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Don't set a default-for-all ovlHashBits, let it be set based on the g…
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…enome size.
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brianwalenz committed Mar 29, 2018
1 parent eda92ac commit a580131
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion src/pipelines/canu/Defaults.pm
Expand Up @@ -688,7 +688,7 @@ sub setOverlapDefaults ($$$) {

setOverlapDefault($tag, "OvlHashBlockLength", undef, "Amount of sequence (bp) to load into the overlap hash table");
setOverlapDefault($tag, "OvlRefBlockLength", undef, "Amount of sequence (bp) to search against the hash table per batch");
setOverlapDefault($tag, "OvlHashBits", ($tag eq "cor") ? 18 : 23, "Width of the kmer hash. Width 22=1gb, 23=2gb, 24=4gb, 25=8gb. Plus 10b per ${tag}OvlHashBlockLength");
setOverlapDefault($tag, "OvlHashBits", undef, "Width of the kmer hash. Width 22=1gb, 23=2gb, 24=4gb, 25=8gb. Plus 10b per ${tag}OvlHashBlockLength");
setOverlapDefault($tag, "OvlHashLoad", 0.75, "Maximum hash table load. If set too high, table lookups are inefficent; if too low, search overhead dominates run time; default 0.75");
setOverlapDefault($tag, "OvlMerSize", ($tag eq "cor") ? 19 : 22, "K-mer size for seeds in overlaps");
setOverlapDefault($tag, "OvlMerThreshold", "auto", "K-mer frequency threshold; mers more frequent than this count are ignored; default 'auto'");
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