modal accuracy, faster cram parsing, fix for stdin, remote files, deprecating checksum

This release adds modal accuracy to the output, is faster to parse crams (probably 2x), includes a fix by @mbhall88 to read from stdin, and can run on remote files (using an HTTPS, FTP, or s3 URL). Calculating a checksum is now deprecated, but please let me know if you thought that was useful, and I will put it back in.