Allow snpEff to process genbank files

Author: bbimber

SequenceAnalysis/resources/web/SequenceAnalysis/field/GenomeFileSelectorField.js

@@ -26,7 +26,7 @@ Ext4.define('SequenceAnalysis.field.GenomeFileSelectorField', {
                     load: function(store){
                         if (this.extensions) {
                             Ext4.Array.forEach(store.getRange(), function (r) {
-                                if (this.extensions.indexOf(r.get('fileid/FileExtension')) == -1){
+                                if (this.extensions.indexOf(r.get('fileid/FileExtension')) === -1){
                                     store.remove(r);
                                 }
                             }, this);
@@ -50,7 +50,7 @@ Ext4.define('SequenceAnalysis.field.GenomeFileSelectorField', {
                     }
                 }
                 else if (parent.libraryIds){
-                    if (parent.libraryIds.length == 1){
+                    if (parent.libraryIds.length === 1){
                         this.updateStoreFilters(parent.libraryIds[0]);
                     }
                     else if (!parent.libraryIds.length){

SequenceAnalysis/resources/web/SequenceAnalysis/window/ImportTrackWindow.js

@@ -51,8 +51,8 @@ Ext4.define('SequenceAnalysis.window.ImportTrackWindow', {
                     name: 'track',
                     allowBlank: false,
                     validator: function(){
-                        var matcher = /^.*\.(bed|gff|gff3|gtf|vcf|bigwig|bw)$/i;
-                        return matcher.test(this.getValue()) ? true : 'File must be either: .bed, .gff, .gff3, .gtf, .vcf, .bigwig, or .bw';
+                        var matcher = /^.*\.(bed|gff|gff3|gtf|vcf|bigwig|bw|gbk)$/i;
+                        return matcher.test(this.getValue()) ? true : 'File must be either: .bed, .gff, .gff3, .gtf, .gbk, .vcf, .bigwig, or .bw';
                     }
                 },{
                     xtype: 'textfield',

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/LofreqAnalysis.java

@@ -96,7 +96,7 @@ public Provider()
             super("LofreqAnalysis", "LoFreq Analysis", null, "This will run LowFreq, a tool designed to call low-frequency mutations in a sample, such as viral populations or bacteria.  It is recommended to run GATK's BQSR and IndelRealigner upstream of this tool.", Arrays.asList(
                     ToolParameterDescriptor.createExpDataParam(SNPEffStep.GENE_PARAM, "Gene File", "This is the ID of a GTF or GFF3 file containing genes from this genome.", "sequenceanalysis-genomefileselectorfield", new JSONObject()
                     {{
-                        put("extensions", Arrays.asList("gtf", "gff"));
+                        put("extensions", Arrays.asList("gtf", "gff", "gbk"));
                         put("width", 400);
                         put("allowBlank", false);
                     }}, null),

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java

@@ -91,7 +91,7 @@ public MergeLoFreqVcfHandler()
                 }}, 25),
                 ToolParameterDescriptor.createExpDataParam(SNPEffStep.GENE_PARAM, "Gene File", "This is the ID of a GTF or GFF3 file containing genes from this genome.", "sequenceanalysis-genomefileselectorfield", new JSONObject()
                 {{
-                    put("extensions", Arrays.asList("gtf", "gff"));
+                    put("extensions", Arrays.asList("gtf", "gff", "gbk"));
                     put("width", 400);
                     put("allowBlank", false);
                 }}, null)

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SnpEffWrapper.java

@@ -127,6 +127,10 @@ else if ("gff".equalsIgnoreCase(ext))
         {
             params.add("-gff3");
         }
+        else if ("gbk".equalsIgnoreCase(ext))
+        {
+            params.add("-genbank");
+        }
         else
         {
             throw new PipelineJobException("unable to process extension: " + ext);

SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java

@@ -81,6 +81,7 @@ public static enum FILETYPE
         sff(".sff"),
         gtf(".gtf"),
         gff(Arrays.asList(".gff", ".gff3"), false),
+        gbk(".gbk"),
         bed(".bed"),
         vcf(Arrays.asList(".vcf"), true),
         gvcf(Arrays.asList(".g.vcf"), true);