Fix an edge case in deletions

run_grid_scan.py

@@ -1,5 +1,6 @@
 import subprocess
 import sys
+from tqdm import tqdm
 
 weed_cmd_rep = "ska weed -o no_ambig.skf --min-freq 1 --filter no-ambig-or-const test_grid.skf"
 weed_cmd_norep = "ska weed -o ambig.skf --min-freq 1 --filter no-const test_grid.skf"
@@ -31,25 +32,47 @@ def compare_hits(repeats: bool):
         for line in f:
             expected.add(str(line.rstrip().split("\t")[0:2]))
         f.close()
-    power = len(found.intersection(expected)) / len(expected)
+    if len(expected) > 0:
+        power = len(found.intersection(expected)) / len(expected)
+    else:
+        power = 1.0
     return power
 
-print(f"k\tpi\tindel_rate\tRepeats\tPower")
-for k in [17, 31, 63]:
-    for dist in [0.000001, 0.00001, 0.0001, 0.001, 0.01, 0.1]:
-        for indel_rate in [0.05, 0.1, 0.2]:
-            for repeat in range(10):
-                sim_cmd = f"ska_sim -k {k} -e {dist} -i {indel_rate} > seq.fa"
-                subprocess.run(sim_cmd, shell=True)
-                ska_cmd = f"ska build --single-strand -k {k} -o test_grid pneumo.fa seq.fa"
-                subprocess.run(ska_cmd, shell=True, stderr=subprocess.DEVNULL)
-
-                subprocess.run(weed_cmd_rep, shell=True, stderr=subprocess.DEVNULL)
-                overlap = compare_hits(True)
-                print(f"{k}\t{dist}\t{indel_rate}\t{repeat}\tNo ambiguity\t{overlap}")
-
-                subprocess.run(weed_cmd_norep, shell=True, stderr=subprocess.DEVNULL)
-                overlap = compare_hits(False)
-                print(f"{k}\t{dist}\t{indel_rate}\t{repeat}\tAllow ambiguity\t{overlap}")
-
-sys.exit(0)
+def avg_range(overlaps: list):
+    overlaps.sort()
+    overlaps = overlaps[1:20:]
+    avg = sum(overlaps) / len(overlaps)
+    top = max(overlaps)
+    bottom = min(overlaps)
+    return (bottom, avg, top)
+
+def main():
+    print(f"k\tpi\tindel_rate\tPower_b\tAverage power\tPower_t")
+    with tqdm(total=3*7*3*20) as pbar:
+        for k in [17, 31, 63]:
+            for dist in [0.000001, 0.00001, 0.0001, 0.001, 0.01, 0.03, 0.1]:
+                for indel_rate in [0.0, 0.1, 0.2]:
+                    overlap_rep = list()
+                    overlap_norep = list()
+                    for _repeat in range(20):
+                        sim_cmd = f"ska_sim -k {k} -e {dist} -i {indel_rate} > seq.fa"
+                        subprocess.run(sim_cmd, shell=True)
+                        ska_cmd = f"ska build --single-strand -k {k} -o test_grid pneumo.fa seq.fa"
+                        subprocess.run(ska_cmd, shell=True, stderr=subprocess.DEVNULL)
+
+                        subprocess.run(weed_cmd_rep, shell=True, stderr=subprocess.DEVNULL)
+                        overlap_rep.append(compare_hits(True))
+                        subprocess.run(weed_cmd_norep, shell=True, stderr=subprocess.DEVNULL)
+                        overlap_norep.append(compare_hits(False))
+                        pbar.update(1)
+
+                    stats = avg_range(overlap_rep)
+                    print(f"{k}\t{dist}\t{indel_rate}\tNo ambiguity\t{stats[0]}\t{stats[1]}\t{stats[2]}")
+                    stats = avg_range(overlap_norep)
+                    print(f"{k}\t{dist}\t{indel_rate}\tAllow ambiguity\t{stats[0]}\t{stats[1]}\t{stats[2]}")
+
+
+    sys.exit(0)
+
+if __name__ == "__main__":
+    main()

src/main.rs

@@ -205,17 +205,18 @@ fn main() {
                 new_weights.append(&mut site_rates(size, &gamma, &mut rng));
                 weights.splice(mutated_pos..(mutated_pos + 1), new_weights);
             } else {
-                // Deletion
-                sites -= size;
                 /*
                 eprintln!(
                     "DEL {mutated_pos}:{}",
                     String::from_utf8(start_seq[mutated_pos..(mutated_pos + size)].to_vec())
                         .unwrap()
                 );
                 */
-                start_seq.drain(mutated_pos..(mutated_pos + size));
-                weights.drain(mutated_pos..(mutated_pos + size));
+                let end_del = sites.min(mutated_pos + size);
+                start_seq.drain(mutated_pos..end_del);
+                weights.drain(mutated_pos..end_del);
+                // Deletion
+                sites -= size;
             }
             // Need new gamma heterogeneity
             pos_dist = WeightedIndex::new(&weights).unwrap();