Better description of how to run the tool would be helpful about discovery HOT 3 OPEN

I should add that when I run the example, it reports that a proportion of 1.0 for each and every contig. That seems really strange -- it would be strange example. How can I know whether this is expected or if instead it's an indication somethings wrong with my installation of the program?

from discovery.

In the current readme, the threshold output by discoverY.py is described as "proportion_shared_with_female". But I think it is really "proportion_NOT_shared_with_female".

Thus values closer to 1 mean a contig is more likely to be from Y.

from discovery.

Agree!

Output of DiscoverY in README.md should be corrected to "proportion_NOT_shared_with_female", because after running DiscorerY, contig file has the following header: '>Sc0000000 7492748 0.012910911534003885 102.0'; while the printed results in the terminal are:
'No. of contigs seen so far: 1
Current contig ID is : Sc0000000
Median is: 102.0
Total No. of k-mers from this contig: 7492732
No. of k-mers not shared with female: 96738
Proportion is: 0.012910911534003885'

Another correction that should be made is the description on how to calculate k-mers from male reads, because it indicates:
"cd dependency
ln -s ../data/female.fasta #make sure the correct reads file is provided to DSK
./run_dsk_Linux.sh r1.fastq 25"
which is misleading for new users. Why do the user needs to soft link female.fasta to dependency if it is completely unnecessary for running DSK?

from discovery.