Possible problem with use case 4

walaj / VariantBam

Filtering and profiling of next-generational sequencing data using region-specific rules

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Possible problem with use case 4 #3

Closed maplesond closed 8 years ago

maplesond commented 8 years ago

I'm trying to run use case 4 on my own datasets,I'm not getting any output when the '-x' option is used. I expected just some count information rather than the BAM. Removing the '-x' and replacing with '-o' behaves as expected.

maplesond commented 8 years ago

After looking at this a bit closer. I think the example use case should be updated to include the '-c ' option as well '-x'

walaj commented 8 years ago

Good catch, the option parser was not grabbing the argument to -x. This is fixed in the latest commit. The proper usage is now as described in case 4.