The Scramble conversion tool
James Bonfield · Bioinformatics · 2014
Abstract 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. Contact: [email protected] Supplementary information : Supplementary data are available at Bioinformatics online.