tech debt: htslib 1.10+ breaking ABI changes

dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects

Apache License 2.0

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tech debt: htslib 1.10+ breaking ABI changes #208

Open mlin opened 4 years ago

mlin commented 4 years ago

htslib 1.10 widens a couple of fields in bcf1_t from 32-bit to 64-bit. We'll need to update BCFSerialize.cc & tests to match, and invalidate/upgrade existing databases.

Info: https://github.com/samtools/htslib/blob/develop/README.large_positions.md

wip: https://github.com/dnanexus-rnd/GLnexus/tree/mlin-htslib-1.10

ASLeonard commented 2 months ago

I tried update the read/write methods based on the htslib changes in samtools/htslib@9583bf8, but alas was not that simple. I'm not sure how many other changes would really be necessary, but it seems like it should be relatively straightforward.