Bugfix to CellRangerVDJ

bbimber · bbimber · commit 15b342259431 · 2024-07-31T21:13:27.000-07:00
diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java
@@ -490,11 +490,11 @@ else if (discordantBarcodes.contains(barcode))
                     while (i.hasNext())
                     {
                         Map<String, Object> fastaRecord = i.next();
-                        String header = (String) fastaRecord.get("header");
+                        String header = "vdj_t<>" + fastaRecord.get("header");
                         j++;
                         if (uniqueContigNames.contains(header))
                         {
-                            sequenceMap.put("vdj_t<>" + header, (String) fastaRecord.get("sequence"));
+                            sequenceMap.put(header, (String) fastaRecord.get("sequence"));
                         }
                     }
                 }

Original file line number	Diff line number	Diff line change
`@@ -490,11 +490,11 @@ else if (discordantBarcodes.contains(barcode))`
`490`	`490`	`while (i.hasNext())`
`491`	`491`	`{`
`492`	`492`	`Map<String, Object> fastaRecord = i.next();`
`493`		`- String header = (String) fastaRecord.get("header");`
	`493`	`+ String header = "vdj_t<>" + fastaRecord.get("header");`
`494`	`494`	`j++;`
`495`	`495`	`if (uniqueContigNames.contains(header))`
`496`	`496`	`{`
`497`		`- sequenceMap.put("vdj_t<>" + header, (String) fastaRecord.get("sequence"));`
	`497`	`+ sequenceMap.put(header, (String) fastaRecord.get("sequence"));`
`498`	`498`	`}`
`499`	`499`	`}`
`500`	`500`	`}`