Segfault when working with VCF with multiple contigs

Intel-HLS / GenomicsDB

GenomicsDB

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Segfault when working with VCF with multiple contigs #142

Closed jackgoldsmith4 closed 6 years ago

jackgoldsmith4 commented 7 years ago

Hi, I turned this VCF into a TileDB array and then tried to query that array, but it resulted in a segfault. This VCF is different from previous VCFs I have used in that it has multiple contigs. The JSON files that go along with it are in the same directory as the VCF in my forked hail repo. Is there anything that should be done differently when working with VCFs with multiple contigs? Thanks

kgururaj commented 7 years ago

We hadn't really well tested the concatenate field operation - found a bug. Included in PR https://github.com/Intel-HLS/GenomicsDB/pull/140. Thanks for bringing this to our notice.

kgururaj commented 6 years ago

Just FYI - the genomicsdb 0.7.0 jar released on Maven central fixes this bug.

Another item that you were interested in previously: FILTER fields are now returned by the query .See produce_FILTER_field option in this page

jackgoldsmith4 commented 6 years ago

Thanks.