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Performance improvements for v6.0.0 HAC models on Blackwell GPUs

Performance of v5.0.0+ SUP models has also been improved, especially for short reads

Feature improvements and bug fixes for Dorado smallvar:

• Improve the CPU efficiency of read splitting.
• Support gVCF output from Dorado smallvar via the --gvcf option.
• Correctly report variants in Dorado smallvar when the reference is lower case.
• Sort and deduplicate processed_regions.bed file in Dorado smallvar.
• Add --hemizygous-regions option to Dorado smallvar, to specify regions in which haploid variant calls are expected.
• Remove duplicated fileformat header line from VCF output.
• Bug fix for overlapping simple variants by removing redundant allele coverage check in Dorado smallvar.
• Fix output of overlapping variants due to trimming of processed regions before merging.

Other updates and improvements:

• Add --MD, --cs and --rmq to the list of supported minimap options.
• No longer create a .fai index file on disk alongside alignment references.
• Fix sp:i tag to contain the correct split points in all cases when a read has been split multiple times.
• Add support for single-ended dual barcode arrangements (two barcodes at one end of a read) and arrangements with split inter-barcode flanking regions.
• Update to minimap2 v2.31.
• Pin POD5 version to 0.3.39.
• Fix batch size benchmarking while running LSTM models with variable chunk sizes.