Add a filtering step by canonical chromosomes before spliting by chromosomes

[mAGLAVE]

Idea of optimization (to test for memory and time consuming):

Actually:

1. concat all bam files from the alignement.
2. split by chromsome (allow to filter to keep canonical chromosomes) -> used for methylation calling.
3. reconcat all bam files -> used for variants calling and QC.

That could be better:

1. concat all bam files from the alignement.
2. filter the bam to keep canonical chromosomes -> used for variants calling and QC.
3. split by chromsome -> used for methylation calling.

The advantage is not having to do the splitting if we don't do the methylation.