From 569db6316c607170cc1b9589265496bb6d2b2226 Mon Sep 17 00:00:00 2001
From: "N. Tessa Pierce-Ward" <ntpierce@gmail.com>
Date: Mon, 28 Aug 2023 17:28:29 -0700
Subject: [PATCH] rm threshold

---
 src/lib.rs                              | 6 ++----
 src/python/pyo3_branchwater/__init__.py | 5 +----
 2 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/src/lib.rs b/src/lib.rs
index 9cf3d37d..ca04ffa5 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -763,7 +763,6 @@ fn build_template(ksize: u8, scaled: usize) -> Sketch {
 fn index<P: AsRef<Path>>(
     siglist: P,
     template: Sketch,
-    threshold: f64,
     output: P,
     save_paths: bool,
     colors: bool,
@@ -777,7 +776,7 @@ fn index<P: AsRef<Path>>(
     let db = RevIndex::create(output.as_ref(), colors);
 
     // Index the signatures using the loaded template, threshold, and save_paths option
-    db.index(index_sigs, &template, threshold, save_paths);
+    db.index(index_sigs, &template, 0.0, save_paths);
 
     Ok(())
 }
@@ -1134,14 +1133,13 @@ fn set_global_thread_pool(num_threads: usize) -> PyResult<usize> {
 fn do_index(siglist: String,
             ksize: u8,
             scaled: usize,
-            threshold: f64,
             output: String,
             save_paths: bool,
             colors: bool,
 ) -> anyhow::Result<u8>{
     // build template from ksize, scaled
     let template = build_template(ksize, scaled);
-    match index(siglist, template, threshold, output,
+    match index(siglist, template, output,
                 save_paths, colors) {
         Ok(_) => Ok(0),
         Err(e) => {
diff --git a/src/python/pyo3_branchwater/__init__.py b/src/python/pyo3_branchwater/__init__.py
index c3a6667f..3a96a4d6 100755
--- a/src/python/pyo3_branchwater/__init__.py
+++ b/src/python/pyo3_branchwater/__init__.py
@@ -159,8 +159,6 @@ def __init__(self, p):
                        help="a text file containing paths to .sig/.sig.gz files")
         p.add_argument('-o', '--output', required=True,
                        help='output file for the index')
-        p.add_argument('-t', '--threshold', default=0.01, type=float,
-                       help='containment threshold for reporting matches')
         p.add_argument('-k', '--ksize', default=31, type=int,
                        help='k-mer size at which to select sketches')
         p.add_argument('-s', '--scaled', default=1000, type=int,
@@ -171,7 +169,7 @@ def __init__(self, p):
                        help='number of cores to use (default is all available)')
 
     def main(self, args):
-        notify(f"ksize: {args.ksize} / scaled: {args.scaled} / threshold: {args.threshold}")
+        notify(f"ksize: {args.ksize} / scaled: {args.scaled}")
 
         num_threads = set_thread_pool(args.cores)
 
@@ -180,7 +178,6 @@ def main(self, args):
         status = pyo3_branchwater.do_index(args.siglist,
                                                 args.ksize,
                                                 args.scaled,
-                                                args.threshold,
                                                 args.output,
                                                 args.save_paths,
                                                 False) # colors - currently must be false?