Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. It is part of the genomic analysis toolkit (GATK). It uses zlib compression and can be re-directed to load AOCL-Compression library at runtime as follows:
# Run picard to process a BAM file and mark duplicates
LD_PRELOAD="path/to/aocl_compression.so" java -Xmx32G -jar picard.jar MarkDuplicates \
INPUT="path/to/inp_file_name.bam" COMPRESSION_LEVEL=6 \
OUTPUT="path/to/out_file_name.bam" \
METRICS_FILE="path/to/metrics_file.txt" \
OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 CREATE_INDEX=true TMP_DIR=/tmp