Skip to content

Commit

Permalink
fix: customize CYP2C19 definition to support set-missing-to-reference
Browse files Browse the repository at this point in the history
  • Loading branch information
@markwoon
markwoon committed Mar 19, 2024
1 parent 86640e7 commit 1f796c2
Show file tree
Hide file tree
Showing 13 changed files with 116 additions and 54 deletions.
2 changes: 1 addition & 1 deletion Dockerfile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ FROM python:3.10

# apt-utils line due to https://github.com/phusion/baseimage-docker/issues/319
RUN apt-get update && \
apt-get install -y --no-install-recommends apt-utils apt-transport-https gnupg && \
apt-get install -y --no-install-recommends apt-utils apt-transport-https gnupg libncurses5-dev && \
apt-get -y upgrade && \
apt-get -y install bzip2 build-essential wget

Expand Down
2 changes: 1 addition & 1 deletion docs/examples/pharmcat.example.match.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -234,7 +234,7 @@ <h3>VKORC1</h3>
<hr />
<footer class="container-fluid">
<p>
<small>Generated on 03/11/24.</small>
<small>Generated on 03/19/24.</small>
</p>
</footer>
</div>
Expand Down
2 changes: 1 addition & 1 deletion docs/examples/pharmcat.example.match.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
"namedAlleleMatcherVersion": "2.0.0",
"genomeBuild": "GRCh38.p13",
"inputFilename": "pharmcat.example.vcf",
"timestamp": "2024-03-11T16:40:18.457Z",
"timestamp": "2024-03-19T20:25:39.927Z",
"topCandidatesOnly": true,
"findCombinations": false,
"callCyp2d": false
Expand Down
6 changes: 6 additions & 0 deletions docs/examples/pharmcat.example.phenotype.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2179,6 +2179,7 @@
"*13",
"*14",
"*15",
"*16",
"*17",
"*18",
"*19",
Expand All @@ -2189,9 +2190,11 @@
"*26",
"*28",
"*29",
"*30",
"*31",
"*32",
"*33",
"*34",
"*35",
"*39"
],
Expand Down Expand Up @@ -16160,6 +16163,7 @@
"*13",
"*14",
"*15",
"*16",
"*17",
"*18",
"*19",
Expand All @@ -16170,9 +16174,11 @@
"*26",
"*28",
"*29",
"*30",
"*31",
"*32",
"*33",
"*34",
"*35",
"*39"
],
Expand Down
12 changes: 9 additions & 3 deletions docs/examples/pharmcat.example.report.html
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<!DOCTYPE html>
!DOCTYPE html>
<html class="no-js" lang="en">
<head>
<meta charset="utf-8" />
Expand Down Expand Up @@ -404,8 +404,8 @@
</div>
<div class="metadata">
<table>
<tr><th>Date created</th><td>March 11, 2024</td></tr>
<tr><th>PharmCAT Version</th><td>v2.9.0-28-gfe7ecab4</td></tr>
<tr><th>Date created</th><td>March 19, 2024</td></tr>
<tr><th>PharmCAT Version</th><td>v2.9.0-29-g86640e71</td></tr>
<tr><th>CPIC Version</th><td>v1.38.0-1-g39f50e7</td></tr>
</table>
</div>
Expand Down Expand Up @@ -15972,6 +15972,8 @@ <h4>Calls at Positions</h4>

<li>*15 - Normal function</li>

<li>*16 - Decreased function</li>

<li>*17 - Increased function</li>

<li>*18 - Normal function</li>
Expand All @@ -15992,12 +15994,16 @@ <h4>Calls at Positions</h4>

