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brentp / goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
MIT License
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ndexcv: excluding chromosome: NC_031965 because of exclude-pattern: ^chrEBV$|^NC|_random$|Un_|^HLA\-|_alt$|hap\d #56

Closed astridboehne closed 5 years ago

astridboehne commented 5 years ago

Hi Brent I tried to run indexcov on my bam files but it excludes all my chromosomes but one which has a different naming. I am working with an NCBI reference genome and chromosomes are named NC_12344. How can I overwrite the default setting which excludes this pattern? I tried this way: ./goleft_linux64 indexcov --chrom NC_031983 --directory /scicore/home/salzburg/boehne/test/ /scicore/home/salzburg/boehne/*realn.bam which did nor work and the same command without the --chrom flag Any help would be great Thanks Astrid

brentp commented 5 years ago

Just set a new exclude pattern like:

--excludepatt "ZZZZZZ"

that won't match anything.

astridboehne commented 5 years ago

perfect, thank you, solved the issue