TY - JOUR T1 - The Scramble Conversion Tool JF - bioRxiv DO - 10.1101/003640 SP - 003640 AU - James K Bonfield Y1 - 2014/01/01 UR - http://biorxiv.org/content/early/2014/03/28/003640.abstract N2 - Motivation The reference CRAM file format implementation is in Java. We present “Scramble”: a new C implementation of SAM, BAM and CRAM file I/O.Results The C API for CRAM is 1.5–1.7x slower than BAM at decoding, but 1.8–2.6x faster at encoding. We see file size savings of 40–50%.Availability Source code is available from http://sourceforge.net/projects/staden/files/io_lib/ ER -