<li>*29 - Uncertain function</li>

<li>*30 - Uncertain function</li>

<li>*31 - Uncertain function</li>

<li>*32 - Uncertain function</li>

<li>*33 - Uncertain function</li>

<li>*34 - Uncertain function</li>

<li>*35 - No function</li>

<li>*39 - Uncertain function</li>
Expand Down
10 changes: 8 additions & 2 deletions docs/examples/pharmcat.example.report.json
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"title": "pharmcat.example",
"timestamp": "2024-03-11T16:40:22.298Z",
"pharmcatVersion": "v2.9.0-28-gfe7ecab4",
"timestamp": "2024-03-19T20:25:43.971Z",
"pharmcatVersion": "v2.9.0-29-g86640e71",
"cpicVersion": "v1.38.0-1-g39f50e7",
"dpwgVersion": "2024-03-11-09-29",
"genes": {
Expand Down Expand Up @@ -2289,6 +2289,7 @@
"*13",
"*14",
"*15",
"*16",
"*17",
"*18",
"*19",
Expand All @@ -2299,9 +2300,11 @@
"*26",
"*28",
"*29",
"*30",
"*31",
"*32",
"*33",
"*34",
"*35",
"*39"
],
Expand Down Expand Up @@ -16842,6 +16845,7 @@
"*13",
"*14",
"*15",
"*16",
"*17",
"*18",
"*19",
Expand All @@ -16852,9 +16856,11 @@
"*26",
"*28",
"*29",
"*30",
"*31",
"*32",
"*33",
"*34",
"*35",
"*39"
],
Expand Down
4 changes: 2 additions & 2 deletions docs/examples/pharmcat.example2.match.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ <h3>CYP2C19</h3>
<table class="table table-striped table-hover table-sm">
<tr><th class="first">Definition Position</th><th>94761900</th><th>94762706</th><th>94762712</th><th>94762715</th><th>94762755</th><th>94762760</th><th>94762788</th><th>94762856</th><th>94775106</th><th>94775121</th><th>94775160</th><th>94775185</th><th>94775367</th><th>94775416</th><th>94775423</th><th>94775453</th><th>94775489</th><th>94775507</th><th>94780574</th><th>94780579</th><th>94780653</th><th>94781858</th><th>94781859</th><th>94781944</th><th>94781999</th><th>94842861</th><th>94842866</th><th>94842879</th><th>94842995</th><th>94849995</th><th>94852738</th><th>94852765</th><th>94852785</th><th>94852914</th></tr> <tr><th></th><th>rs12248560</th><th>rs28399504</th><th>rs367543002</th><th>rs367543003</th><th>rs55752064</th><th>rs17882687</th><th>rs1564656981</th><th>rs1564657013</th><th>rs145328984</th><th>rs1564660997</th><th>rs118203756</th><th>rs1288601658</th><th>rs12769205</th><th>rs41291556</th><th>rs17885179</th><th>rs72552267</th><th>rs17884712</th><th>rs58973490</th><th>rs140278421</th><th>rs370803989</th><th>rs4986893</th><th>rs6413438</th><th>rs4244285</th><th>rs375781227</th><th>rs72558186</th><th>rs138142612</th><th>rs3758581</th><th>rs118203757</th><th>rs113934938</th><th>rs17879685</th><th>rs56337013</th><th>rs192154563</th><th>rs118203759</th><th>rs55640102</th></tr> <tr><th class="first">VCF Position</th><th>94761900</th><th>94762706</th><th>94762712</th><th>94762715</th><th>94762755</th><th>94762760</th><th>94762788</th><th>94762856</th><th>94775106</th><th>94775121</th><th>94775160</th><th>94775185</th><th>94775367</th><th>94775416</th><th>94775423</th><th>94775453</th><th>94775489</th><th>94775507</th><th>94780574</th><th>94780579</th><th>94780653</th><th>94781858</th><th>94781859</th><th>94781944</th><th>94781999</th><th>94842861</th><th>94842866</th><th>94842879</th><th>94842995</th><th>94849995</th><th>94852738</th><th>94852765</th><th>94852785</th><th>94852914</th></tr> <tr><th class="first">VCF REF,ALTs</th><th>C,T</th><th>A,G</th><th>C,T</th><th>T,C</th><th>T,C</th><th>A,C</th><th>A,T</th><th>A,G</th><th>C,T</th><th>C,T</th><th>G,C</th><th>A,G</th><th>A,G</th><th>T,C</th><th>A,C</th><th>G,A</th><th>G,A</th><th>G,A</th><th>G,C</th><th>G,A</th><th>G,A</th><th>C,T</th><th>G,A</th><th>G,A</th><th>T,A</th><th>G,A</th><th>A,G</th><th>G,A</th><th>G,A</th><th>C,T</th><th>C,T</th><th>C,T</th><th>C,G</th><th>A,C</th></tr>
<tr class="table-success"><th class="first">VCF Call</th><th>C/C</th><th>A/A</th><th>C/C</th><th>T/T</th><th>T/T</th><th>A/A</th><th>A/A</th><th>A/A</th><th>C/C</th><th>C/C</th><th>G/G</th><th>A/A</th><th class="table-danger">G/G</th><th>T/T</th><th>A/A</th><th>G/G</th><th>G/G</th><th>G/G</th><th>G/G</th><th>G/G</th><th>G/G</th><th>C/C</th><th class="table-danger">A/A</th><th>G/G</th><th>T/T</th><th>G/G</th><th class="table-danger">G/G</th><th>G/G</th><th>G/G</th><th>C/C</th><th>C/C</th><th>C/C</th><th>C/C</th><th>A/A</th></tr>
<tr class="table-info"><th class="first">*2</th><td><b>C</b></td><td><b>A</b></td><td><b>C</b></td><td><b>T</b></td><td><b>T</b></td><td><b>A</b></td><td><b>A</b></td><td><b>A</b></td><td><b>C</b></td><td><b>C</b></td><td><b>G</b></td><td><b>A</b></td><td class="table-danger"><b>G</b></td><td><b>T</b></td><td><b>A</b></td><td><b>G</b></td><td><b>G</b></td><td><b>[AG]</b></td><td><b>G</b></td><td><b>G</b></td><td><b>G</b></td><td><b>C</b></td><td class="table-danger"><b>A</b></td><td><b>G</b></td><td><b>T</b></td><td><b>G</b></td><td class="table-danger"><b>G</b></td><td><b>G</b></td><td><b>G</b></td><td><b>C</b></td><td><b>C</b></td><td><b>C</b></td><td><b>C</b></td><td><b>A</b></td></tr>
<tr class="table-info"><th class="first">*2</th><td><b>C</b></td><td><b>A</b></td><td><b>C</b></td><td><b>T</b></td><td><b>T</b></td><td><b>A</b></td><td><b>A</b></td><td><b>A</b></td><td><b>C</b></td><td><b>C</b></td><td><b>G</b></td><td><b>A</b></td><td class="table-danger"><b>[AG]</b></td><td><b>T</b></td><td><b>A</b></td><td><b>G</b></td><td><b>G</b></td><td><b>[AG]</b></td><td><b>G</b></td><td><b>G</b></td><td><b>G</b></td><td><b>C</b></td><td class="table-danger"><b>A</b></td><td><b>G</b></td><td><b>T</b></td><td><b>G</b></td><td class="table-danger"><b>[AG]</b></td><td><b>G</b></td><td><b>G</b></td><td><b>C</b></td><td><b>C</b></td><td><b>C</b></td><td><b>C</b></td><td><b>A</b></td></tr>
<tr><th class="first"></th><td>C</td><td>A</td><td>C</td><td>T</td><td>T</td><td>A</td><td>A</td><td>A</td><td>C</td><td>C</td><td>G</td><td>A</td><td class="table-danger">G</td><td>T</td><td>A</td><td>G</td><td>G</td><td>G</td><td>G</td><td>G</td><td>G</td><td>C</td><td class="table-danger">A</td><td>G</td><td>T</td><td>G</td><td class="table-danger">G</td><td>G</td><td>G</td><td>C</td><td>C</td><td>C</td><td>C</td><td>A</td></tr>
</table>

