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added zdrop, gapopen and gapextend as parameters in redundancy reduction

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AnnSeidel committed Feb 6, 2020
1 parent a66c02c commit 4d3db848bec825ad5736ddb9e88d86f8ed22560a
Showing with 7 additions and 1 deletion.
  1. +1 −1 lib/mmseqs
  2. +3 −0 src/commons/LocalParameters.h
  3. +3 −0 src/workflow/Nuclassembler.cpp
@@ -113,6 +113,9 @@ class LocalParameters : public Parameters {
reduceredundancy.push_back(&PARAM_C);
reduceredundancy.push_back(&PARAM_MAX_SEQ_LEN);
reduceredundancy.push_back(&PARAM_WRAPPED_SCORING);
reduceredundancy.push_back(&PARAM_GAP_OPEN);
reduceredundancy.push_back(&PARAM_GAP_EXTEND);
reduceredundancy.push_back(&PARAM_ZDROP);

// nucl assembler workflow
nuclassemblerworkflow.push_back(&PARAM_CYCLE_CHECK);
@@ -112,6 +112,9 @@ int nuclassembler(int argc, const char **argv, const Command &command) {
par.covMode = 1;
par.wrappedScoring = true;
par.ignoreMultiKmer = true;
par.zdrop = 200;
par.gapOpen = 5;
par.gapExtend = 2;
cmd.addVariable("CLUSTER_PAR", par.createParameterString(par.reduceredundancy).c_str());

cmd.addVariable("THREADS_PAR", par.createParameterString(par.onlythreads).c_str());

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