From 83591adf2d154c45ecf5e64c87e4ba1635e874b6 Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Mon, 24 Jul 2023 09:24:15 +0200
Subject: [PATCH] start of CSQ code

see #146
---
 docker/Dockerfile |  2 +-
 js/csq.js         | 34 ++++++++++++++++++++++++++++++++++
 2 files changed, 35 insertions(+), 1 deletion(-)
 create mode 100644 js/csq.js

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 451d784..b2bd723 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -52,7 +52,7 @@ RUN cd / && \
     export PATH=/nim/bin:$PATH && \
     git clone https://github.com/iffy/nim-argparse && cd nim-argparse && git checkout v0.10.1 && nimble install -y && \
     cd .. && rm -rf nim-argparse && \
-    git clone --depth 1 git://github.com/brentp/slivar.git && \
+    git clone --depth 1 https://github.com/brentp/slivar.git && \
     cd slivar && \
     sed -i 's/-no-pie//' nim.cfg && \
     nimble install -y &&  \
diff --git a/js/csq.js b/js/csq.js
new file mode 100644
index 0000000..09e5cbe
--- /dev/null
+++ b/js/csq.js
@@ -0,0 +1,34 @@
+var CSQ = function (info_csq, csq_names, numeric_fields) {
+    var csq = this;
+    csq._values = info_csq.split('|');
+    csq._numeric_fields = numeric_fields;
+    // create an object of key => index from vcf_csq
+    csq._names = {};
+    csq_names.forEach(function (name, index) { csq._names[name] = index; });
+
+    return new Proxy(csq, {
+        get: function (target, name) {
+            if (name in target._names) {
+                var result = target._values[target._names[name]];
+                if (target._numeric_fields[name]) {
+                    result = parseFloat(result);
+                }
+
+                return result
+            }
+            throw "unknown CSQ field: " + name;
+        }
+    });
+};
+
+function CSQs(csq_string, vcf_csq, numeric_fields) {
+    // if numeric fields is an array, turn it into an object
+    if (Array.isArray(numeric_fields)) {
+        var numeric_fields_obj = {};
+        numeric_fields.forEach(function (field) { numeric_fields_obj[field] = true; });
+        numeric_fields = numeric_fields_obj;
+    }
+
+    csqs = csq_string.split(',');
+    return csqs.map(function (csq) { return new CSQ(csq, vcf_csq, numeric_fields); });
+}
\ No newline at end of file