Bugfix to SRA download with multiple file pairs

bbimber · bbimber · commit 31629fd54944 · 2025-01-05T17:54:25.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java
@@ -1977,8 +1977,10 @@ else if (sraIDs.contains(rd.getSra_accession()))
                                 }
                             });
                         }
-
-                        outDir.mkdirs();
+                        else
+                        {
+                            outDir.mkdirs();
+                        }
 
                         Pair<File, File> downloaded = sra.downloadSra(rd.getSra_accession(), unzippedOutDir, rd.isPairedEnd());
                         File moved1 = new File(outDir, downloaded.first.getName());

Original file line number	Diff line number	Diff line change
`@@ -1977,8 +1977,10 @@ else if (sraIDs.contains(rd.getSra_accession()))`
`1977`	`1977`	`}`
`1978`	`1978`	`});`
`1979`	`1979`	`}`
`1980`		`-`
`1981`		`- outDir.mkdirs();`
	`1980`	`+ else`
	`1981`	`+ {`
	`1982`	`+ outDir.mkdirs();`
	`1983`	`+ }`
`1982`	`1984`
`1983`	`1985`	`Pair<File, File> downloaded = sra.downloadSra(rd.getSra_accession(), unzippedOutDir, rd.isPairedEnd());`
`1984`	`1986`	`File moved1 = new File(outDir, downloaded.first.getName());`