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query -f "%GT" does not raise error #119

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jeromekelleher opened this issue Jan 14, 2025 · 0 comments
Open

query -f "%GT" does not raise error #119

jeromekelleher opened this issue Jan 14, 2025 · 0 comments
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@jeromekelleher
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$ python3 -m vcztools query performance/data/sim_10k.vcz -f '%POS\t%GT\n'  | head
245     <map object at 0x7f9e5c0e3190>
427     <map object at 0x7f9e5c0e2590>
479     <map object at 0x7f9e6a86c5b0>
571     <map object at 0x7f9e6a86c850>
689     <map object at 0x7f9e5c0e2350>
712     <map object at 0x7f9e6a86c7f0>
719     <map object at 0x7f9e5c2747f0>
737     <map object at 0x7f9e6a86c7c0>
961     <map object at 0x7f9e5c0e2590>
996     <map object at 0x7f9e6a86c850>

Correct output is:

$ bcftools query performance/data/sim_10k.vcf.gz -f '%POS\t%GT\n' 
Error: no such tag defined in the VCF header: INFO/GT. FORMAT fields must be enclosed in square brackets, e.g. "[ %GT]"
@jeromekelleher jeromekelleher added the bug Something isn't working label Jan 14, 2025
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