Friday, July 4, 2014

Fwd: The Scramble conversion tool

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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 1.5-1.7x slower than BAM at decoding but 1.8-2.6x 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:jkb@sanger.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

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(Via Bioinformatics - Advance Access.)