Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branch…

…water into refactor_tests

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "sourmash_plugin_branchwater"
-version = "0.9.8"
+version = "0.9.9-dev"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

src/fastgather.rs

@@ -14,14 +14,14 @@ pub fn fastgather(
     against_filepath: String,
     threshold_bp: usize,
     scaled: usize,
-    selection: &Selection,
+    selection: Selection,
     gather_output: Option<String>,
     prefetch_output: Option<String>,
     allow_failed_sigpaths: bool,
 ) -> Result<()> {
     let query_collection = load_collection(
         &query_filepath,
-        selection,
+        &selection,
         ReportType::Query,
         allow_failed_sigpaths,
     )?;
@@ -40,7 +40,7 @@ pub fn fastgather(
     let query_md5 = query_sig.md5sum();
 
     // clone here is necessary b/c we use full query_sig in consume_query_by_gather
-    let query_sig_ds = query_sig.select(selection)?; // downsample
+    let query_sig_ds = query_sig.select(&selection)?; // downsample
     let query_mh = match query_sig_ds.try_into() {
         Ok(query_mh) => query_mh,
         Err(_) => {
@@ -50,7 +50,7 @@ pub fn fastgather(
     // load collection to match against.
     let against_collection = load_collection(
         &against_filepath,
-        selection,
+        &selection,
         ReportType::Against,
         allow_failed_sigpaths,
     )?;

src/fastmultigather.rs

@@ -29,8 +29,8 @@ pub fn fastmultigather(
     query_filepath: String,
     against_filepath: String,
     threshold_bp: usize,
-    scaled: usize,
-    selection: &Selection,
+    scaled: Option<usize>,
+    selection: Selection,
     allow_failed_sigpaths: bool,
     save_matches: bool,
     create_empty_results: bool,
@@ -40,11 +40,26 @@ pub fn fastmultigather(
     // load query collection
     let query_collection = load_collection(
         &query_filepath,
-        selection,
+        &selection,
         ReportType::Query,
         allow_failed_sigpaths,
     )?;
 
+    let scaled = match scaled {
+        Some(s) => s,
+        None => {
+            let scaled = query_collection.max_scaled().expect("no records!?").clone() as usize;
+            eprintln!(
+                "Setting scaled={} based on max scaled in query collection",
+                scaled
+            );
+            scaled
+        }
+    };
+
+    let mut against_selection = selection;
+    against_selection.set_scaled(scaled as u32);
+
     let threshold_hashes: u64 = {
         let x = threshold_bp / scaled;
         if x > 0 {
@@ -60,12 +75,12 @@ pub fn fastmultigather(
     // load against collection
     let against_collection = load_collection(
         &against_filepath,
-        selection,
+        &against_selection,
         ReportType::Against,
         allow_failed_sigpaths,
     )?;
     // load against sketches into memory, downsampling on the way
-    let against = against_collection.load_sketches(selection)?;
+    let against = against_collection.load_sketches(&against_selection)?;
 
     // Iterate over all queries => do prefetch and gather!
     let processed_queries = AtomicUsize::new(0);

src/index.rs

@@ -8,7 +8,7 @@ use sourmash::collection::{Collection, CollectionSet};
 
 pub fn index<P: AsRef<Path>>(
     siglist: String,
-    selection: &Selection,
+    selection: Selection,
     output: P,
     colors: bool,
     allow_failed_sigpaths: bool,
@@ -18,7 +18,7 @@ pub fn index<P: AsRef<Path>>(
 
     let multi = match load_collection(
         &siglist,
-        selection,
+        &selection,
         ReportType::General,
         allow_failed_sigpaths,
     ) {
@@ -31,15 +31,15 @@ pub fn index<P: AsRef<Path>>(
     let collection = match Collection::try_from(multi.clone()) {
         // conversion worked!
         Ok(c) => {
-            let cs: CollectionSet = c.select(selection)?.try_into()?;
+            let cs: CollectionSet = c.select(&selection)?.try_into()?;
             Ok(cs)
         }
         // conversion failed; can we/should we load it into memory?
         Err(_) => {
             if use_internal_storage {
                 eprintln!("WARNING: loading all sketches into memory in order to index.");
                 eprintln!("See 'index' documentation for details.");
-                let c: Collection = multi.load_all_sigs(selection)?;
+                let c: Collection = multi.load_all_sigs(&selection)?;
                 let cs: CollectionSet = c.try_into()?;
                 Ok(cs)
             } else {

src/lib.rs

@@ -39,7 +39,7 @@ fn do_manysearch(
     ignore_abundance: Option<bool>,
 ) -> anyhow::Result<u8> {
     let againstfile_path: PathBuf = siglist_path.clone().into();
-    let selection = build_selection(ksize, scaled, &moltype);
+    let selection = build_selection(ksize, Some(scaled), &moltype);
     eprintln!("selection scaled: {:?}", selection.scaled());
     let allow_failed_sigpaths = true;
 
