pipeline expects different format of *.bed.cov* files

[marnec]

Numerous scripts along the pipeline expects .bed.cov files format to be something along

chr1  start  end  name  offset  coverage

When their actual format is

chr1  start  end  name   coverage  strand  many_other_fields

While I could fix this in pipeline/scripts/{gap_annotator.py, qc_report.py} and in pipeline_stages_congif-groovy at line 939, I instead couldn't at line 1214.