Skip header when parsing cellranger vdj output

bbimber · bbimber · commit 2f1472073517 · 2022-01-08T12:58:20.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java b/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java
@@ -454,9 +454,11 @@ public AlignmentStep.AlignmentOutput performAlignment(Readset rs, List<File> inp
                         String line;
                         int totalD = 0;
                         int totalG = 0;
+                        int lineIdx = 0;
                         while ((line = reader.readLine()) != null)
                         {
-                            if (line.contains("g,") || line.contains("d,"))
+                            lineIdx++;
+                            if (lineIdx > 1 && (line.contains("g,") || line.contains("d,")))
                             {
                                 //Infer correct chain from the V, J and C genes
                                 String[] tokens = line.split(",");

Original file line number	Diff line number	Diff line change
`@@ -454,9 +454,11 @@ public AlignmentStep.AlignmentOutput performAlignment(Readset rs, List<File> inp`
`454`	`454`	`String line;`
`455`	`455`	`int totalD = 0;`
`456`	`456`	`int totalG = 0;`
	`457`	`+ int lineIdx = 0;`
`457`	`458`	`while ((line = reader.readLine()) != null)`
`458`	`459`	`{`
`459`		`- if (line.contains("g,") \|\| line.contains("d,"))`
	`460`	`+ lineIdx++;`
	`461`	`+ if (lineIdx > 1 && (line.contains("g,") \|\| line.contains("d,")))`
`460`	`462`	`{`
`461`	`463`	`//Infer correct chain from the V, J and C genes`
`462`	`464`	`String[] tokens = line.split(",");`