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Should CheckIlluminaDirectory be able to handle a non-standard read structure

alecwalecw Member, Broadie

I have a flowcell (from a 10x library) in which the 'natural' read structure is 178T8B14B5T. However, I want to interpret the flowcell as 178T8B14T5S, so that is what I passed to CheckIlluminaDirectory. I get the exception below. It looks like the code is trying to check all the cycles, including the skips. However, CbclReader.outputCycles is initialized only with enough elements to hold the non-skip cycles. Is this a bug? Or is it wrong to pass a read structure with skips in it?

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 200
at picard.illumina.parser.readers.CbclReader.readSurfaceTile(CbclReader.java:119)
at picard.illumina.parser.readers.CbclReader.(CbclReader.java:102)
at picard.illumina.CheckIlluminaDirectory.doWork(CheckIlluminaDirectory.java:170)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)

Issue · Github
by Sheila

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