From d78c972dcc8e8eb4fa3dd82d343c1e256690ea42 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Wed, 5 Jun 2024 13:10:04 -0700
Subject: [PATCH] Set chainier R10 parameters and swap count and length presets
 for HiFi to follow swapped parameters

---
 src/subcommand/giraffe_main.cpp | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/subcommand/giraffe_main.cpp b/src/subcommand/giraffe_main.cpp
index ce2e7f40825..b440cb73dfe 100644
--- a/src/subcommand/giraffe_main.cpp
+++ b/src/subcommand/giraffe_main.cpp
@@ -859,8 +859,8 @@ int main_giraffe(int argc, char** argv) {
         // Use downsampling instead of max unique minimizer count
         .add_entry<size_t>("max-min", 0)
         .add_entry<size_t>("num-bp-per-min", 1000)
-        .add_entry<size_t>("downsample-window-count", 125)
-        .add_entry<size_t>("downsample-window-length", 120)
+        .add_entry<size_t>("downsample-window-count", 120)
+        .add_entry<size_t>("downsample-window-length", 125)
         // Don't use the hit-cap||score-fraction filter because it doesn't do anything after downsampling
         .add_entry<size_t>("hit-cap", 0)
         .add_entry<double>("score-fraction", 1.0)
@@ -909,14 +909,14 @@ int main_giraffe(int argc, char** argv) {
         .add_entry<size_t>("watchdog-timeout", 30)
         .add_entry<size_t>("batch-size", 10)
         // Use downsampling instead of max unique minimizer count
-        .add_entry<size_t>("max-min", 100)
-        .add_entry<size_t>("num-bp-per-min", 500)
-        .add_entry<size_t>("downsample-window-count", 500)
-        .add_entry<size_t>("downsample-window-length", 20)
+        .add_entry<size_t>("max-min", 79)
+        .add_entry<size_t>("num-bp-per-min", 152)
+        .add_entry<size_t>("downsample-window-count", 15)
+        .add_entry<size_t>("downsample-window-length", 227)
         // Don't use the hit-cap||score-fraction filter because it doesn't do anything after downsampling
         .add_entry<size_t>("hit-cap", 0)
         .add_entry<double>("score-fraction", 1.0)
-        .add_entry<size_t>("hard-hit-cap", 20000)
+        .add_entry<size_t>("hard-hit-cap", 13614)
         .add_entry<double>("mapq-score-scale", 1)
         .add_entry<size_t>("mapq-score-window", 150)
         .add_entry<double>("zipcode-tree-score-threshold", 100.0)
@@ -940,10 +940,10 @@ int main_giraffe(int argc, char** argv) {
         .add_entry<int>("min-chaining-problems", 6)
         .add_entry<int>("max-chaining-problems", std::numeric_limits<int>::max())
         .add_entry<size_t>("max-lookback-bases", 20000)
-        .add_entry<double>("max-lookback-bases-per-base", 0.15)
+        .add_entry<double>("max-lookback-bases-per-base", 0.10501002120802233)
         .add_entry<int>("item-bonus", 20)
         .add_entry<int>("item-scale", 1)
-        .add_entry<double>("gap-scale", 2.75)
+        .add_entry<double>("gap-scale", 0.06759721757973396)
         .add_entry<size_t>("max-indel-bases", 5000)
         .add_entry<double>("max-indel-bases-per-base", 2.45)
         .add_entry<double>("chain-score-threshold", 100.0)