@@ -51,7 +51,7 @@ fn do_manysearch(
         match mastiff_manysearch::mastiff_manysearch(
             querylist_path,
             againstfile_path,
-            &selection,
+            selection,
             threshold,
             output_path,
             allow_failed_sigpaths,
@@ -66,7 +66,7 @@ fn do_manysearch(
         match manysearch::manysearch(
             querylist_path,
             siglist_path,
-            &selection,
+            selection,
             threshold,
             output_path,
             allow_failed_sigpaths,
@@ -94,15 +94,15 @@ fn do_fastgather(
     output_path_prefetch: Option<String>,
     output_path_gather: Option<String>,
 ) -> anyhow::Result<u8> {
-    let selection = build_selection(ksize, scaled, &moltype);
+    let selection = build_selection(ksize, Some(scaled), &moltype);
     let allow_failed_sigpaths = true;
 
     match fastgather::fastgather(
         query_filename,
         siglist_path,
         threshold_bp,
         scaled,
-        &selection,
+        selection,
         output_path_prefetch,
         output_path_gather,
         allow_failed_sigpaths,
@@ -123,7 +123,7 @@ fn do_fastmultigather(
     siglist_path: String,
     threshold_bp: usize,
     ksize: u8,
-    scaled: usize,
+    scaled: Option<usize>,
     moltype: String,
     output_path: Option<String>,
     save_matches: bool,
@@ -138,7 +138,7 @@ fn do_fastmultigather(
         match mastiff_manygather::mastiff_manygather(
             query_filenames,
             againstfile_path,
-            &selection,
+            selection.clone(),
             threshold_bp,
             output_path,
             allow_failed_sigpaths,
@@ -158,7 +158,7 @@ fn do_fastmultigather(
             siglist_path,
             threshold_bp,
             scaled,
-            &selection,
+            selection,
             allow_failed_sigpaths,
             save_matches,
             create_empty_results,
@@ -199,11 +199,11 @@ fn do_index(
     colors: bool,
     use_internal_storage: bool,
 ) -> anyhow::Result<u8> {
-    let selection = build_selection(ksize, scaled, &moltype);
+    let selection = build_selection(ksize, Some(scaled), &moltype);
     let allow_failed_sigpaths = false;
     match index::index(
         siglist,
-        &selection,
+        selection,
         output,
         colors,
         allow_failed_sigpaths,
@@ -237,7 +237,7 @@ fn do_multisearch(
     siglist_path: String,
     threshold: f64,
     ksize: u8,
-    scaled: usize,
+    scaled: Option<usize>,
     moltype: String,
     estimate_ani: bool,
     output_path: Option<String>,
@@ -251,7 +251,7 @@ fn do_multisearch(
         querylist_path,
         siglist_path,
         threshold,
-        &selection,
+        selection,
         allow_failed_sigpaths,
         estimate_ani,
         output_path,
@@ -277,12 +277,12 @@ fn do_pairwise(
     write_all: bool,
     output_path: Option<String>,
 ) -> anyhow::Result<u8> {
-    let selection = build_selection(ksize, scaled, &moltype);
+    let selection = build_selection(ksize, Some(scaled), &moltype);
     let allow_failed_sigpaths = true;
     match pairwise::pairwise(
         siglist_path,
         threshold,
-        &selection,
+        selection,
         allow_failed_sigpaths,
         estimate_ani,
         write_all,

src/manysearch.rs

@@ -19,7 +19,7 @@ use sourmash::sketch::minhash::KmerMinHash;
 pub fn manysearch(
     query_filepath: String,
     against_filepath: String,
-    selection: &Selection,
+    selection: Selection,
     threshold: f64,
     output: Option<String>,
     allow_failed_sigpaths: bool,
@@ -28,18 +28,18 @@ pub fn manysearch(
     // Load query collection
     let query_collection = load_collection(
         &query_filepath,
-        selection,
+        &selection,
         ReportType::Query,
         allow_failed_sigpaths,
     )?;
 
     // load all query sketches into memory, downsampling on the way
-    let query_sketchlist = query_collection.load_sketches(selection)?;
+    let query_sketchlist = query_collection.load_sketches(&selection)?;
 
     // Against: Load collection, potentially off disk & not into memory.
     let against_collection = load_collection(
         &against_filepath,
-        selection,
+        &selection,
         ReportType::Against,
         allow_failed_sigpaths,
     )?;

src/mastiff_manygather.rs

@@ -15,7 +15,7 @@ use crate::utils::{
 pub fn mastiff_manygather(
     queries_file: String,
     index: PathBuf,
-    selection: &Selection,
+    selection: Selection,
     threshold_bp: usize,
     output: Option<String>,
     allow_failed_sigpaths: bool,
@@ -29,7 +29,7 @@ pub fn mastiff_manygather(
 
     let query_collection = load_collection(
         &queries_file,
-        selection,
+        &selection,
         ReportType::Query,
         allow_failed_sigpaths,
     )?;

src/mastiff_manysearch.rs

@@ -18,7 +18,7 @@ use crate::utils::{
 pub fn mastiff_manysearch(
     queries_path: String,
     index: PathBuf,
-    selection: &Selection,
+    selection: Selection,
     minimum_containment: f64,
     output: Option<String>,
     allow_failed_sigpaths: bool,
@@ -35,7 +35,7 @@ pub fn mastiff_manysearch(
     // Load query paths
     let query_collection = load_collection(
         &queries_path,
-        selection,
+        &selection,
         ReportType::Query,
         allow_failed_sigpaths,
     )?;