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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PAF export #31

Closed glennhickey closed 1 year ago

glennhickey commented 1 year ago

This PR adds -p and -P options to taffy view to change the output format to PAF. So this lets multiple alignments (MAF or TAF) format be converted into their constituent pairwise alignments. -p will report the alignment of rows 1-N to row 0. -P will report all pairs.

The goal here is mostly debugging (ie visualize a pairwise alignment within Cactus's output using tools that depend on PAF), There may be other uses though..