Bugfix to CellRangerVDJ

bbimber · bbimber · commit 350e9a2b9929 · 2024-07-31T20:45:19.000-07:00
diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java b/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java
@@ -821,7 +821,7 @@ private static void processCSV(PrintWriter writer, boolean printHeader, File inp
                 {
                     if (printHeader)
                     {
-                        writer.println(line + "\tchain_type");
+                        writer.println(line + ",chain_type");
                     }
 
                     continue;
@@ -897,7 +897,7 @@ else if (uniqueChains.size() == 2)
 
                 if (acceptableChains.contains(tokens[5]))
                 {
-                    writer.println(StringUtils.join(tokens, ",") + "\t" + chainType);
+                    writer.println(StringUtils.join(tokens, ",") + "," + chainType);
                 }
             }
 

Original file line number	Diff line number	Diff line change
`@@ -821,7 +821,7 @@ private static void processCSV(PrintWriter writer, boolean printHeader, File inp`
`821`	`821`	`{`
`822`	`822`	`if (printHeader)`
`823`	`823`	`{`
`824`		`- writer.println(line + "\tchain_type");`
	`824`	`+ writer.println(line + ",chain_type");`
`825`	`825`	`}`
`826`	`826`
`827`	`827`	`continue;`
`@@ -897,7 +897,7 @@ else if (uniqueChains.size() == 2)`
`897`	`897`
`898`	`898`	`if (acceptableChains.contains(tokens[5]))`
`899`	`899`	`{`
`900`		`- writer.println(StringUtils.join(tokens, ",") + "\t" + chainType);`
	`900`	`+ writer.println(StringUtils.join(tokens, ",") + "," + chainType);`
`901`	`901`	`}`
`902`	`902`	`}`
`903`	`903`