Bug Fixes

mutectcaller and haplotypecaller: Fixed a wrong alignment offset value in smith-waterman algorithm.

mutectcaller and haplotypecaller: Fixed a crash on GPU when running in low memory mode.

mutectcaller: Fixed the wrong active probability value when the pileup size is 0.

mutectcaller: Fixed a max coverage overflow bug.

rna_fq2bam: Fixed an error when passing "WithinBAM_SoftClip" or "WithinBAM_HardClip" to --out-chim-type.

minimap2: Fixed support for Oxford Nanopore Technologies (ONT) data with minimap2.

fq2bamfast : Fix rare erroneous assertion (Workspace not big enough, expected desiredSize <= cubWorkspaceSize, exiting). Case will now be handled correctly and fall back to CPU recovery if needed.

deepvariant: Fixed bug related to Smith-Waterman computation on CPU.