Unclear documentation

[lczech]

Hi there,

I noted that the README.md does not quite seem fitting with the output. It says in Run ntCard that F numbers are printed to terminal, and a tab separated file with three columns is produced with k-mer values. However, running

ntcard -k `seq -s, 16 31` -p counts -t 48 @ref_cat_fasta_list.txt

only printed runtime to terminal, and gave separate files per value of k, with columns

F1	14775493891180
F0	34372442646
1	251806
2	736852
3	1892607
4	3833951
5	6560879
...

I don't know if the README simply has not been updated to match the current output format, or if I am missing something.

Furthermore, the parameters section also might need an update:

• There does not seem to be a flag to activate F2 and F∞ (which it says in the Output are not printed by default)
• The -c option is described as "maximum coverage", where the meaning of "coverage" is not clear in this context. Looking at my output files, it looks like it's meant to mean k-mers that occur more often than that? Maybe "maximum occurrence (i.e., histogram cutoff)" might be more clear here.

Cheers and so long
Lucas