preventing duplicate read ids from bit-gen-reads

Author: Mike Lee

CHANGELOG.md

@@ -13,6 +13,13 @@
 
 -->
 
+## v1.13.14 (13-Mar-2026)
+
+### Fixed
+- `bit-gen-reads` previously may have by chance created reads with identical headers (since only coordinates were being added), now there is also a counter to prevent this
+
+---
+
 ## v1.13.13 (12-Mar-2026)
 
 ### Added

bit/cli/gen_reads.py

@@ -115,6 +115,4 @@ def main():
     elif not args.read_length:
         args.read_length = 150
 
-    print(args)
-
     generate_reads(args)

bit/modules/gen_reads.py

@@ -106,6 +106,7 @@ def gen_paired_reads(args, proportions):
         num_fragments = args.num_reads // 2
         reads_remaining = num_fragments
         remainder = 0.0
+        read_count = 0
 
         for fasta_file in tqdm(args.input_fastas, desc = "    Generating reads from each input FASTA file"):
 
@@ -131,12 +132,13 @@ def gen_paired_reads(args, proportions):
 
                     quality_scores = "I" * args.read_length
 
-                    fw.write(f"@{seq_id}_{start}/1\n")
+                    read_count += 1
+                    fw.write(f"@{seq_id}_{read_count}_{start}/1\n")
                     fw.write(f"{forward_read}\n")
                     fw.write(f"+\n")
                     fw.write(f"{quality_scores}\n")
 
-                    rw.write(f"@{seq_id}_{start}/2\n")
+                    rw.write(f"@{seq_id}_{read_count}_{start}/2\n")
                     rw.write(f"{reverse_read}\n")
                     rw.write(f"+\n")
                     rw.write(f"{quality_scores}\n")
@@ -159,12 +161,13 @@ def gen_paired_reads(args, proportions):
                 reverse_read = fragment[-args.read_length:][::-1].translate(str.maketrans("ACGT", "TGCA"))
                 quality_scores = "I" * args.read_length
 
-                fw.write(f"@{seq_id}_{start}/1\n")
+                read_count += 1
+                fw.write(f"@{seq_id}_{read_count}_{start}/1\n")
                 fw.write(f"{forward_read}\n")
                 fw.write(f"+\n")
                 fw.write(f"{quality_scores}\n")
 
-                rw.write(f"@{seq_id}_{start}/2\n")
+                rw.write(f"@{seq_id}_{read_count}_{start}/2\n")
                 rw.write(f"{reverse_read}\n")
                 rw.write(f"+\n")
                 rw.write(f"{quality_scores}\n")
@@ -185,6 +188,7 @@ def gen_single_reads(args, proportions):
 
         reads_remaining = args.num_reads
         remainder = 0.0
+        read_count = 0
 
         for fasta_file in tqdm(args.input_fastas, desc = "    Generating reads from each input FASTA file"):
 
@@ -210,7 +214,8 @@ def gen_single_reads(args, proportions):
 
                     quality_scores = "I" * len(read)
 
-                    fw.write(f"@{seq_id}_{start}\n")
+                    read_count += 1
+                    fw.write(f"@{seq_id}_{read_count}_{start}\n")
                     fw.write(f"{read}\n")
                     fw.write(f"+\n")
                     fw.write(f"{quality_scores}\n")
@@ -234,7 +239,8 @@ def gen_single_reads(args, proportions):
                 read, start = extract_subsequence(sequence, seq_length, read_len, args.circularize)
 
                 quality_scores = "I" * len(read)
-                fw.write(f"@{seq_id}_{start}\n")
+                read_count += 1
+                fw.write(f"@{seq_id}_{read_count}_{start}\n")
                 fw.write(f"{read}\n")
                 fw.write(f"+\n")
                 fw.write(f"{quality_scores}\n")

bit/tests/test_gen_reads.py

@@ -37,7 +37,7 @@ def test_gen_reads(tmp_path):
         expected = f.read().splitlines()
 
     observed = [
-        "@partial-NC_003131.1_550/1",
+        "@partial-NC_003131.1_1_550/1",
         "GTGGACGACT",
         "+",
         "IIIIIIIIII"