cnvkit batch - generate target_bed in output_dir if given #940
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Hi!
Small edit here.
I noticed that the target BED generated by
cnvkit.py batch
was created in the working directory, NOT the specified output directory. This PR add some logic to fix this.For context I am running
cnvkit batch
in WGS mode using only a FASTA while specifying an output directory, this is the command:This generates a target BED based on the FASTA, but despite giving an output directory this BED (
genome.bed
in this case) was generated in the current directory.