Updates to repeat resolution, correction, and alignment #213
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re-estimate local coverage even in low coverage regions avoid marking very short low coverage nodes uniques
…meric nodes based on telomere bed file
… (w/modifications) rather than untip_relative
…haligner uses a read to close a gap prefer that alignment
…r output and fix error checking
working version of updated read filtering
…om being clipped, keep longest
…e didn't use winnowmap mappings for after gapfill
dont update to snakemake 8
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…es when estimating memory, fix error checking for indexing
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This addresses issues #198, #200, and #201. The tests on human and primate show similar or slightly better assembly with this branch compared to release while being much faster. Will require parallelizing/splitting the correction overlap computation and improving a few remaining regions which were resolved before but are not resolved now.