Expand Down Expand Up @@ -236,7 +236,7 @@ <h3>VKORC1</h3>
<hr />
<footer class="container-fluid">
<p>
<small>Generated on 03/11/24.</small>
<small>Generated on 03/19/24.</small>
</p>
</footer>
</div>
Expand Down
14 changes: 7 additions & 7 deletions docs/examples/pharmcat.example2.match.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
"namedAlleleMatcherVersion": "2.0.0",
"genomeBuild": "GRCh38.p13",
"inputFilename": "pharmcat.example2.vcf",
"timestamp": "2024-03-11T16:40:47.661Z",
"timestamp": "2024-03-19T20:26:02.661Z",
"topCandidatesOnly": true,
"findCombinations": false,
"callCyp2d": false
Expand Down Expand Up @@ -1551,7 +1551,7 @@
"C",
"G",
"A",
"G",
"R",
"T",
"A",
"G",
Expand All @@ -1565,7 +1565,7 @@
"G",
"T",
"G",
"G",
"R",
"G",
"G",
"C",
Expand Down Expand Up @@ -1637,7 +1637,7 @@
"C",
"G",
"A",
"G",
"R",
"T",
"A",
"G",
Expand All @@ -1651,7 +1651,7 @@
"G",
"T",
"G",
"G",
"R",
"G",
"G",
"C",
Expand Down Expand Up @@ -1727,7 +1727,7 @@
"C",
"G",
"A",
"G",
"R",
"T",
"A",
"G",
Expand All @@ -1741,7 +1741,7 @@
"G",
"T",
"G",
"G",
"R",
"G",
"G",
"C",
Expand Down
6 changes: 6 additions & 0 deletions docs/examples/pharmcat.example2.phenotype.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2171,6 +2171,7 @@
"*13",
"*14",
"*15",
"*16",
"*17",
"*18",
"*19",
Expand All @@ -2181,9 +2182,11 @@
"*26",
"*28",
"*29",
"*30",
"*31",
"*32",
"*33",
"*34",
"*35",
"*39"
],
Expand Down Expand Up @@ -16084,6 +16087,7 @@
"*13",
"*14",
"*15",
"*16",
"*17",
"*18",
"*19",
Expand All @@ -16094,9 +16098,11 @@
"*26",
"*28",
"*29",
"*30",
"*31",
"*32",
"*33",
"*34",
"*35",
"*39"
],
Expand Down
10 changes: 8 additions & 2 deletions docs/examples/pharmcat.example2.report.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -404,8 +404,8 @@
</div>
<div class="metadata">
<table>
<tr><th>Date created</th><td>March 11, 2024</td></tr>
<tr><th>PharmCAT Version</th><td>v2.9.0-28-gfe7ecab4</td></tr>
<tr><th>Date created</th><td>March 19, 2024</td></tr>
<tr><th>PharmCAT Version</th><td>v2.9.0-29-g86640e71</td></tr>
<tr><th>CPIC Version</th><td>v1.38.0-1-g39f50e7</td></tr>
</table>
</div>
Expand Down Expand Up @@ -11948,6 +11948,8 @@ <h4>Calls at Positions</h4>

