From 06886515f8d13d769d10373771b38bdbc1e404d7 Mon Sep 17 00:00:00 2001
From: Felix Wiegand <fxwiegand@wgdnet.de>
Date: Mon, 19 Apr 2021 10:37:01 +0200
Subject: [PATCH] Stop displaying undefined values in side table of vcf-report
 (#145)
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* Stop displaying undefined values in side table of vcf-report
This fixes #144.

* Update CHANGELOG.md

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
---
 CHANGELOG.md                      |  5 ++--
 src/bcf/report/js/table-report.js | 44 +++++++++++++++++--------------
 2 files changed, 27 insertions(+), 22 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0a0a167f..7e094469 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,9 +3,10 @@ All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [0.20.5] - 2021-04-19
+### Changed
+- Bugfix for `rbt vcf-report` that stops displaying undefined values in the table-report.
 ### Added
-- New parameter `--pin-until` for `rbt csv-report`.
-- `--pin-until` pins the table until the given column such that scrolling to the right does not hide the given column and those before.
+- New parameter `--pin-until` for `rbt csv-report`. `--pin-until` pins the table until the given column such that scrolling to the right does not hide the given column and those before.
 
 ## [0.20.4] - 2021-04-15
 ### Changed
diff --git a/src/bcf/report/js/table-report.js b/src/bcf/report/js/table-report.js
index 2b9a1eaa..c285bc28 100644
--- a/src/bcf/report/js/table-report.js
+++ b/src/bcf/report/js/table-report.js
@@ -83,29 +83,33 @@ $(document).ready(function () {
                 let ix = x + 1;
                 let field = 'ann[' + j + '][' + ix + ']';
                 let vl = $(that).data(field);
-                if (name === "Existing_variation" && vl) {
-                    let fields = vl.split('&');
-                    let result = "";
-                    for (var o = 0; o < fields.length; o++) {
-                        let val = fields[o];
-                        if (val.startsWith("rs")) {
-                            result = result + "<a href='https://www.ncbi.nlm.nih.gov/snp/" + val + "'>" + val + "</a>";
-                        } else if (val.startsWith("COSM")) {
-                            let num = val.replace( /^\D+/g, '');
-                            result = result + "<a href='https://cancer.sanger.ac.uk/cosmic/mutation/overview?id=" + num + "'>" + val + "</a>";
-                        } else if (val.startsWith("COSN")) {
-                            let num = val.replace( /^\D+/g, '');
-                            result = result + "<a href='https://cancer.sanger.ac.uk/cosmic/ncv/overview?id=" + num + "'>" + val + "</a>";
-                        } else {
-                            result = result + val;
-                        }
-                        if (!(o === fields.length - 1)) {
-                            result = result + ", ";
+                if (vl) {
+                    if (name === "Existing_variation") {
+                        let fields = vl.split('&');
+                        let result = "";
+                        for (var o = 0; o < fields.length; o++) {
+                            let val = fields[o];
+                            if (val.startsWith("rs")) {
+                                result = result + "<a href='https://www.ncbi.nlm.nih.gov/snp/" + val + "'>" + val + "</a>";
+                            } else if (val.startsWith("COSM")) {
+                                let num = val.replace( /^\D+/g, '');
+                                result = result + "<a href='https://cancer.sanger.ac.uk/cosmic/mutation/overview?id=" + num + "'>" + val + "</a>";
+                            } else if (val.startsWith("COSN")) {
+                                let num = val.replace( /^\D+/g, '');
+                                result = result + "<a href='https://cancer.sanger.ac.uk/cosmic/ncv/overview?id=" + num + "'>" + val + "</a>";
+                            } else {
+                                result = result + val;
+                            }
+                            if (!(o === fields.length - 1)) {
+                                result = result + ", ";
+                            }
                         }
+                        vl = result;
                     }
-                    vl = result;
+                    $('#ann-sidebar').append('<td>' + vl + '</td>');
+                } else {
+                    $('#ann-sidebar').append('<td></td>');
                 }
-                $('#ann-sidebar').append('<td>' + vl + '</td>');
             }
             $('#ann-sidebar').append('</tr>');
         });