I'm trying to use FindPeaks with some data mapped in ELAND via GERALD. At the moment I'm stuck on using SeparateReads.jar. Below is a sample of the data from the input "s_X_sorted.txt" file:
I read in another thread that I could specify the aligner as "elandext", but to no avail. I get the following error message from SeparateReads.jar:
Is this a problem with the input file? I can't find any specification for the eland/elandext inputs for FindPeaks anywhere.
Code:
HWI-EAS486 19 4 26 19288 17610 0 1 GCTTGTGTATCACTGGCGCAGCAGAGAGTCTGAGCATG hhhhhhhhhghhhhhhfhfhcgdggcffchggfghfgh chr10.fa 55 F 38131 HWI-EAS486 19 4 65 12362 19698 0 1 CTGGTTAGAACAGCTAGGCCCTTGGGCCTCACTGTACA hhhhhhghhhhhhhhhghhhhhhhhgfhhhhhhhfhhh chr10.fa 145 F 38131 HWI-EAS486 19 4 79 19730 5608 0 1 GCCAGCCTGGCAACTATCAGGCCACAAGGTGACATAAG gggggggggdffc_fggggfc]ffWfcfadffffea_[ chr10.fa 309 F 19T18 88
Code:
Version: Initializing class Log_Buffer $Revision: 2530 $ Version: Vancouver Short Read Analysis Package 4.0.16-dev.jars Version: Initializing class SeparateReads $Revision: 3125 $ Version: Initializing class Generic_AlignRead_Iterator $Revision: 3118 $ Version: Initializing class ElandExtIterator $Revision: 2933 $ Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 38 at java.lang.StringBuffer.setCharAt(StringBuffer.java:210) at src.lib.ioInterfaces.ElandExtUtilities.parse_mismatches(ElandExtUtilities.java:23) at src.lib.ioInterfaces.ElandExtIterator.next(ElandExtIterator.java:213) at src.lib.ioInterfaces.ElandExtIterator.next(ElandExtIterator.java:22) at src.lib.ioInterfaces.Generic_AlignRead_Iterator.hasNext(Generic_AlignRead_Iterator.java:121) at src.fileUtilities.SeparateReads.main(SeparateReads.java:70)
Comment