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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': $!\n";
Thank you.
The text was updated successfully, but these errors were encountered:
Hi, I'm reporting a simple issue on deduplicate_bismark.
There's a "--samtools_path" option to specify the path to samtools while deduplicating bam file.
However, while deduplicating with multiple bam files, it doesn't use the samtools I specified, but the samtools on environmental variables.
It's written on the 157th line of deduplicate_bismark like below.
open (IN,"$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.
The text was updated successfully, but these errors were encountered: