@molgenis/vip-report-template 3.1.1 → 3.1.2

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Files changed (4) hide show
  1. package/package.json +1 -1
  2. package/src/__tests__/query.test.ts +15 -3
  3. package/src/mocks/GRCh37/vcf/family.vcf.blob +1 -1
  4. package/src/utils/query.ts +8 -1
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@molgenis/vip-report-template",
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- "version": "3.1.1",
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+ "version": "3.1.2",
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  "description": "Report Template for Variant Call Format (VCF) Report Generator",
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  "scripts": {
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  "build": "vite build",
package/src/__tests__/query.test.ts CHANGED
@@ -12,7 +12,7 @@ import {
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  sampleSelector,
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  selectorKey,
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  } from "../utils/query";
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- import { Item, Person, QueryClause, Sample } from "@molgenis/vip-report-api/src/Api";
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+ import { Item, Person, Query, QueryClause, Sample } from "@molgenis/vip-report-api/src/Api";
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  describe("query utilities", () => {
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  let fieldMetaCsq: FieldMetadata = {
@@ -55,7 +55,13 @@ describe("query utilities", () => {
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  test("create sample query - filters", () => {
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  const sample = { data: { index: 1 } } as Item<Sample>;
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- const queryClause: QueryClause = { selector: ["s", 1, "GT", "t"], operator: "!=", args: "hom_r" };
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+ const queryClause: Query = {
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+ operator: "and",
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+ args: [
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+ { selector: ["s", 1, "GT", "t"], operator: "!=", args: "hom_r" },
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+ { selector: ["s", 1, "GT", "t"], operator: "!=", args: "miss" },
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+ ],
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+ };
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  const filterQueryClause: QueryClause = { selector: ["n", "CSQ", "*", 0], operator: "==", args: [0] };
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  const filterQueries: FilterQueries = {
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  "CSQ/field1": filterQueryClause,
@@ -68,7 +74,13 @@ describe("query utilities", () => {
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  test("create sample query - undefined search and undefined filters", () => {
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  const sample = { data: { index: 1 } } as Item<Sample>;
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- const queryClause: QueryClause = { selector: ["s", 1, "GT", "t"], operator: "!=", args: "hom_r" };
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+ const queryClause: Query = {
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+ operator: "and",
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+ args: [
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+ { selector: ["s", 1, "GT", "t"], operator: "!=", args: "hom_r" },
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+ { selector: ["s", 1, "GT", "t"], operator: "!=", args: "miss" },
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+ ],
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+ };
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  expect(createSampleQuery(sample, undefined, undefined, meta)).toStrictEqual(queryClause);
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  });
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package/src/mocks/GRCh37/vcf/family.vcf.blob CHANGED
@@ -95,7 +95,7 @@
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  17 29556064 . AC A . PASS CSQ=-|frameshift_variant|HIGH|NF1|4763|Transcript|NM_000267.3|protein_coding|21/57||NM_000267.3:c.2433del|NP_000258.1:p.Ile812LeufsTer9|2816/12362|2433/8457|811/2818|T/X|acC/ac||1||1|||EntrezGene|||||||1|||||||||||-22|-11|12|25|0.00|0.00|0.00|0.00|NF1|VUS|0.9913782|HP:0000951|1|AD|LP|||||||||||LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|NF1|4763|Transcript|NM_001042492.3|protein_coding|21/58||NM_001042492.3:c.2433del|NP_001035957.1:p.Ile812LeufsTer9|2766/12373|2433/8520|811/2839|T/X|acC/ac||1||1||1|EntrezGene|||||||1|||||||||||-22|-11|12|25|0.00|0.00|0.00|0.00|NF1|VUS|0.9913782|HP:0000951|1|AD|LP|||||||||||LP|filter&vkgl&exit_lp| GT:AD:DP:VIC:VID:VIM 1|1:0,50:50:.:1:0 1|1:0,50:50:.:.:. 0|0:50,0:50:.:.:. 1|0:25,25:50:.:.:. 0|0:50,0:50:.:.:. 1|0:25,25:50:.:.:.
