Feat/finalize paper #33
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Changed do_align to accept an arbitrary aligner function. Began writing a wfmash module to allow for more accurate hits.
Decided to make one temporary direction that is cleaned upon completion. This allows us to control the file suffixes. No testing has been done, just the idea sketched out.
can now call wfmash as backend. tested on one small example.
wfmash now reflected in documentation. types defined at more global scale
query and reference files were being opened and never closed before reading from them. now we close files after writing for the explicit flush. odd error when we were trying to capture the output directly with a pipe. write to a file and then read from it unfortunately now, but at least reliably doesn't deadlock
error is thrown if binaries aren't detected on path
wfmash also removes duplicates on self-maps.
Fixed the cigar parsing. I temporarily run the alignment in single-threaded mode to make debugging simpler.
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Adding
mmseqs2as alternative alignment kernel and updating analysis and documentation accordingly