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add /1 or /2 information back into read name if missing #1

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merged 2 commits into from
Jul 31, 2023
Merged

add /1 or /2 information back into read name if missing #1

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63c96f3
add /1 or /2 info back into read name if missing
bluegenes Jul 17, 2023
866ed6d
add pysam read name code
bluegenes Jul 20, 2023
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14 changes: 14 additions & 0 deletions subtract/calc-coverage-diff-2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,20 @@ def main():

#print('XXX', chr, start, end)

# add /1 or /2 if read is paired and is read 1 or read 2
if read.is_paired:
if read.is_read1:
if '/1' not in read.qname:
read.qname += '/1'
elif read.is_read2:
if '/2' not in read.qname:
read.qname += '/2'
else:
raise ValueError(f"read {read.qname} is paired but not read 1 or read 2")
else:
if '/1' not in read.qname:
read.qname += '/1'

# for each position in query read, get coverage
sum_cov = []
for pos in range(start, end + 1):
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14 changes: 14 additions & 0 deletions subtract/calc-coverage-diff-sam-bam.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,20 @@ def main():
start = read.reference_start
end = read.reference_end

# add /1 or /2 if read is paired and is read 1 or read 2
if read.is_paired:
if read.is_read1:
if '/1' not in read.qname:
read.qname += '/1'
elif read.is_read2:
if '/2' not in read.qname:
read.qname += '/2'
else:
raise ValueError(f"read {read.qname} is paired but not read 1 or read 2")
else:
if '/1' not in read.qname:
read.qname += '/1'

# for each position in query read, get coverage
sum_cov = []
for i in range(start, end + 1):
Expand Down