feat(data): remove F5

PharmGKB · Mar 26, 2024 · 0c6123b · 0c6123b
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diff --git a/docs/Genes-and-Drugs.md b/docs/Genes-and-Drugs.md
@@ -51,7 +51,6 @@ HLA calls, respectively, using sequencing data.
 | Gene | CPIC | PharmGKB-DPWG |
 | :--- | :---: | :---: |
 | [CYP2D6](/Phenotypes-List#cyp2d6) | :heavy_check_mark: | :heavy_check_mark: |
-| [F5](/Phenotypes-List#f5) |  | :heavy_check_mark: |
 | [HLA-A](/Phenotypes-List#hla-a) | :heavy_check_mark: | :heavy_check_mark: |
 | [HLA-B](/Phenotypes-List#hla-b) | :heavy_check_mark: | :heavy_check_mark: |
 | [MT-RNR1](/Phenotypes-List#mt-rnr1) | :heavy_check_mark: |  |
@@ -104,7 +103,6 @@ The following table lists drugs for which PharmCAT has recommendations for, alon
 | gentamicin | :heavy_check_mark: |  |
 | haloperidol |  | :heavy_check_mark: |
 | halothane | :heavy_check_mark: |  |
-| hormonal contraceptives for systemic use |  | :heavy_check_mark: |
 | hydrocodone | :heavy_check_mark: |  |
 | ibuprofen | :heavy_check_mark: |  |
 | imipramine | :heavy_check_mark: | :heavy_check_mark: |

diff --git a/docs/Phenotypes-List.md b/docs/Phenotypes-List.md
@@ -165,18 +165,6 @@ If you are using [outside calls](/using/Outside-Call-Format), you can see how we
 </tr>
 </table>
 
-### F5
-<table>
-<tr>
-<th style="text-align: left">Variants</th>
-<th style="text-align: left">DPWG Phenotypes</th>
-</tr>
-<tr>
-<td style="vertical-align: top"><ul style="padding-left: 1rem"><li>rs6025 C</li><li>rs6025 T (Factor V Leiden)</li></ul></td>
-<td style="vertical-align: top"><ul style="padding-left: 1rem"><li>Factor V Leiden absent</li><li>Factor V Leiden heterozygous</li><li>Factor V Leiden homozygous</li></ul></td>
-</tr>
-</table>
-
 ### G6PD
 <table>
 <tr>

diff --git a/docs/examples/pharmcat.example.match.html b/docs/examples/pharmcat.example.match.html
@@ -147,15 +147,6 @@ <h3>DPYD</h3>
   <tr><th class="first"></th><td>G</td><td>C</td><td>C</td><td>C</td><td>A</td><td>G</td><td>T</td><td>T</td><td>T</td><td>T</td><td>T</td><td>C</td><td>G</td><td>C</td><td>T</td><td>T</td><td>C</td><td>G</td><td>G</td><td>G</td><td>A</td><td>C</td><td>G</td><td>C</td><td>C</td><td>C</td><td>T</td><td>C</td><td>G</td><td>TG</td><td>A</td><td>A</td><td>C</td><td>C</td><td>G</td><td>C</td><td>A</td><td>T</td><td>C</td><td>C</td><td>G</td><td>C</td><td>C</td><td>T</td><td>G</td><td>G</td><td>G</td><td>G</td><td>G</td><td>A</td><td>C</td><td>C</td><td>A</td><td>C</td><td>C</td><td>G</td><td>C</td><td>T</td><td>G</td><td>C</td><td>C</td><td>C</td><td>G</td><td>A</td><td>T</td><td>T</td><td>G</td><td>T</td><td>T</td><td>T</td><td>C</td><td>C</td><td>T</td><td>T</td><td>T</td><td>C</td><td>GATGA</td><td>A</td><td>C</td><td>G</td><td>G</td></tr>
 </table>
 
