Bug Fixes

Resolved potential deadlock conditions that could occur when work queues become saturated.

Fixed error which could trigger if --bwa-cpu-thread-pool was set to 1 thread.

Fixed benign error which was reported when setting the environment variable CUDA_LOG_FILE=stderr.

Fixed a memory leak when the --align-only option is on and outputs an unsorted bam file.

Fixed a missing comparison between the sum of base qualities and INT8_MAX / 2 in mark duplicates.

Fixed a bug where batches could fail to enter CPU recovery mode when an error occurred during GPU extension.