Allow additional filetypes as sequence outputs

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java

@@ -571,6 +571,10 @@ else if (_fastaFileType.isType(f))
             ret.add(f.getName() + ".gz.gzi");
             ret.add(f.getName() + ".gz.fai");
         }
+        else if (new FileType("txt.gz").isType(f))
+        {
+            ret.add(f.getName() + ".tbi");
+        }
 
         // NOTE: this allows modules to register handlers for extra ancillary files, such as seurat metadata
         SequenceAnalysisServiceImpl.get().getAccessoryFileProviders().forEach(fn -> {

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

@@ -11,6 +11,6 @@ public class SequenceOutputFileType extends FileType
 {
     public SequenceOutputFileType()
     {
-        super(Arrays.asList(".bam", ".cram", ".gff", ".gtf", ".bed", ".vcf", ".rds", ".bw"), ".bed", FileType.gzSupportLevel.SUPPORT_GZ);
+        super(Arrays.asList(".bam", ".cram", ".gff", ".gtf", ".bed", ".vcf", ".rds", ".bw", ".txt"), ".bed", FileType.gzSupportLevel.SUPPORT_GZ);
     }
 }