Input from BSMAP
genefish:bsmap-2.73 Steven$ ./bsmap -a /Users/Shared/data/filtered_Unlabeled_NoIndex_L003_R1wID_trimmed.fastq -d /Users/Shared/data/oyster.v9_M.fa -o /Volumes/web/cnidarian/BSMAP_v9_M.BAM -p
OUTPUT
http://eagle.fish.washington.edu/cnidarian/BSMAP_v9_M.BAM
...