add default option to strip leading chevrons

3 files changed, 20 insertions, 6 deletions

diff --git a/index.html b/index.html
index 6e0aa55..d0da373 100644
--- a/index.html
+++ b/index.html
@@ -14,8 +14,11 @@
         <label for='pni-threshold'>threshold:</label>
         <input id='pni-threshold' name='pni-threshold' type='text' size='5' value='90.5'>%
         <br>
+        <label for='strip-chevron'>strip leading chevron (<code>&gt;</code>)</label>
+        <input id='strip-chevron' name='strip-chevron' type='checkbox' checked>
+        <br>
         <label for='ignore-header'>ignore header line:</label>
-        <input id='ignore-header' name='ignore-header' type=checkbox checked>
+        <input id='ignore-header' name='ignore-header' type='checkbox'>
         <br>
         <label for='csv-input'>upload:</label>
         <input id='csv-input' name='csv-input' type='file' accept='text/csv' required>
diff --git a/pnit-form.mjs b/pnit-form.mjs
index f85457b..50624c0 100644
--- a/pnit-form.mjs
+++ b/pnit-form.mjs
@@ -17,6 +17,10 @@ export default class extends HTMLElement {
         return this.form.querySelector('input[name="ignore-header"]').checked;
     }
 
+    get stripChevron() {
+        return this.form.querySelector('input[name="strip-chevron"]').checked;
+    }
+
     get threshold() {
         return Number(this.form.querySelector('input[name="pni-threshold"]').value);
     }
@@ -81,6 +85,7 @@ export default class extends HTMLElement {
         }
         this.files.forEach(file => {
             worker.postMessage({
+                stripChevron: this.stripChevron,
                 ignoreHeader: this.ignoreHeader,
                 threshold: this.threshold,
                 file
diff --git a/worker.js b/worker.js
index 4812203..b469e92 100644
--- a/worker.js
+++ b/worker.js
@@ -1,10 +1,12 @@
 import CSVParse from './csv-parse.mjs';
 
+let stripChevron = true;
+let threshold = 0;
 let ignoreLines = 0;
 let sequenceNames = [];
 
-function process(threshold, row) {
-    const name = row[0];
+function process(row) {
+    let name = row[0];
     if (name === undefined || /^\s*$/.test(name)) {
         return;
     }
@@ -12,6 +14,9 @@ function process(threshold, row) {
         ignoreLines--;
         return;
     }
+    if (stripChevron && name[0] === '>') {
+        name = name.substring(1);
+    }
     sequenceNames.push(name);
 
     let i = 0;
@@ -32,8 +37,9 @@ onmessage = e => {
     console.debug('reading file');
 
     console.debug('e.data', e.data);
-    const { ignoreHeader, threshold, file } = e.data;
-    console.debug('threshold', threshold, 'file', file);
+    stripChevron = e.data.stripChevron;
+    threshold = e.data.threshold;
+    const { ignoreHeader, file } = e.data;
 
     const reader = new FileReader();
     reader.onload = e => {
@@ -44,7 +50,7 @@ onmessage = e => {
         if (ignoreHeader) {
             ignoreLines = 1;
         }
-        parser.results.forEach(row => process(threshold, row));
+        parser.results.forEach(process);
     }
     reader.progress = e => {
         console.debug('reader.progress', e);