bugfix genbank file import

bbimber · bbimber · commit 2eabfbe6e3ca · 2020-09-16T12:47:42.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java
@@ -287,11 +287,13 @@ else if (SequenceUtil.FILETYPE.vcf.getFileType().isType(file))
             else
             {
                 getJob().getLogger().info("skipping VCF sort");
+                SequenceAnalysisService.get().ensureVcfIndex(file, getJob().getLogger());
             }
         }
         else if (SequenceUtil.FILETYPE.gbk.getFileType().isType(file))
         {
             getJob().getLogger().debug("no processing needed: " + file.getName());
+            FileUtils.moveFile(file, outputFile);
         }
         else
         {

Original file line number	Diff line number	Diff line change
`@@ -287,11 +287,13 @@ else if (SequenceUtil.FILETYPE.vcf.getFileType().isType(file))`
`287`	`287`	`else`
`288`	`288`	`{`
`289`	`289`	`getJob().getLogger().info("skipping VCF sort");`
	`290`	`+ SequenceAnalysisService.get().ensureVcfIndex(file, getJob().getLogger());`
`290`	`291`	`}`
`291`	`292`	`}`
`292`	`293`	`else if (SequenceUtil.FILETYPE.gbk.getFileType().isType(file))`
`293`	`294`	`{`
`294`	`295`	`getJob().getLogger().debug("no processing needed: " + file.getName());`
	`296`	`+ FileUtils.moveFile(file, outputFile);`
`295`	`297`	`}`
`296`	`298`	`else`
`297`	`299`	`{`