GRCh37 chromosome names are pure integers (1, 2, 3, ... in oppose to chr1, chr2, chr3... in hg19/hg38), and at some point when a coverage or a fasta file is read into a dataframe, they get automatically parsed as ints, making this further chunk crash:

  File "/g/data3/gx8/extras/vlad/miniconda/envs/sequana/lib/python3.6/site-packages/sequana/scripts/coverage.py", line 421, in run_analysis
    directory += os.sep + chrom.chrom_name
TypeError: must be str, not numpy.int64

I guess in order to work with GRCh37, converting chrom_name into a str at some point might be needed.

Vlad