Feat: Built-in scoring for HMMRATAC

[mrendleman]

Describe the solution you'd like I'd like the option to calculate scores for peaks when running MACS3 HMMRATAC, similar to the original HMMRATAC implementation (the old command line option --score <max || ave || med || fc || zscore || all>). This would be useful for comparing peaks within a sample and enable downstream between-replicate reproducibility with methods like IDR.

Describe alternatives you've considered An alternative would be any type of informative peak scoring. Another suggestion would be a different version of the "fc" option where instead of reporting fold-change relative to the whole genome's average coverage, it reports fold change relative to the chromosome's average or a sliding-window local average.

Additional context Currently, the gappedPeak files output by macs3 hmmratac contain all zeros for the score/signalValue/pValue/qValue columns, giving the impression that no peaks are higher confidence than the others.

[taoliu]

A good suggestion. We will consider adding that. The way in JAVA HMMRATAC is to take the called regions and revisit the pileup signal tracks to compute these values.