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genome / bam-readcount

Count bases in BAM/CRAM files
MIT License
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print-individual-mapq not working #58

Open fkokocinski opened 5 years ago

fkokocinski commented 5 years ago

Running with other options works great, but -D or --print-individual-mapq with either of 1, true, yes or a few other things throws an error:

bam-readcount -w 10 -f ${fasta}.fa -D true ${sample}.bam ${region}

Minimum mapping quality is set to 0
libc++abi.dylib: terminating with uncaught exception of type char const*
Abort trap: 6

This is on OS X 10.14 in a conda environment. Many thanks, Felix

susannasiebert commented 5 years ago

This might just be an error in the documentation but since this is a flag, I wouldn't expect it to take an argument. Have you tried to run it with just -D without an argument?

fkokocinski commented 5 years ago

Thanks, but yes, this was the result:

libc++abi.dylib: terminating with uncaught exception of type boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_bool_value> >: 
the argument ('filengs.bam') for option '--mapq' is invalid. 
Valid choices are 'on|off', 'yes|no', '1|0' and 'true|false'
Abort trap: 6