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ComparativeGenomicsToolkit / taffy

This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files
MIT License
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make sure taf-writing tools all have -sc #55

Closed glennhickey closed 4 months ago

glennhickey commented 4 months ago

This PR makes sure that taffy norm, add-gap-bases, sort and annotate all have 

-s --repeatCoordinatesEveryNColumns : Repeat coordinates of each sequence at least every n columns. By default: 10000
-c --useCompression : Write the output using bgzip compression.

The -s option is particularly important as without it, taffy index does not work very well (you can end up with just one record / contig).