iterator interface (v0.3) #34
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kose-y
commented
Jun 17, 2025
src/iterator.jl
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| VCFRow | ||
| end | ||
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| function Base.iterate(itr::VCFIterator, state=1) |
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Let's use VariantCallFormat.Reader as a state instead of an integer.
src/iterator.jl
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| if state <= 0 || state > rows | ||
| return nothing | ||
| else | ||
| reader = VCF.Reader(openvcf(itr.vcffile, "r")) |
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This opens a VCF file, and if we do this, we are opening/decompressing(vcf.gz) n times from the beginning of the file, which is very slow.
src/iterator.jl
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| reader = VCF.Reader(openvcf(itr.vcffile, "r")) | ||
| count = 0 | ||
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| for record in reader |
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This for loop should be removed, and each call to this function should be O(N) time, where N is the number of samples. It should be constant in terms of number of genetic variants.
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