search

nmdp-bioinformatics / pipeline

Consensus assembly and allele interpretation pipeline.
GNU Lesser General Public License v3.0
7 stars 7 forks source link

ArrayIndexOutOfBoundsException when filtering all HLA(-A) exons #56

Closed ckennedy-nmdp closed 9 years ago

ckennedy-nmdp commented 9 years ago

This is the command that I ran:

ybolon@yung-tsione:/mnt/common/data/incoming/ucla/ex014/verify/HLA-A_ALLEXONS$ /home/ybolon/loop.dogroovyAintcompSeq /mnt/common/data/incoming/ucla/ex014

Caught: java.lang.ArrayIndexOutOfBoundsException: 1 java.lang.ArrayIndexOutOfBoundsException: 1 at splice-bam$_run_closure2.doCall(splice-bam.groovy:77) at splice-bam.run(splice-bam.groovy:76) ….

ckennedy-nmdp commented 9 years ago

Mark please reformat the .txt files in /mnt/common/data/reference/regions/ replacing \s (spaces) with \t (tab) and then close the issue. Thanks!

ybolon-nmdp commented 9 years ago

Excellent, I was just going to post about this. I have lots of output with the new reverse-complement capable splice-bam.groovy, but there are too many allele options coming out -- hoping that having all the exon sequences pushed to the interpretation service will pare down the output.

ckennedy-nmdp commented 9 years ago

Closing, new code change doesn't require alteration of input regions files.