Switch nimble to use custom alignment percentage, rather than alignment length

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', 'scoreThreshold']
+					fields: ['genomeId', 'template', 'grouping', 'scorePercent']
 				},
 				columns: [{
 					dataIndex: 'genomeId',
@@ -82,9 +82,9 @@ Ext4.define('SingleCell.panel.NimbleAlignPanel', {
 						xtype: 'checkbox'
 					}
 				},{
-					dataIndex: 'scoreThreshold',
+					dataIndex: 'scorePercent',
 					width: 150,
-					header: 'Score Threshold',
+					header: 'Min Pct Aligned',
 					editor: {
 						xtype: 'ldk-integerfield',
 						minValue: 0
@@ -99,7 +99,7 @@ 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.scoreThreshold || '']);
+			ret.push([r.data.genomeId, r.data.template, r.data.grouping || false, r.data.scorePercent || '']);
 		}, this);
 
 		return Ext4.isEmpty(ret) ? null : JSON.stringify(ret);
@@ -136,7 +136,7 @@ Ext4.define('SingleCell.panel.NimbleAlignPanel', {
 					genomeId: row[0],
 					template: row[1],
 					grouping: row[2],
-					scoreThreshold: row.length > 3 ? row[3] : null
+					scorePercent: row.length > 3 ? row[3] : null
 				});
 				grid.store.add(rec);
 			}, this);

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

@@ -179,7 +179,7 @@ public void doNimbleAlign(File bam, PipelineStepOutput output, Readset rs, Strin
             output.addIntermediateFile(genomeFasta);
             output.addIntermediateFile(refJson);
 
-            String description = genome.getScoreThreshold() > 0 ? "score_threshold: " + genome.getScoreThreshold() : null;
+            String description = genome.getScorePercent() > 0 ? "score_percent: " + genome.getScorePercent() : null;
             output.addSequenceOutput(results, basename + ": nimble align", "Nimble Alignment", rs.getRowId(), null, genome.getGenomeId(), description);
         }
     }
@@ -231,6 +231,7 @@ private void updateNimbleConfigFile(File configFile, NimbleGenome genome) throws
                 config.put("num_mismatches", 10);
                 config.put("intersect_level", 0);
                 config.put("score_threshold", 45);
+                config.put("score_percent", 0.75);
                 config.put("score_filter", 25);
                 //discard_multiple_matches: false
                 //discard_multi_hits: ?
@@ -240,7 +241,8 @@ else if ("strict".equals(alignTemplate))
             {
                 config.put("num_mismatches", 0);
                 config.put("intersect_level", 0);
-                config.put("score_threshold", 50);
+                config.put("score_percent", 0.99);
+                config.put("score_threshold", 45);
                 config.put("score_filter", 25);
             }
             else
@@ -255,10 +257,10 @@ else if ("strict".equals(alignTemplate))
 
             config.put("max_hits_to_report", genome.maxHitsToReport);
 
-            if (genome.getScoreThreshold() > 0)
+            if (genome.getScorePercent() > 0)
             {
-                getPipelineCtx().getLogger().debug("Using custom score_threshold: " + genome.getScoreThreshold());
-                config.put("score_threshold", genome.getScoreThreshold());
+                getPipelineCtx().getLogger().debug("Using custom score_percent: " + genome.getScorePercent());
+                config.put("score_percent", genome.getScorePercent());
             }
 
             getPipelineCtx().getLogger().info("Final config:");
@@ -487,7 +489,7 @@ private static class NimbleGenome
         private final String template;
         private final boolean doGroup;
         private final int maxHitsToReport;
-        private final int scoreThreshold;
+        private final double scorePercent;
 
         public NimbleGenome(String genomeStr, int maxHitsToReport) throws PipelineJobException
         {
@@ -502,7 +504,7 @@ public NimbleGenome(String genomeStr, int maxHitsToReport) throws PipelineJobExc
             doGroup = arr.getBoolean(2);
 
             String rawScore = arr.length() > 3 ? StringUtils.trimToNull(arr.getString(3)) : null;
-            scoreThreshold = rawScore == null ? -1 : Integer.parseInt(rawScore);
+            scorePercent = rawScore == null ? -1.0 : Double.parseDouble(rawScore);
 
             this.maxHitsToReport = maxHitsToReport;
         }
@@ -522,9 +524,9 @@ public boolean isDoGroup()
             return doGroup;
         }
 
-        public int getScoreThreshold()
+        public double getScorePercent()
         {
-            return scoreThreshold;
+            return scorePercent;
         }
     }