Bed file validation not following bed specifications

[duartemolha]

I tried using mosdepth with a bed file that has the fields separated by spaces instead of tabs and it complains: [mosdepth] skipping bad bed line:chrY 7711640 7711641 rs879195003

This is not correct since a bed tile is white space delimited so both spaces and tabs are acceptable

also, the output of the regions.bed.gz removes part of the input bed file used in --by

for example if my input bed file defining the regions is

chrX 77504877 77508629 ATRX 1 +

the output for the regions bed file is

chrX 77504877 77508629 ATRX 324.95

The score field and the strand fields are removed. It would be good if they could be retained and the counts just added as an additional column.

Thanks

[brentp]

mosdepth requires tab-delimited files. I'd accept a PR to inject the depth into the 5th column when a file has more than 5 columns.

[duartemolha]

yes... that would be better to just removing the columns :) thanks