The Scramble conversion tool

Bioinformatics. 2014 Oct;30(19):2818-9. doi: 10.1093/bioinformatics/btu390. Epub 2014 Jun 14.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Computers
  • Escherichia coli / genetics
  • Genome, Bacterial
  • Genome, Human
  • Humans
  • Information Storage and Retrieval
  • Programming Languages*
  • Software