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add_cpg_counts does not work #105

@ecmra

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@ecmra

wgbstools add_cpg_counts --verbose <filename.bam>

stops with

FileNotFoundError: [Errno 2] No such file or directory: './<filename>_chr15.output.bam'

(filename.bam only contains reads mapping on chr15).

It also creates an indexed output file <filename.counts.bam>
which is empty

samtools view <filename.counts.bam> | wc -l
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