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Strand correction #74

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ahanden wants to merge 4 commits into from
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Strand correction #74

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0ffa61e
Changed reference sequence from list to generator
uchicago-handena Feb 11, 2026
67b1aba
Changed -C to behave like REDI1 instead of REDI2
uchicago-handena Feb 26, 2026
256aec8
Changed help documentation for strand correction
uchicago-handena Feb 26, 2026
fca0092
Undid refseq changes from wrong branch
uchicago-handena Mar 5, 2026
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4 changes: 3 additions & 1 deletion reditools/analyze.py
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Original file line number Diff line number Diff line change
Expand Up @@ -375,7 +375,9 @@ def parse_options(): # noqa:WPS213
'--strand-correction',
default=False,
help='Strand correction. Once the strand has been inferred, ' +
'only bases according to this strand will be selected.',
'only bases according to this strand will be selected. If ' +
'edits are detected on the reverse strand, the base complements ' +
'will be reported.',
action='store_true',
)
parser.add_argument(
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5 changes: 2 additions & 3 deletions reditools/reditools.py
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Expand Up @@ -380,6 +380,8 @@ def analyze(self, alignment_manager, region=None): # noqa:WPS231,WPS213
if bases is not None and self._use_strand_correction:
strand = bases.get_strand(threshold=self.strand_confidence_threshold)
bases.filter_by_strand(strand)
if strand == '-':
bases.complement()
if not self._rtqc.check(self, bases):
continue
column = self._get_column(position, bases, region)
Expand Down Expand Up @@ -435,9 +437,6 @@ def _get_column(self, position, bases, region):
region.stop,
)
return None
strand = bases.get_strand(threshold=self.strand_confidence_threshold)
if strand == '-':
bases.complement()

return RTResult(bases, strand, region.contig, position)

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