Bug Fixes

Added the missing read group (RG) header line in the normal sample BAM/CRAM output defined by --mutect-bam-output.

Addressed an issue preventing --markdups-assume-sortorder-queryname from taking effect when combined with --gpusort.

Fixed a potential GPU out-of-memory condition when --num-streams-per-gpu was set to auto (default).

Fixed missing alignments for reads with a high degree of multimapping.

Fixed a memory leak that occurred during CPU recovery.

Fixed an issue where --bwa-nstreams auto (default value) and --gpuwrite could potentially run out of device memory with GPUs having more than 16 GB but less than 22 GB of memory.

Fixed a potential out-of-bounds device write when using --gpuwrite for accelerated BAM and CRAM writing. This risk was more likely to appear on ARM systems such as NVIDIA GB10.

Fixed --preserve-file-symlinks to work properly with methylation reference genome and indexes.

Fixed a potential deadlock in paired-end mode that could occur when an input file had very few batches and all of them entered CPU recovery mode.

Fixed an issue where null padding could appear in output query names when using BAM input.