Output formats

Output formats

The output format can be changed with --format FORMAT. Default format is 'bed', and the alternative is 'counts'.

"counts" format

The "counts" format will print the reference sequence name in FASTA format (i. e. using > as prefix), then a two columns table: coverage in the first column, and span (number of bases covered in the second column).

Examples

BED format

EMPTY           0       414     0
NC_001416.1     0       2       0
NC_001416.1     2       6       1
NC_001416.1     6       7       2
NC_001416.1     7       12      3

Counts format

>EMPTY
0       414
>NC_001416.1
0       2
1       4
2       1
3       5
4       6
5       3
6       1