[reformat.sh] sam output instead of bam with sambamba

[Juke34]

Hi,

I have added sambamba to the conda bbmap recipe in order to use reformat.sh but I realised it creates sam output instead of bam, while using samtools instead of sambamba I get expected bam output. I will modify the conda recipe to use samtools instead of sambamba but I was thinking it shoulkd not make any difference in theory, isn't it?
If my assumption is true either something is wrong in reformat.sh, otherwise the problem comes from the sambamba conda version.
I hope you could help me to decipher the problem.

Best regards,

Jacques

poke @bbushnell