#119 mimodd reheader bug with renaming ref sequences in BAM

[Wolfgang Maier]

Traceback (most recent call last):
  File "/usr/local/tools/_conda/envs/__MiModD@0.1.8/bin/mimodd", line 7, in <module>
    __main__.parse()
  File "/usr/local/tools/_conda/envs/__MiModD@0.1.8/lib/python3.6/site-packages/MiModD/__main__.py", line 1197, in parse
    result = funcs[-1](**args)
  File "/usr/local/tools/_conda/envs/__MiModD@0.1.8/lib/python3.6/site-packages/MiModD/convert.py", line 727, in clparse_reheader
    co_specs = specs['co'], **args)
  File "/usr/local/tools/_conda/envs/__MiModD@0.1.8/lib/python3.6/site-packages/MiModD/convert.py", line 596, in reheader
    sam2bam (inputfile, outputfile, iformat = 'bam', oformat = 'bam', reheader = reheader)
  File "/usr/local/tools/_conda/envs/__MiModD@0.1.8/lib/python3.6/site-packages/MiModD/convert.py", line 466, in sam2bam
    read.tid = sqids_to_groom[new_rname]
KeyError: 'NC_045512.2'

It looks as if the tool tries to look up the new sequence name instead of the old one here.