Output metrics to a single file

Illumina / REViewer

A tool for visualizing alignments of reads in regions containing tandem repeats

GNU General Public License v3.0

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Output metrics to a single file #38

Closed egor-dolzhenko closed 2 years ago

egor-dolzhenko commented 2 years ago

This pull request will:

Output all metrics into a single file (currently REViewer produces a separate metrics file for each repeat)
Rename DiplotypePaths to Diplotype; this change is consistent with the underlying conceptual model where (1) a local haplotype is a graph path and (2) a local diplotype is a pair of paths; the code becomes more readable because collections DiplotypePaths can now be called Diplotypes instead of harder-to-understand phrases like DiplotypePathsSet.

egor-dolzhenko commented 2 years ago

Not given this a very detailed look but it sounds sensible.

You might consider whether this would be a good point to add more documentation for the new metrics outputs? Or to add a simple demo dataset which includes an example of the metrics output?

Absolutely! I already started working on documentation. I'll add it in as soon as we finalize the output file format.