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Showing content from https://github.com/marbl/canu/commit/f40a20407cd32135ff24300a378d025463ae30ff below:

don't use the first read when we're backing up · marbl/canu@f40a204 · GitHub

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lines changed Original file line number Diff line number Diff line change

@@ -381,7 +381,7 @@ unitigConsensus::generateTemplateStitch(void) {

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bool first = (nm == 0);

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bool save = false;

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if ((nm < _utgpos[ii].max()) && (thick || first) && badToAdd.count(ii) == 0) {

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if ((nm < _utgpos[ii].max()) && (thick || (first && !allowContains)) && badToAdd.count(ii) == 0) {

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save = true;

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nr = ii;

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nm = _utgpos[ii].max();

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