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44 OpenVariant Bug breaks when input has empty lines #45

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merged 1 commit into from
Mar 14, 2025
Merged

44 OpenVariant Bug breaks when input has empty lines #45

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12 changes: 10 additions & 2 deletions openvariant/variant/variant.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
import ctypes
import gzip
import lzma
import warnings
from fnmatch import fnmatch
from functools import lru_cache
import mmap
Expand Down Expand Up @@ -242,8 +243,15 @@ def _parser(self, file_path: str, annotation: Annotation, group_by: str, display

if row and not _exclude(line_dict, annotation.excludes):
yield row

except (ValueError, IndexError, KeyError) as e:
except IndexError as e:
if line == ['']:
warnings.warn(f"Warning: empty line {lnum} on {file_path}.", UserWarning)
pass
else:
self.mm.close()
self.file.close()
raise ValueError(f"Error parsing line: {lnum} {file_path}: {e}")
except (ValueError, KeyError) as e:
self.mm.close()
self.file.close()
raise ValueError(f"Error parsing line: {lnum} {file_path}: {e}")
Expand Down