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Quickstart VCFTable example doesn't work #95

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ovesh opened this issue Sep 23, 2024 · 0 comments

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ovesh commented Sep 23, 2024 •

edited

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Trying to open the file in the example results in this error:

>>> vcf = VCFTable.from_vcf("test.vcf.gz", Genome("hg19"), info_ids=["AF"], fmt_ids=["GT", "AD"])
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/foo/GenomeKit/genome_kit/vcf_table.py", line 247, in from_vcf
    VCFTable.build_vcfbin(
ValueError: src/variant_table.cpp:983: In VCF file: test.vcf.gz:9
  src/variant_table.cpp:751: Invalid REF "-".

The correct contents of the file are in demos/query_vcf.py

The text was updated successfully, but these errors were encountered:

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