Improvements

Supports CRAM file write on queryname-based sorting. It auto-detects cram file extension on output file.

Updates to match the baseline version v1.6.

Reduced reader buffer size to shorten the time it takes to start processing.

Speed improvements.

Added support for BWA MEM options: -B (values up to 15), -T, -L, and -U.

Added support for reads longer than 500 bp using CPU recovery mode (note that speed will be slower and memory usage will be higher). Set --max-read-length to the desired max read length for the FASTQ filter.

Better messaging in filehandle when reading index files to avoid user confusion.

Better error checking when reading FASTQ files: checks that each FASTQ read name line starts with '@'.