- add ZarrTracks for much faster performance than D4. - finish deprecating parallel GVL.
Fix
- implementation of Haplotypes with re-alignment of tracks, no runtime errors. Pending unit tests. - implementation of Haplotypes with re-alignment of tracks, no runtime errors. Pending unit tests. - deprecate vcf, tiledb, and zarr readers and associated types.
0.2.5
Fix
- raise informative error for unnormalized VCFs. - remove print statement and add zarr dependency. - VCFGenos needed offset information. - bug in construct_haplotypes, updated shift too early. feat: support for VCF and Zarr/Tensorstore for parallel access to genotypes.
0.2.3
Fix
- wrong syntax with in_memory FASTA and cast queries to 1d for FastaVariants.
0.2.2
0.2.1
Fix
- update seqpro version. - update seqpro version.
0.2.0
Feat
- rename RLE table to intervals. WIP generalizing to arbitrary groupings and value columns. - rename RLE table to intervals. WIP generalizing to arbitrary groupings and value columns.
Fix
- include tqdm dependency - non-contiguous genotypes array when using multiple regions in pgen. - update tests to use relative paths and reflect changes to API - handle contig normalization when file has mixed contigs prefixes. - bug in Buffer class - bug in Buffer class - infer contig prefix for FASTA. - return NDArray from Reader instead of DataArray for greater portability and performance. - only slice batch_dims when fetching buffers. - faster FASTA reads, skip sequences that aren't needed. - broadcast track to have ploid dimension.