Updated samtools doesn't work with hisat2 in mapping pipeline

[microbialman]

Having just done a new CGAT install I ended up with the latest version of samtools (1.10) it has a new way of handling BAM headers that throws an error when I used hisat2 in the mapping pipline (in the step using samtools view to pipe to bam2bam).

I tested using samtools version 1.9 locally and this seems to work still so I guess samtools version might need to be limited? Not sure why the BAM output from hisat2 causes problems.

[Acribbs]

Thanks for the comment, I can take a look at this over the xmas break