Don't set a default-for-all ovlHashBits, let it be set based on the g…

…enome size.
marbl · Mar 29, 2018 · a580131 · a580131
1 parent eda92ac
commit a580131
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/pipelines/canu/Defaults.pm b/src/pipelines/canu/Defaults.pm
@@ -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'");