title: The Scramble conversion tool.
abstract: BACKGROUND
  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%.
  
  
  METHODS
  Source code is available at http://sourceforge.net/projects/staden/files/io_lib/ under the BSD software licence.
authors.affiliation: DNA Pipelines, Wellcome Trust Sanger Institute, Cambridgeshire, CB10 1SA, UK.
authors.forename: James K
authors.initials: JK
authors.lastname: Bonfield
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003201:Computers; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D015894:Genome, Human; D006801:Humans; D016247:Information Storage and Retrieval; D011381:Programming Languages; D012984:Software