Add more cellranger debugging

bbimber · bbimber · commit cca6c224131b · 2021-12-30T15:19:01.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java b/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java
@@ -479,7 +479,7 @@ else if (val.contains("TRBTRD"))
                                     {
                                         if (!originalChain.equals("TRA") && !"None".equals(originalChain))
                                         {
-                                            getPipelineCtx().getLogger().error("Unexpected chain: was " + originalChain + ", to " + chain);
+                                            getPipelineCtx().getLogger().error("Unexpected chain: was " + originalChain + ", updated to " + chain + ". " + tokens[6] + "/" + tokens[8] + "/" + tokens[9]);
                                         }
 
                                         totalG++;
@@ -488,7 +488,7 @@ else if (chain.equals("TRD"))
                                     {
                                         if (!originalChain.equals("TRB") && !"None".equals(originalChain))
                                         {
-                                            getPipelineCtx().getLogger().error("Unexpected chain: was " + originalChain + ", to " + chain);
+                                            getPipelineCtx().getLogger().error("Unexpected chain: was " + originalChain + ", updated to " + chain + ". " + tokens[6] + "/" + tokens[8] + "/" + tokens[9]);
                                         }
 
                                         totalD++;
@@ -502,7 +502,7 @@ else if (chain.equals("TRD"))
                                 }
                                 else
                                 {
-                                    getPipelineCtx().getLogger().warn("Multiple chains detected [" + StringUtils.join(chains, ",")+ "], leaving original call alone: " + originalChain);
+                                    getPipelineCtx().getLogger().warn("Multiple chains detected [" + StringUtils.join(chains, ",")+ "], leaving original call alone: " + originalChain  + ". " + tokens[6] + "/" + tokens[8] + "/" + tokens[9]);
                                 }
                             }
 

Original file line number	Diff line number	Diff line change
`@@ -479,7 +479,7 @@ else if (val.contains("TRBTRD"))`
`479`	`479`	`{`
`480`	`480`	`if (!originalChain.equals("TRA") && !"None".equals(originalChain))`
`481`	`481`	`{`
`482`		`- getPipelineCtx().getLogger().error("Unexpected chain: was " + originalChain + ", to " + chain);`
	`482`	`+ getPipelineCtx().getLogger().error("Unexpected chain: was " + originalChain + ", updated to " + chain + ". " + tokens[6] + "/" + tokens[8] + "/" + tokens[9]);`
`483`	`483`	`}`
`484`	`484`
`485`	`485`	`totalG++;`
`@@ -488,7 +488,7 @@ else if (chain.equals("TRD"))`
`488`	`488`	`{`
`489`	`489`	`if (!originalChain.equals("TRB") && !"None".equals(originalChain))`
`490`	`490`	`{`
`491`		`- getPipelineCtx().getLogger().error("Unexpected chain: was " + originalChain + ", to " + chain);`
	`491`	`+ getPipelineCtx().getLogger().error("Unexpected chain: was " + originalChain + ", updated to " + chain + ". " + tokens[6] + "/" + tokens[8] + "/" + tokens[9]);`
`492`	`492`	`}`
`493`	`493`
`494`	`494`	`totalD++;`
`@@ -502,7 +502,7 @@ else if (chain.equals("TRD"))`
`502`	`502`	`}`
`503`	`503`	`else`
`504`	`504`	`{`
`505`		`- getPipelineCtx().getLogger().warn("Multiple chains detected [" + StringUtils.join(chains, ",")+ "], leaving original call alone: " + originalChain);`
	`505`	`+ getPipelineCtx().getLogger().warn("Multiple chains detected [" + StringUtils.join(chains, ",")+ "], leaving original call alone: " + originalChain + ". " + tokens[6] + "/" + tokens[8] + "/" + tokens[9]);`
`506`	`506`	`}`
`507`	`507`	`}`
`508`	`508`