Improved parsing of INFO and FORMAT lines #374
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This fixes a canonicalization check that was looking at span instead of SVLEN. It also checks against canonicalizing variants whose end positions would fall outside the contig. Those are incorrect in the VCF and can't safely be canonicalized.
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I got a warning that this PR failed a CI test from the vgteam fork: https://github.com/vgteam/vcflib/actions/runs/4724980520 However, this test is also currently failing in the master branch, so I strongly suspect that it is unrelated to this PR: https://github.com/vcflib/vcflib/actions/runs/4508941622/jobs/7938130394 |
adamnovak
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Apr 24, 2023
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I'll take a look at this. |
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Thanks! |
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The current parsing code assumes that the required fields (ID, Number, Format, Description) will occur in a set orientation. My reading of the VCF spec is that this ordering is not required, although it's definitely a bit ambiguous:
This parsing issue shows up, in particular, in some of the VCFs from the newer high-coverage VCFs of the 1000GP samples. My updated parsing code allows these keys to occur in any order.
(I'm also pulling in some useful-looking warnings from Adam)