Allow import of genbank files as genome tracks

bbimber · bbimber · commit 04836ac98583 · 2020-09-16T12:15:32.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java
@@ -289,6 +289,10 @@ else if (SequenceUtil.FILETYPE.vcf.getFileType().isType(file))
                 getJob().getLogger().info("skipping VCF sort");
             }
         }
+        else if (SequenceUtil.FILETYPE.gbk.getFileType().isType(file))
+        {
+            getJob().getLogger().debug("no processing needed: " + file.getName());
+        }
         else
         {
             throw new PipelineJobException("Unsupported filetype: " + file.getName());

Original file line number	Diff line number	Diff line change
`@@ -289,6 +289,10 @@ else if (SequenceUtil.FILETYPE.vcf.getFileType().isType(file))`
`289`	`289`	`getJob().getLogger().info("skipping VCF sort");`
`290`	`290`	`}`
`291`	`291`	`}`
	`292`	`+ else if (SequenceUtil.FILETYPE.gbk.getFileType().isType(file))`
	`293`	`+ {`
	`294`	`+ getJob().getLogger().debug("no processing needed: " + file.getName());`
	`295`	`+ }`
`292`	`296`	`else`
`293`	`297`	`{`
`294`	`298`	`throw new PipelineJobException("Unsupported filetype: " + file.getName());`