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Fix coverage calculation to reduce false positives #22

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Fix coverage calculation to reduce false positives #22

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f62c4a9
Only include pairs in which both reads are mapped.
pontushojer Jul 28, 2021
9d00a12
Chromosome length should be used for coverage calculation
pontushojer Jan 26, 2022
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1 change: 0 additions & 1 deletion src/get_reads.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,6 @@ def make_barcodeDict(chrom):
disc_mate_pairs = dict()
split_reads = collections.defaultdict(list)
LRs_by_pos = collections.defaultdict(list)
lengths = sum(reads.lengths)
iterator = reads.fetch(chrom)
starttime = time.time()
prevtime = starttime
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9 changes: 5 additions & 4 deletions src/global_vars.py
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Expand Up @@ -77,17 +77,18 @@ def estimate_lmin_lmax():
num = 0
for i,chrm in enumerate(reads.references):
for read in reads.fetch(chrm):
if read.is_unmapped or read.mate_is_unmapped:
continue

num += 1
if num > 1000000:
break
if read.query_name in mate_pairs:
if read.reference_start > mate_pairs[read.query_name][0]:
dist = read.reference_start-mate_pairs[read.query_name][1]
else:
try:
dist = mate_pairs[read.query_name][0]-read.reference_end
except:
pass
dist = mate_pairs[read.query_name][0]-read.reference_end

if abs(dist) < 2000:
length.append(read.query_length)
ls.append(dist)
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