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Brian Fulton-Howard

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Latest activity by Brian Fulton-Howard
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    Brian Fulton-Howard commented,

    It's a fairly simple algorithm with some modifications for speed. Basically it reads in the fasta file line by line, directly from compressed in binary mode. If the line starts with ">", it will de...

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    Brian Fulton-Howard commented,

    I am modifying the qName field programmatically using python3 with a lookup table in pandas. I am pretty sure at this point that it's not the chain file that's the problem though, but the fasta fil...

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    Brian Fulton-Howard commented,

    Thanks for the quick reply!I have done some further troubleshooting and determined that it is NOT due to the source genotype file (it also fails with the HGDP WGS vcf files. Though I am modifying t...

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    Brian Fulton-Howard commented,

    I'm getting the same problem, and I know my vcf file is sorted sequentially, and that all of the target contigs are in the reference fasta. What's more, it only fails on chr18. All of the other chr...