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  17 29585422 . A G . PASS CSQ=G|missense_variant|MODERATE|NF1|4763|Transcript|NM_000267.3|protein_coding|31/57||NM_000267.3:c.4171A>G|NP_000258.1:p.Arg1391Gly|4554/12362|4171/8457|1391/2818|R/G|Aga/Gga|rs1555618515&CM1211610|1||1|||EntrezGene|||||0|0.962||pathogenic||1&1||||||||-48|2|28|-27|0.00|0.00|0.01|0.00|NF1|VUS|0.6458939|HP:0000951|1|AD|LP|||||||457686|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,G|missense_variant|MODERATE|NF1|4763|Transcript|NM_001042492.3|protein_coding|32/58||NM_001042492.3:c.4234A>G|NP_001035957.1:p.Arg1412Gly|4567/12373|4234/8520|1412/2839|R/G|Aga/Gga|rs1555618515&CM1211610|1||1||1|EntrezGene|||||0|0.988||pathogenic||1&1||||||||-48|2|28|-27|0.00|0.00|0.01|0.00|NF1|VUS|0.7539552|HP:0000951|1|AD|LP|||||||457686|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIM 1|1:0,50:50:AR:.:1:0 0|1:.:10:.:.:.:. 0|0:50,0:50:.:.:.:. 0|0:50,0:50:.:.:.:. 0|0:50,0:50:.:.:.:. 0|0:50,0:50:.:.:.:.
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  17 29663879 . T G . PASS CSQ=G|missense_variant|MODERATE|NF1|4763|Transcript|NM_000267.3|protein_coding|41/57||NM_000267.3:c.6311T>G|NP_000258.1:p.Leu2104Arg|6694/12362|6311/8457|2104/2818|L/R|cTg/cGg|CM141499&CM143458|1||1|||EntrezGene|||||0|0.994||||1&1||||||||-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.8564539|HP:0000951|1|AD|LP|||||||996527|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&exit_lp|,G|missense_variant|MODERATE|NF1|4763|Transcript|NM_001042492.3|protein_coding|42/58||NM_001042492.3:c.6374T>G|NP_001035957.1:p.Leu2125Arg|6707/12373|6374/8520|2125/2839|L/R|cTg/cGg|CM141499&CM143458|1||1||1|EntrezGene|||||0|0.993||||1&1||||||||-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.8564539|HP:0000951|1|AD|LP|||||||996527|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS 1|0:25,25:50:AR,AD:17_29683983_C_T:0:4763:1:AD_IP,AR_C 0|0:50,0:50:.:.:.:.:.:. 1|0:25,25:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:.
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- 17 29683983 . C T . PASS CSQ=T|stop_gained|HIGH|NF1|4763|Transcript|NM_000267.3|protein_coding|52/57||NM_000267.3:c.7681C>T|NP_000258.1:p.Gln2561Ter|8064/12362|7681/8457|2561/2818|Q/*|Cag/Tag|CM143479|1||1|||EntrezGene||||||||||1||||||||24|-5|24|36|0.02|0.00|0.00|0.00|NF1|VUS|0.99177766|HP:0000951|1|AD|LP|||||||||||LP|filter&vkgl&exit_lp|,T|stop_gained|HIGH|NF1|4763|Transcript|NM_001042492.3|protein_coding|53/58||NM_001042492.3:c.7744C>T|NP_001035957.1:p.Gln2582Ter|8077/12373|7744/8520|2582/2839|Q/*|Cag/Tag|CM143479|1||1||1|EntrezGene||||||||||1||||||||24|-5|24|36|0.02|0.00|0.00|0.00|NF1|VUS|0.9919058|HP:0000951|1|AD|LP|||||||||||LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS 1|0:25,25:50:AR,AD:17_29663879_T_G:1:4763:1:AR_C 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:.
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+ 17 29683983 . C T . PASS CSQ=T|stop_gained|HIGH|NF1|4763|Transcript|NM_000267.3|protein_coding|52/57||NM_000267.3:c.7681C>T|NP_000258.1:p.Gln2561Ter|8064/12362|7681/8457|2561/2818|Q/*|Cag/Tag|CM143479|1||1|||EntrezGene||||||||||1||||||||24|-5|24|36|0.02|0.00|0.00|0.00|NF1|VUS|0.99177766|HP:0000951|1|AD|LP|||||||||||LP|filter&vkgl&exit_lp|,T|stop_gained|HIGH|NF1|4763|Transcript|NM_001042492.3|protein_coding|53/58||NM_001042492.3:c.7744C>T|NP_001035957.1:p.Gln2582Ter|8077/12373|7744/8520|2582/2839|Q/*|Cag/Tag|CM143479|1||1||1|EntrezGene||||||||||1||||||||24|-5|24|36|0.02|0.00|0.00|0.00|NF1|VUS|0.9919058|HP:0000951|1|AD|LP|||||||||||LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS .|.:25,25:50:AR,AD:17_29663879_T_G:1:4763:1:AR_C 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.:.
