PT  - JOURNAL ARTICLE
AU  - James K Bonfield
TI  - The Scramble Conversion Tool
AID  - 10.1101/003640
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 003640
4099  - http://biorxiv.org/content/early/2014/03/28/003640.short
4100  - http://biorxiv.org/content/early/2014/03/28/003640.full
AB  - 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/