From 5a3df4b6805b02ea9299549dda3e7d181fabeaf2 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Fri, 16 Feb 2018 02:47:48 -0500
Subject: [PATCH] Parse autosql table

---
 src/JBrowse/Store/SeqFeature/BigBed.js        |  2 +-
 src/JBrowse/Store/SeqFeature/BigWig.js        | 37 +++++++++++++++++++
 .../Store/SeqFeature/BigWig/RequestWorker.js  | 21 +++++++++--
 src/JBrowse/Store/SeqFeature/BigWig/Window.js |  3 +-
 4 files changed, 58 insertions(+), 5 deletions(-)

diff --git a/src/JBrowse/Store/SeqFeature/BigBed.js b/src/JBrowse/Store/SeqFeature/BigBed.js
index dcbe0880eb..32ad5d78d8 100644
--- a/src/JBrowse/Store/SeqFeature/BigBed.js
+++ b/src/JBrowse/Store/SeqFeature/BigBed.js
@@ -72,7 +72,7 @@ return declare(BigWig,
             if (nzl) {
                 cirLen = this.zoomLevels[0].dataOffset - this.unzoomedIndexOffset;
             }
-            this.unzoomedView = new Window( this, this.unzoomedIndexOffset, cirLen, false );
+            this.unzoomedView = new Window( this, this.unzoomedIndexOffset, cirLen, false, this.autoSql );
         }
         return this.unzoomedView;
     }
diff --git a/src/JBrowse/Store/SeqFeature/BigWig.js b/src/JBrowse/Store/SeqFeature/BigWig.js
index 249ea512e2..09f63e4b23 100644
--- a/src/JBrowse/Store/SeqFeature/BigWig.js
+++ b/src/JBrowse/Store/SeqFeature/BigWig.js
@@ -134,6 +134,7 @@ return declare([ SeqFeatureStore, DeferredFeaturesMixin, DeferredStatsMixin ],
             this.totalSummaryOffset = data.getUint64();
             this.uncompressBufSize = data.getUint32();
 
+
             // dlog('bigType: ' + this.type);
             // dlog('chromTree at: ' + this.chromTreeOffset);
             // dlog('uncompress: ' + this.uncompressBufSize);
@@ -152,6 +153,19 @@ return declare([ SeqFeatureStore, DeferredFeaturesMixin, DeferredStatsMixin ],
                 this.zoomLevels.push({reductionLevel: zlReduction, dataOffset: zlData, indexOffset: zlIndex});
             }
 
+            var string = "";
+            var c = 0;
+            data.getBytes(72);
+
+            
+            while(true) {
+                c = data.getChar();
+                if(c.charCodeAt() == 0) break;
+                string += c;
+            }
+            this.parseAutoSql(string);
+
+
             // parse the totalSummary if present (summary of all data in the file)
             if( this.totalSummaryOffset ) {
                 (function() {
@@ -340,6 +354,29 @@ return declare([ SeqFeatureStore, DeferredFeaturesMixin, DeferredStatsMixin ],
         return this.getUnzoomedView();
     },
 
+    parseAutoSql: function(string) {
+        var res = string.split('\n');
+        this.autoSql = {
+            name: /table (\w+)/.exec(res[0])[1],
+            description: /"([\w\s]+)"/.exec(res[1])[1],
+            fields: []
+        };
+        var i = 3;
+        var field;
+        while(res[i].trim() != ')') {
+            if(field = /([\w\[\]0-9]+)\s*(\w+)\s*;\s*"(.*)"/.exec(res[i].trim())) {
+                this.autoSql.fields.push({
+                    type: field[1],
+                    name: field[2],
+                    description: field[3]
+                });
+            } else {
+                console.warn('autosql line not parsed', res[i]);
+            }
+            i++;
+        }
+    },
+
 
     saveStore: function() {
         return {
diff --git a/src/JBrowse/Store/SeqFeature/BigWig/RequestWorker.js b/src/JBrowse/Store/SeqFeature/BigWig/RequestWorker.js
index 1659b1e1a4..1914972b9a 100644
--- a/src/JBrowse/Store/SeqFeature/BigWig/RequestWorker.js
+++ b/src/JBrowse/Store/SeqFeature/BigWig/RequestWorker.js
@@ -304,6 +304,20 @@ var RequestWorker = declare( null,
             } else if (chromId == this.chr && start <= this.max && end >= this.min) {
                 // Complex-BED?
                 // FIXME this is currently a bit of a hack to do Clever Things with ensGene.bb
+                var auto = this.window.autoSql;
+                for(var i = 0; i < auto.fields.length-3; i++) {
+                    featureOpts[auto.fields[i+3].name] = bedColumns[i];
+                }
+                delete featureOpts.blockCount;
+                delete featureOpts.blockSizes;
+                delete featureOpts.thickStart;
+                delete featureOpts.thickEnd;
+                delete featureOpts.reserved;
+                delete featureOpts.chromStarts;
+                delete featureOpts.strand;
+                delete featureOpts.score;
+                delete featureOpts.name;
+                delete featureOpts.override_color;
 
                 var thickStart = bedColumns[3]|0;
                 var thickEnd   = bedColumns[4]|0;
@@ -311,13 +325,14 @@ var RequestWorker = declare( null,
                 var blockSizes = bedColumns[7].split(',');
                 var blockStarts = bedColumns[8].split(',');
 
-                var grp = {
+
+                var grp = dojo.mixin(featureOpts, {
                     id: bedColumns[0]+'_'+chromId+'_'+start+'_'+end,
                     type: 'mRNA',
                     notes: [],
-                    strand: featureOpts.orientation=="+"?1:-1,
+                    strand: featureOpts.orientation == "+"?1:-1,
                     subfeatures: []
-                };
+                });
 
                 if (bedColumns.length > 10) {
                     var geneId = bedColumns[9];
diff --git a/src/JBrowse/Store/SeqFeature/BigWig/Window.js b/src/JBrowse/Store/SeqFeature/BigWig/Window.js
index 817f3b730c..28c72ea4bc 100644
--- a/src/JBrowse/Store/SeqFeature/BigWig/Window.js
+++ b/src/JBrowse/Store/SeqFeature/BigWig/Window.js
@@ -21,8 +21,9 @@ return declare( null,
      * Explorer by Thomas Down.
      * @constructs
      */
-    constructor: function(bwg, cirTreeOffset, cirTreeLength, isSummary) {
+    constructor: function(bwg, cirTreeOffset, cirTreeLength, isSummary, autoSql) {
         this.bwg = bwg;
+        this.autoSql = autoSql;
         if( !( cirTreeOffset >= 0 ) )
             throw "invalid cirTreeOffset!";
         if( !( cirTreeLength > 0 ) )