The Scramble conversion tool.

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 implementation of for CRAM is 1.5-1.7× slower than BAM at decoding but 1.8-2.6× faster at encoding. We see file size savings of 34-55%. AVAILABILITY AND IMPLEMENTATION: Source code is available at http://sourceforge.net/projects/staden/files/io_lib/ under the BSD software licence.