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  19 11224051 . C CGTGGTCGCTCTGGACACGGAG . PASS CSQ=TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_000527.5|protein_coding|9/18||NM_000527.5:c.1289_1309dup|NP_000518.1:p.Val430_Val436dup|1395-1396/5173|1309-1310/2583|437/860|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1||1|EntrezGene|||||||25||||||||||||||||||||VUS|0.27201134|HP:0000951&HP:0003124||AD&AR|LP|||||||||||LP|filter&vkgl&exit_lp|,TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_001195798.2|protein_coding|9/18||NM_001195798.2:c.1289_1309dup|NP_001182727.1:p.Val430_Val436dup|1395-1396/5167|1309-1310/2577|437/858|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1|||EntrezGene|||||||25||||||||||||||||||||VUS|0.27201134|HP:0000951&HP:0003124||AD&AR|LP|||||||||||LP|filter&vkgl&exit_lp|,TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_001195799.2|protein_coding|8/17||NM_001195799.2:c.1166_1186dup|NP_001182728.1:p.Val389_Val395dup|1272-1273/5050|1186-1187/2460|396/819|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1|||EntrezGene|||||||25||||||||||||||||||||VUS|0.26963568|HP:0000951&HP:0003124||AD&AR|LP|||||||||||LP|filter&vkgl&exit_lp|,TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_001195800.2|protein_coding|7/16||NM_001195800.2:c.785_805dup|NP_001182729.1:p.Val262_Val268dup|891-892/4669|805-806/2079|269/692|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1|||EntrezGene|||||||25||||||||||||||||||||VUS|0.3952981|HP:0000951&HP:0003124||AD&AR|LP|||||||||||LP|filter&vkgl&exit_lp|,TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_001195803.2|protein_coding|8/16||NM_001195803.2:c.908_928dup|NP_001182732.1:p.Val303_Val309dup|1014-1015/4639|928-929/2049|310/682|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1|||EntrezGene|||||||25||||||||||||||||||||VUS|0.30903387|HP:0000951&HP:0003124||AD&AR|LP|||||||||||LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM 1|1:.:10:AR:.:0:3949:1 0|1:.:10:.:.:.:.:. 1|0:25,25:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:. 0|0:50,0:50:.:.:.:.:.
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  19 17449399 . C T . PASS . GT:AD:DP:VI:VIC:VID:VIM 1|0:25,25:50:AD:.:1:0 0|0:50,0:50:.:.:.:. 0|0:50,0:50:.:.:.:. 0|0:50,0:50:.:.:.:. 0|0:50,0:50:.:.:.:. 0|0:50,0:50:.:.:.:.
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  19 17451997 . GA G . PASS CSQ=-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_001128855.3|protein_coding|8/9||NM_001128855.3:c.1058del|NP_001122327.1:p.Asn353ThrfsTer26|1117/2503|1058/1416|353/471|N/X|aAc/ac||1||1|||EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.9804278|HP:0000951||AR|LP|||||||||||LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_001195422.1|protein_coding|8/9||NM_001195422.1:c.1187del|NP_001182351.1:p.Asn396ThrfsTer26|1209/2595|1187/1545|396/514|N/X|aAc/ac||1||1|||EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.98119754|HP:0000951||AR|LP|||||||||||LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_032620.4|protein_coding|8/9||NM_032620.4:c.1121del|NP_116009.2:p.Asn374ThrfsTer26|1180/2566|1121/1479|374/492|N/X|aAc/ac||1||1|||EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.98185974|HP:0000951||AR|LP|||||||||||LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_133644.4|protein_coding|7/8||NM_133644.4:c.1217del|NP_598399.2:p.Asn406ThrfsTer26|1276/2662|1217/1575|406/524|N/X|aAc/ac||1||1||1|EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.97986597|HP:0000951||AR|LP|||||||||||LP|filter&vkgl&exit_lp| GT:AD:DP:VIC:VID:VIM 1|1:0,50:50:.:1:0 0|0:10,0:10:.:.:. 0|0:50,0:50:.:.:. 1|0:25,25:50:.:.:. 1|1:0,50:50:.:.:. 1|1:0,50:50:.:.:.
package/src/utils/query.ts CHANGED
@@ -18,7 +18,14 @@ export function createSampleQuery(
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  filters: FilterQueries | undefined,
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  metadata: Metadata
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  ): Query | null {
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- const sampleQuery: QueryClause = { selector: ["s", sample.data.index, "GT", "t"], operator: "!=", args: "hom_r" };
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+ const genotypeSelector: Selector = ["s", sample.data.index, "GT", "t"];
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+ const sampleQuery: Query = {
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+ operator: "and",
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+ args: [
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+ { selector: genotypeSelector, operator: "!=", args: "hom_r" },
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+ { selector: genotypeSelector, operator: "!=", args: "miss" },
27
+ ],
28
+ };
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  const searchFilterQuery = createQuery(search, filters, metadata);
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  const query: Query =
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  searchFilterQuery !== null ? { operator: "and", args: [sampleQuery, searchFilterQuery] } : sampleQuery;