Bug Fixes

Updated the logic used to determine valid mapped mates for a read, now mirroring Google DeepVariant.

Added a better error message when header information is missing in the supplied input sample.

Fixed a bug causing print statements to appear in incorrect order.

Properly parse user-supplied pangenome sample and pangenome reference names.

Fixed invalid .tbi index generation in certain edge cases.

Fixed an issue where a .tbi index could appear older than its corresponding data file.

Fixed a BGZF writer crash during vcf.gz writing on records larger than 64 KB.

Fixed a potential race condition and also ensure bit-identical results across architectures.

Fixed an incorrect error message for invalid tumor/normal sample names.

Fixed a possible crash when processing batches that contain only short reads (below 29 bp) that produce no minimizers.

Fixed two potential out-of-bounds writes in the Dozeu alignment kernel.

Fixed several GPU alignment edge cases involving empty chains, short-seed scoring, large-read scratch data, and reads with many seeds.

Fixed paired-end long-read CPU recovery mode to allow reads longer than --max-read-size-gpu to be processed on CPU.

Fixed a case that could result in a crash if all reads in a batch were below BWA-MEM's minimum seed length, which by default is 19 bp.

Fixed an out of bounds access caused by reads that skipped alignment in the splice:sr preset.

Fixed a bug that could cause junction values to not be used in splice-aware alignments.

Fixed a bug in the GPU CRAM writer that caused samtools index to fail on the GPU generated CRAM file.