Fix extract methylation MT/LAMBDA script

As per now, it is executed twice, once for the MT chr and once for the LAMBDA. The script apps/ext_chr_srt.py should accept multiple command line arguments, each being a chromosome.

IDEAS

• Remove the test for "Bismark" start of line on each iteration, leave it just for the first line
• Open one file handle for each input chromosome and output reads there

This script is executed in the main pipeline (wgbs-pipeline.sh) and that call will need to be updated consequentially.