Revert "Revert "Use stable distribution in fasta_to_fastq""

This reverts commit 1154fb9.

Author: Donaim

micall/utils/fasta_to_fastq.py

@@ -15,6 +15,7 @@
 from Bio.SeqRecord import SeqRecord, Seq
 from typing import Sequence, Iterator
 from pathlib import Path
+from micall.utils.stable_random_distribution import stable_random_distribution
 
 MAX_QUALITY = 40
 
@@ -52,19 +53,16 @@ def simulate_reads(reference: Seq,
 
     ref_len = len(reference)
     file_num = 2 if is_reversed else 1
+    rng = stable_random_distribution(maximum=(ref_len - min_length))
 
     for i in range(n_reads):
         # Choose a read length uniformly between min_length and max_length.
         read_length = random.randint(min_length, max_length)
-
-        # Choose a random start index ensuring the read fits within
-        # the reference.
-        if ref_len - read_length <= 0:
-            start = 0
-        else:
-            start = random.randrange(0, ref_len - read_length + 1)
-
+        # Choose a start index from a fair distribution.
+        start = next(rng)
         end = start + read_length
+
+        # Get the read nucleotides.
         read_seq_seq = reference[start:end]
         read_seq_str = str(read_seq_seq)
         read_seq = Seq(read_seq_str)