diff --git a/src/subcommand/giraffe_main.cpp b/src/subcommand/giraffe_main.cpp index 9557600ecd..471d3b9253 100644 --- a/src/subcommand/giraffe_main.cpp +++ b/src/subcommand/giraffe_main.cpp @@ -920,6 +920,7 @@ int main_giraffe(int argc, char** argv) { presets["default"] // This is always on in the non-chaining codepath right now, but just to be sure... .add_entry("explored-cap", true); + presets["hifi"] .add_entry("align-from-chains", true) .add_entry("explored-cap", false) @@ -962,11 +963,11 @@ int main_giraffe(int argc, char** argv) { .add_entry("item-bonus", 20) .add_entry("item-scale", 1.0) .add_entry("gap-scale", 0.2) - .add_entry("chain-score-threshold", 100.0) - .add_entry("min-chains", 4) - .add_entry("min-chain-score-per-base", 0.06) + .add_entry("chain-score-threshold", 200.0) + .add_entry("min-chains", 2) + .add_entry("min-chain-score-per-base", 0.1) .add_entry("max-chains-per-tree", 3) - .add_entry("max-min-chain-score", 100) + .add_entry("max-min-chain-score", 1100) .add_entry("max-skipped-bases", 1000) .add_entry("max-alignments", 3) .add_entry("max-chain-connection", 233) @@ -981,6 +982,7 @@ int main_giraffe(int argc, char** argv) { .add_entry("wfa-max-mismatches-per-base", 0.05) .add_entry("wfa-max-max-mismatches", 15); + presets["r10"] .add_entry("align-from-chains", true) .add_entry("explored-cap", false) @@ -1018,17 +1020,19 @@ int main_giraffe(int argc, char** argv) { .add_entry("min-chaining-problems", 6) .add_entry("max-chaining-problems", std::numeric_limits::max()) .add_entry("max-graph-lookback-bases", 20000) - .add_entry("max-graph-lookback-bases-per-base", 0.10501002120802233) + .add_entry("max-graph-lookback-bases-per-base", 0.036) + .add_entry("max-read-lookback-bases", 20000) + .add_entry("max-read-lookback-bases-per-base", 0.036) .add_entry("max-indel-bases", 5000) .add_entry("max-indel-bases-per-base", 2.45) .add_entry("item-bonus", 20) .add_entry("item-scale", 1.0) .add_entry("gap-scale", 0.06759721757973396) - .add_entry("chain-score-threshold", 100.0) + .add_entry("chain-score-threshold", 160.0) .add_entry("min-chains", 2) .add_entry("max-chains-per-tree", 3) - .add_entry("min-chain-score-per-base", 0.06) - .add_entry("max-min-chain-score", 500.0) + .add_entry("min-chain-score-per-base", 0.052) + .add_entry("max-min-chain-score", 1900.0) .add_entry("max-skipped-bases", 1000) .add_entry("max-alignments", 3) .add_entry("max-chain-connection", 233)