The Scramble conversion tool.
Ontology highlight
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
Publications
<h4>Motivation</h4>The reference CRAM file format implementation is in Java. We present 'Scramble': a new C implementation of SAM, BAM and CRAM file I/O.<h4>Results</h4>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%.<h4>Availability and implementation</h4>Source code is available at http://sourceforge.net/projects/staden/files/io_lib/ under the BSD software licence. ...[more]
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