cnvkit batch - generate target_bed in output_dir if given

[pontushojer]

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:

cnvkit.py batch path/to/my.cram -n -m wgs -f path/to/genome.fa -d output

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.

[pontushojer]

Relates to: https://github.com/etal/cnvkit/issues/781

[etal]

Thanks!