Allow nimble runs to provide a custom value for num_mismatches

Author: bbimber

singlecell/resources/web/singlecell/panel/NimbleAlignPanel.js

@@ -41,7 +41,7 @@ Ext4.define('SingleCell.panel.NimbleAlignPanel', {
 				},LABKEY.ext4.GRIDBUTTONS.DELETERECORD()],
 				store: {
 					type: 'array',
-					fields: ['genomeId', 'template', 'grouping', 'scorePercent']
+					fields: ['genomeId', 'template', 'grouping', 'scorePercent', 'numMismatches']
 				},
 				columns: [{
 					dataIndex: 'genomeId',
@@ -85,6 +85,16 @@ Ext4.define('SingleCell.panel.NimbleAlignPanel', {
 					dataIndex: 'scorePercent',
 					width: 150,
 					header: 'Min Pct Aligned',
+					editor: {
+						xtype: 'ldk-numberfield',
+						minValue: 0,
+						maxValue: 1,
+						decimalPrecision: 2
+					}
+				},{
+					dataIndex: 'numMismatches',
+					width: 150,
+					header: 'Max Mismatches',
 					editor: {
 						xtype: 'ldk-integerfield',
 						minValue: 0
@@ -99,7 +109,7 @@ Ext4.define('SingleCell.panel.NimbleAlignPanel', {
 	getValue: function(){
 		var ret = [];
 		this.down('ldk-gridpanel').store.each(function(r, i) {
-			ret.push([r.data.genomeId, r.data.template, r.data.grouping || false, r.data.scorePercent || '']);
+			ret.push([r.data.genomeId, r.data.template, r.data.grouping || false, r.data.scorePercent || '', r.data.numMismatches || '']);
 		}, this);
 
 		return Ext4.isEmpty(ret) ? null : JSON.stringify(ret);
@@ -136,7 +146,8 @@ Ext4.define('SingleCell.panel.NimbleAlignPanel', {
 					genomeId: row[0],
 					template: row[1],
 					grouping: row[2],
-					scorePercent: row.length > 3 ? row[3] : null
+					scorePercent: row.length > 3 ? row[3] : null,
+					numMismatches: row.length > 4 ? row[4] : null
 				});
 				grid.store.add(rec);
 			}, this);

singlecell/src/org/labkey/singlecell/run/NimbleHelper.java

@@ -288,6 +288,12 @@ else if ("strict".equals(alignTemplate))
                 config.put("score_percent", genome.getScorePercent());
             }
 
+            if (genome.getNumMismatches() > 0)
+            {
+                getPipelineCtx().getLogger().debug("Using custom num_mismatches: " + genome.getNumMismatches());
+                config.put("num_mismatches", genome.getNumMismatches());
+            }
+
             getPipelineCtx().getLogger().info("Final config:");
             getPipelineCtx().getLogger().info(config.toString(1));
 
@@ -570,6 +576,7 @@ private static class NimbleGenome
         private final boolean doGroup;
         private final int maxHitsToReport;
         private final double scorePercent;
+        private final int numMismatches;
 
         public NimbleGenome(JSONArray arr, int maxHitsToReport) throws PipelineJobException
         {
@@ -585,6 +592,9 @@ public NimbleGenome(JSONArray arr, int maxHitsToReport) throws PipelineJobExcept
             String rawScore = arr.length() > 3 ? StringUtils.trimToNull(arr.getString(3)) : null;
             scorePercent = rawScore == null ? -1.0 : Double.parseDouble(rawScore);
 
+            String rawMismatches = arr.length() > 4 ? StringUtils.trimToNull(arr.getString(4)) : null;
+            numMismatches = rawMismatches == null ? -1 : Integer.parseInt(rawMismatches);
+
             this.maxHitsToReport = maxHitsToReport;
         }
 
@@ -607,5 +617,10 @@ public double getScorePercent()
         {
             return scorePercent;
         }
+
+        public Integer getNumMismatches()
+        {
+            return numMismatches;
+        }
     }
 }