deduplicat_bismark with multiple bam files require samtools on environmental variable

[Yoonsung1203]

Hi, I'm reporting a simple issue on deduplicate_bismark.

There's a "--samtools_path" option to specify the path to samtools while deduplicating bam file.

However, while deduplicating with multiple bam files, it doesn't use the samtools I specified, but the samtools on environmental variables.
It's written on the 157th line of deduplicate_bismark like below.

open (IN,"$samtools_path cat -h $file @filenames | samtools view -h |") or die "Unable to read from BAM files in '@filenames': $!\n";

I think it must be changed into like this.

open (IN,"$samtools_path cat -h $file @filenames | $samtools_path view -h |") or die "Unable to read from BAM files in '@filenames': $!\n";

Thank you.

[FelixKrueger]

Good catch. I have just changed this in the dev version. Thanks!