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Feature/fix coverage calculation #258

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Merged
joshfactorial merged 2 commits into from
Apr 5, 2026
Merged

Feature/fix coverage calculation #258

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1465517
updating tests
joshfactorial Apr 4, 2026
f420778
Adding tests too will add more in a separate branch
joshfactorial Apr 5, 2026
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1 change: 1 addition & 0 deletions neat/read_simulator/single_runner.py
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Expand Up @@ -4,6 +4,7 @@
import gzip
import os
import pickle
import pdb

import pysam
from Bio import SeqIO, bgzf
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4 changes: 2 additions & 2 deletions neat/read_simulator/utils/generate_reads.py
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Expand Up @@ -49,9 +49,9 @@ def cover_dataset(
number_reads_per_layer = ceil(span_length / fragment_model.fragment_mean)
if options.paired_ended:
# TODO use gc bias to skew this number. Calculate at the runner level.
number_reads = ceil(number_reads_per_layer * (options.coverage/2))
number_reads = ceil(span_length * options.coverage / (2 * options.read_len))
else:
number_reads = ceil(number_reads_per_layer * options.coverage)
number_reads = ceil(span_length * options.coverage / options.read_len)

# step 1: Divide the span up into segments drawn from the fragment pool. Assign reads based on that.
# step 2: repeat above until number of reads exceeds number_reads
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