Request: more information in SEACR log output

[SolKatzman]

During it's run SEACR outputs some helpful progress information.

First, a nitpick: For better readability, each output line should be preceded (not followed) by a timestamp.

Currently:
Normalizing control to experimental bedgraph
Using relaxed threshold
Creating experimental AUC file: Wed Jan 11 08:53:11 PST 2023
Creating control AUC file: Wed Jan 11 08:53:28 PST 2023
Calculating optimal AUC threshold: Wed Jan 11 08:53:39 PST 2023

Preferred:
Wed Jan 11 08:53:01 PST 2023: Normalizing control to experimental bedgraph
Wed Jan 11 08:53:05 PST 2023: Using relaxed threshold
Wed Jan 11 08:53:11 PST 2023: Creating experimental AUC file
Wed Jan 11 08:53:28 PST 2023: Creating control AUC file
Wed Jan 11 08:53:39 PST 2023: Calculating optimal AUC threshold

More substantially, it would be very useful to get information about the processing as it proceeds, to help debug unexpected or questionable results in the output set of peaks. Currently, the only such item that I see in the log is "Empirical false discovery rate".
Some useful items of interest would be the following, but basically any parameter that the program finds would be worthwhile to report:

threshold values calculated for target and control
number of "raw" peaks at threshold in target and control
number of peaks after merging nearby features in target and control
number of peaks for target that were filtered out due to overlap with control

A more demanding request would be for an output file with (data and) figures, such as the graphs (with actual labeled axes) in Figure 2a in the SEACR paper:

"Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling"

Thanks for your attention,
Sol Katzman
UC Santa Cruz Genomics Institute

[bhanco]

A single threshold value is calculated based off the target and control? If I understand correctly.
I was hoping this value would be output as well.