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Fix align_trim to deal with long deletion containing left primer #111

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Fix align_trim to deal with long deletion containing left primer #111

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6eb8787
Fix align_trim to deal with long deletion containing left primer
hsnguyen Jun 20, 2022
00d1658
fix bug of primer coordinates: [start+1,end] instead of [start,end+1]
hsnguyen Sep 19, 2023
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2 changes: 1 addition & 1 deletion artic/align_trim.py
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,7 @@ def trim(segment, primer_pos, end, debug):
break

# calculate how many extra matches are needed in the CIGAR
extra = abs(pos - primer_pos)
extra = min(abs(pos - primer_pos),length)
if debug:
print("extra %s" % (extra), file=sys.stderr)
if extra:
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5 changes: 3 additions & 2 deletions artic/vcf_merge.py
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Expand Up @@ -10,7 +10,8 @@ def vcf_merge(args):
primer_map = defaultdict(dict)

for p in bed:
for n in range(p['start'], p['end']+1):
#for n in range(p['start'], p['end']+1):
for n in range(p['start']+1, p['end']):
primer_map[p['PoolName']][n] = p['Primer_ID']

first_vcf = None
Expand All @@ -19,7 +20,7 @@ def vcf_merge(args):
for param in args.vcflist:
pool_name, file_name = param.split(":")
pool_map[file_name] = pool_name
if not first_vcf:
if not first_vcf:
first_vcf = file_name

vcf_reader = vcf.Reader(filename=first_vcf)
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2 changes: 1 addition & 1 deletion artic/version.py
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = "1.3.0"
__version__ = "1.3.2"