The Scramble conversion tool.

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.

SUBMITTER: Bonfield JK 

PROVIDER: S-EPMC4173023 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature