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Fix parse record error verbiage #175

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JarvisVon opened this issue Jun 24, 2024 · 0 comments · May be fixed by #177
Open

Fix parse record error verbiage #175

JarvisVon opened this issue Jun 24, 2024 · 0 comments · May be fixed by #177

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@JarvisVon
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JarvisVon commented Jun 24, 2024 •
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  • vcfpy version: 0.13.8
  • Python version: 3.12.1
  • Operating System: macOS 14.0

Description

When parsing a file with 9 columns, the 8 required plus an additional FORMAT column, a confusing error is returned of the form "The line contains an invalid number of fields. Was 9 but expected 9".

What I Did

import vcfpy
path = '/path/to/file.vcf'
reader = vcfpy.Reader.from_path(path)
records = []
for record in reader:
  # do work

Stack Trace:
  File "<stdin>", line 1, in <module>
  File "python3.12/site-packages/vcfpy/reader.py", line 175, in __next__
    result = self.parser.parse_next_record()
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "python3.12/site-packages/vcfpy/parser.py", line 804, in parse_next_record
    return self.parse_line(self._read_next_line())
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "python3.12/site-packages/vcfpy/parser.py", line 795, in parse_line
    return self._record_parser.parse_line(line)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "python3.12/site-packages/vcfpy/parser.py", line 425, in parse_line
    arr = self._split_line(line_str)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "python3.12/site-packages/vcfpy/parser.py", line 518, in _split_line
    raise exceptions.InvalidRecordException(
vcfpy.exceptions.InvalidRecordException: The line contains an invalid number of fields. Was 9 but expected 9

The fix would be to update line 521 in vcfpy/parser.py to use self.expected_fields as opposed to 9 + len(self.samples.names), as this distinction is already handled when 9 + len(self.samples.names) is set at lines 399-402 and is used as the error criteria in parser.py line 513
@JarvisVon JarvisVon changed the title Confusing error message in "The line contains an invalid number of fields. Was 9 but expected 9" Fix parse record error verbiage Jun 24, 2024
@JarvisVon JarvisVon linked a pull request Jun 24, 2024 that will close this issue
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fix: Fix parse record error verbiage JarvisVon/vcfpy
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@JarvisVon