<li>*15 - Normal function</li>

<li>*16 - Decreased function</li>

<li>*17 - Increased function</li>

<li>*18 - Normal function</li>
Expand All @@ -11968,12 +11970,16 @@ <h4>Calls at Positions</h4>

<li>*29 - Uncertain function</li>

<li>*30 - Uncertain function</li>

<li>*31 - Uncertain function</li>

<li>*32 - Uncertain function</li>

<li>*33 - Uncertain function</li>

<li>*34 - Uncertain function</li>

<li>*35 - No function</li>

<li>*39 - Uncertain function</li>
Expand Down
10 changes: 8 additions & 2 deletions docs/examples/pharmcat.example2.report.json
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"title": "pharmcat.example2",
"timestamp": "2024-03-11T16:40:51.409Z",
"pharmcatVersion": "v2.9.0-28-gfe7ecab4",
"timestamp": "2024-03-19T20:26:04.520Z",
"pharmcatVersion": "v2.9.0-29-g86640e71",
"cpicVersion": "v1.38.0-1-g39f50e7",
"dpwgVersion": "2024-03-11-09-29",
"genes": {
Expand Down Expand Up @@ -2300,6 +2300,7 @@
"*13",
"*14",
"*15",
"*16",
"*17",
"*18",
"*19",
Expand All @@ -2310,9 +2311,11 @@
"*26",
"*28",
"*29",
"*30",
"*31",
"*32",
"*33",
"*34",
"*35",
"*39"
],
Expand Down Expand Up @@ -16804,6 +16807,7 @@
"*13",
"*14",
"*15",
"*16",
"*17",
"*18",
"*19",
Expand All @@ -16814,9 +16818,11 @@
"*26",
"*28",
"*29",
"*30",
"*31",
"*32",
"*33",
"*34",
"*35",
"*39"
],
Expand Down
Loading

0 comments on commit 1f796c2

Please sign in to comment.