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Disable random dropping (for now) #208

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merged 2 commits into from
Nov 23, 2023
+2 −2
Merged

Disable random dropping (for now) #208

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17f709b
disaple ties dropping for now
AndreaGuarracino Nov 23, 2023
d28e3d5
cleaning
AndreaGuarracino Nov 23, 2023
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4 changes: 2 additions & 2 deletions src/interface/parse_args.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ void parse_args(int argc,
args::Flag drop_low_map_pct_identity(mapping_opts, "K", "drop mappings with estimated identity below --map-pct-id=%", {'K', "drop-low-map-id"});
args::Flag no_filter(mapping_opts, "MODE", "disable mapping filtering", {'f', "no-filter"});
args::ValueFlag<double> map_sparsification(mapping_opts, "FACTOR", "keep this fraction of mappings", {'x', "sparsify-mappings"});
args::Flag keep_ties(mapping_opts, "", "keep all mappings with equal score even if it results in more than n mappings", {'D', "keep-ties"});
//ToFix: args::Flag keep_ties(mapping_opts, "", "keep all mappings with equal score even if it results in more than n mappings", {'D', "keep-ties"});
args::ValueFlag<int64_t> sketch_size(mapping_opts, "N", "sketch size for sketching.", {'w', "sketch-size"});
args::ValueFlag<double> kmer_complexity(mapping_opts, "F", "Drop segments w/ predicted kmer complexity below this cutoff. Kmer complexity defined as #kmers / (s - k + 1)", {'J', "kmer-complexity"});
args::Flag no_hg_filter(mapping_opts, "", "Don't use the hypergeometric filtering and instead use the MashMap2 first pass filtering.", {'1', "no-hg-filter"});
Expand Down Expand Up @@ -352,7 +352,7 @@ void parse_args(int argc,
align_parameters.sam_format = args::get(sam_format);
align_parameters.no_seq_in_sam = args::get(no_seq_in_sam);
map_parameters.split = !args::get(no_split);
map_parameters.dropRand = !args::get(keep_ties);
map_parameters.dropRand = false;//ToFix: !args::get(keep_ties);
align_parameters.split = !args::get(no_split);

map_parameters.mergeMappings = !args::get(no_merge);
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