Made kmer_min_cutoff generic over types that implement UInt

bacpop · Jan 27, 2025 · d45e944 · d45e944
1 parent b06fdca
commit d45e944
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Showing 2 changed files with 21 additions and 33 deletions.
diff --git a/src/io_utils.rs b/src/io_utils.rs
@@ -167,10 +167,9 @@ pub fn get_2_fastq_path(files: &[InputFastx]) -> (String, String) {
 }
 
 /// Calculates minimum kmer cutoff depending on user provided argument
-pub fn kmer_min_cutoff(
+pub fn kmer_min_cutoff<IntT: for<'a> UInt<'a>>(
     v: &Option<ValidMinKmer>,
     files: &[InputFastx],
-    rep_64: bool,
     k: &usize,
     rc: bool,
     verbose: bool,
@@ -192,18 +191,10 @@ pub fn kmer_min_cutoff(
             // auto-calculate & there are enough fastq files
             ValidMinKmer::Auto if count_fastq(files).ge(&2) => {
                 let (fastq_fwd, fastq_rev) = get_2_fastq_path(files);
-                let out: u16;
-                if rep_64 {
-                    let mut cov =
-                        CoverageHistogram::<u64>::new(&fastq_fwd, &fastq_rev, *k, rc, verbose);
-                    out = cov.fit_histogram().expect("Couldn't fit coverage model") as u16;
-                    cov.plot_hist();
-                } else {
-                    let mut cov =
-                        CoverageHistogram::<u128>::new(&fastq_fwd, &fastq_rev, *k, rc, verbose);
-                    out = cov.fit_histogram().expect("Couldn't fit coverage model") as u16;
-                    cov.plot_hist();
-                }
+                let mut cov =
+                    CoverageHistogram::<IntT>::new(&fastq_fwd, &fastq_rev, *k, rc, verbose);
+                let out = cov.fit_histogram().expect("Couldn't fit coverage model") as u16;
+                cov.plot_hist();
                 log::info!("Using inferred minimum kmer value of {}", out);
                 out
             }

diff --git a/src/lib.rs b/src/lib.rs
@@ -504,26 +504,16 @@ pub fn main() {
             // Read input
             let input_files = get_input_list(file_list, seq_files);
             let rc = !*single_strand;
-
-            // Are using 64 or 128 bit representation
-            let rep_64: bool = k.le(&31);
-            if rep_64 {
-                log::info!("k={}: using 64-bit representation", *k);
-            } else {
-                log::info!("k={}: using 128-bit representation", *k);
-            }
-
-            // Calculate minimum kmer cutoff
-            let cutoff = kmer_min_cutoff(min_count, &input_files, rep_64, k, rc, args.verbose);
-
-            let quality = QualOpts {
-                min_count: cutoff,
-                min_qual: *min_qual,
-                qual_filter: *qual_filter,
-            };
-
             // Build, merge
-            if rep_64 {
+            // check for 64 or 128 bit representation
+            if k.le(&31) {
+                log::info!("k={}: using 64-bit representation", *k);
+                let cutoff = kmer_min_cutoff::<u64>(min_count, &input_files, k, rc, args.verbose);
+                let quality = QualOpts {
+                    min_count: cutoff,
+                    min_qual: *min_qual,
+                    qual_filter: *qual_filter,
+                };
                 let merged_dict = build_and_merge::<u64>(
                     &input_files,
                     *k,
@@ -536,6 +526,13 @@ pub fn main() {
                 // Save
                 save_skf(&merged_dict, output);
             } else {
+                log::info!("k={}: using 128-bit representation", *k);
+                let cutoff = kmer_min_cutoff::<u128>(min_count, &input_files, k, rc, args.verbose);
+                let quality = QualOpts {
+                    min_count: cutoff,
+                    min_qual: *min_qual,
+                    qual_filter: *qual_filter,
+                };
                 let merged_dict = build_and_merge::<u128>(
                     &input_files,
                     *k,