Docs2#95
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susannasiebert
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Jul 9, 2026
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I think for now this is fine, but it's probably preferable/more robust to use vcfpy here. Maybe a stretch goal to do in the future.
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Good suggestion - I didn't think that hard about this (quick and dirty script for internal use, etc), but it makes sense. Flipped it around to use vcfpy to be consistent with the rest of the package. Fixed it up.
…s (1 -> 1.0, etc)
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Adding lots of examples to the documentation, along with a minimal set of VCFs and inputs to run all of the examples.
Also includes an amalgamation of minor issue fixes that came from getting the examples to run cleanly and intuitively (no unneeded warnings, etc):
replaces typo of "Gene Expressions" with "Gene Expression" for the GX field (and updates tests accordingly)
updates the mismatch reporter tool to remove extra "INFO:root:" output at the top of the report
removes some warnings that were not useful/unnecessary from several tools
fixed a bug in vcf_info_annotator. When using --overwrite, the indices internal to vcfpy weren't getting updated correctly, so trying to remove the old header line caused a dangling reference and an error. Fixed by rebuilding the indices.