Consistency checking between profile_dists and gas distance units

[apetkau]

Issue

Right now gas call or gas mcluster relies on distances calculated from profile_dists. Distance thresholds are set using the --threshold parameter. However, profile_dists can give distances in two different units: either scaled (number from 0 to 1) or hamming (non-negative number). The distance units passed as thresholds need to be kept in-sync. For example:

• If profile_dists uses scaled, then thresholds need to be from 0 to 1 e.g., --threshold 0.2,0.1
• If profile_dists uses hamming, then thresholds need to be non-negative, e.g., --threshold 10,5,0

Solution

One solution to help with error checking is to add a --distm method to gas, that takes either hamming or scaled (same values as passed to profile_dists). This parameter is used to check numbers passed to --threshold

[apetkau]

Other consistency checks could be:

• If --distm hamming, then all distance values from profile_dists (and passed thresholds) should be integers
• If --distm scaled, then all distance values from profile_dists should be between 0 and 1.

Not sure if it would add a lot more time for consistency checking of calculated distance values though.

[apetkau]

Alternatively, you could change the column output from profile_dists to include the unit. That is:

query_id	ref_id	dist_scaled
A	A	0
A	B	0.5

And then passing --distm scaled to gas would only read from the dist_scaled column (and same for --distm hamming).