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The reason this was happening was due to chromosomes of length greater than 2^29 being indexed which is technically a tabix limit but older versions of tabix allowed it
Tabix 1.2.1 allows it but tabix 1.9 gives a proper error
[E::hts_idx_push] Region 536930580..536930581 cannot be stored in a tbi index. Try using a csi index with min_shift = 14, n_lvls >= 6
tbx_index_build failed: G3116.vcf.gz
Here is a snippet of a vcf with a failing tabix file
failing_tabix.tar.gz
Ends up getting a negative chunkCount
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