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..
This PR adds
-pand-Poptions totaffy viewto change the output format to PAF. So this lets multiple alignments (MAF or TAF) format be converted into their constituent pairwise alignments.-pwill report the alignment of rows 1-N to row 0.-Pwill 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..