-<h3>F5</h3>
-<ul>  <li>rs6025 C/rs6025 C (2)</li></ul>
-<table class="table table-striped table-hover table-sm">
-  <tr><th class="first">Definition Position</th><th>169549811</th></tr>  <tr><th></th><th>rs6025</th></tr>  <tr><th class="first">VCF Position</th><th>169549811</th></tr>  <tr><th class="first">VCF REF,ALTs</th><th>C,T</th></tr>
-  <tr class="table-success"><th class="first">VCF Call</th><th>C/C</th></tr>
-  <tr class="table-info"><th class="first">rs6025 C</th><td><b>C</b></td></tr>
-  <tr><th class="first"></th><td>C</td></tr>
-</table>
-
 <h3>G6PD</h3>
 <ul>  <li>B (reference)/B (reference) (342)</li></ul>
 <table class="table table-striped table-hover table-sm">
@@ -234,7 +225,7 @@ <h3>VKORC1</h3>
   <hr />
   <footer class="container-fluid">
     <p>
-      <small>Generated on 03/11/24.</small>
+      <small>Generated on 03/25/24.</small>
     </p>
   </footer>
 </div>

diff --git a/docs/examples/pharmcat.example.match.json b/docs/examples/pharmcat.example.match.json
@@ -3,7 +3,7 @@
     "namedAlleleMatcherVersion": "2.0.0",
     "genomeBuild": "GRCh38.p13",
     "inputFilename": "pharmcat.example.vcf",
-    "timestamp": "2024-03-11T16:40:18.457Z",
+    "timestamp": "2024-03-26T04:55:24.238Z",
     "topCandidatesOnly": true,
     "findCombinations": false,
     "callCyp2d": false
@@ -2958,7 +2958,7 @@
     },
     {
       "source": "PHARMGKB",
-      "version": "2024-03-11-09-29",
+      "version": "2024-03-25-16-13",
       "chromosome": "chr7",
       "gene": "CYP3A4",
       "diplotypes": [
@@ -5008,102 +5008,6 @@
       "ignoredHaplotypes": [],
       "warnings": []
     },
-    {
-      "source": "PHARMGKB",
-      "version": "2024-03-11-09-29",
-      "chromosome": "chr1",
-      "gene": "F5",
-      "diplotypes": [
-        {
-          "name": "rs6025 C/rs6025 C",
-          "haplotype1": {
-            "name": "rs6025 C",
-            "haplotype": {
-              "name": "rs6025 C",
-              "id": "PA166300382",
-              "alleles": [
-                "C"
-              ],
-              "cpicAlleles": [
-                "C"
-              ],
-              "populationFrequency": null,
-              "reference": true,
-              "numCombinations": 0,
-              "numPartials": 0
-            },
-            "sequences": [
-              "169549811:C;"
-            ]
-          },
-          "haplotype2": {
-            "name": "rs6025 C",
-            "haplotype": {
-              "name": "rs6025 C",
-              "id": "PA166300382",
-              "alleles": [
-                "C"
-              ],
-              "cpicAlleles": [
-                "C"
-              ],
-              "populationFrequency": null,
-              "reference": true,
-              "numCombinations": 0,
-              "numPartials": 0
-            },
-            "sequences": [
-              "169549811:C;"
-            ]
-          },
-          "score": 2
-        }
-      ],
-      "haplotypes": [
-        {
-          "name": "rs6025 C",
-          "haplotype": {
-            "name": "rs6025 C",
-            "id": "PA166300382",
-            "alleles": [
-              "C"
-            ],
-            "cpicAlleles": [
-              "C"
-            ],
-            "populationFrequency": null,
-            "reference": true,
-            "numCombinations": 0,
-            "numPartials": 0
-          },
-          "sequences": [
-            "169549811:C;"
-          ]
-        }
-      ],
-      "haplotypeMatches": [],
-      "phased": false,
-      "variants": [
-        {
-          "position": 169549811,
-          "rsid": "rs6025",
-          "vcfCall": "C/C",
-          "phased": false
-        }
-      ],
-      "variantsOfInterest": [],
-      "matchData": {
-        "missingPositions": [],
-        "positionsWithUndocumentedVariations": [],
-        "treatUndocumentedVariationsAsReference": false,
-        "phased": false,
-        "homozygous": true,
-        "effectivelyPhased": true
-      },
-      "uncallableHaplotypes": [],
-      "ignoredHaplotypes": [],
-      "warnings": null
-    },
     {
       "source": "CPIC",
       "version": "v1.38.0-1-g39f50e7",