene": "CFTR",\n- "phenotype": "ivacaftor non-responsive in CF patients",\n+ "phenotypes": [\n+ "ivacaftor non-responsive in CF patients"\n+ ],\n "variant": null,\n- "lookupKey": "ivacaftor non-responsive in CF patients",\n+ "lookupKey": [\n+ "ivacaftor non-responsive in CF patients"\n+ ],\n "label": "No CPIC variants found"\n }\n ],\n@@ -124,9 +218,13 @@\n "reference": true\n },\n "gene": "CFTR",\n- "phenotype": "ivacaftor non-responsive in CF patients",\n+ "phenotypes": [\n+ "ivacaftor non-responsive in CF patients"\n+ ],\n "variant": null,\n- '..b' "TPMT",\n@@ -6165,7 +6840,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "A",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6178,7 +6854,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "G",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6191,7 +6868,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6204,7 +6882,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6217,7 +6896,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "T",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6230,7 +6910,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "A",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "TPMT",\n@@ -6243,7 +6924,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "T",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n }\n ],\n "variantsOfInterest": [],\n@@ -6288,9 +6970,13 @@\n "reference": true\n },\n "gene": "UGT1A1",\n- "phenotype": "Normal Metabolizer",\n+ "phenotypes": [\n+ "Normal Metabolizer"\n+ ],\n "variant": null,\n- "lookupKey": "Normal Metabolizer",\n+ "lookupKey": [\n+ "Normal Metabolizer"\n+ ],\n "label": "*1/*1"\n }\n ],\n@@ -6309,9 +6995,13 @@\n "reference": true\n },\n "gene": "UGT1A1",\n- "phenotype": "Normal Metabolizer",\n+ "phenotypes": [\n+ "Normal Metabolizer"\n+ ],\n "variant": null,\n- "lookupKey": "Normal Metabolizer",\n+ "lookupKey": [\n+ "Normal Metabolizer"\n+ ],\n "label": "*1/*1"\n }\n ],\n@@ -6329,7 +7019,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "UGT1A1",\n@@ -6346,7 +7037,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "CAT",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "UGT1A1",\n@@ -6359,7 +7051,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "G",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n },\n {\n "gene": "UGT1A1",\n@@ -6372,7 +7065,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n }\n ],\n "variantsOfInterest": [],\n@@ -6432,9 +7126,9 @@\n "reference": true\n },\n "gene": "VKORC1",\n- "phenotype": null,\n+ "phenotypes": [],\n "variant": null,\n- "lookupKey": null,\n+ "lookupKey": [],\n "label": "rs9923231 reference (C)/rs9923231 reference (C)"\n }\n ],\n@@ -6453,9 +7147,9 @@\n "reference": true\n },\n "gene": "VKORC1",\n- "phenotype": null,\n+ "phenotypes": [],\n "variant": null,\n- "lookupKey": null,\n+ "lookupKey": [],\n "label": "rs9923231 reference (C)/rs9923231 reference (C)"\n }\n ],\n@@ -6471,7 +7165,8 @@\n ],\n "phased": false,\n "wildtypeAllele": "C",\n- "mismatch": false\n+ "mismatch": false,\n+ "warnings": []\n }\n ],\n "variantsOfInterest": [],\n' |