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The Scramble conversion tool

Bioinformatics

Oct 1, 2014

James K Bonfield

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Abstract

The reference CRAM file format implementation is in Java. We present 'Scramble': a new C implementation of SAM, BAM and CRAM file I/O. 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%. Source cod...read more

Mentioned in this Paper

CCRL2 gene
Computers, Digital
Genome, Bacterial
Information Extraction
Programming Languages
Computational Molecular Biology
c new
Computer Programs and Programming
Genome, Human
DPYSL5 gene
14
1
34
Paper Details
References
    • References4
    • Citations11
    • References4
    • Citations11
  • The Scramble conversion tool

    Bioinformatics

    Oct 1, 2014

    James K Bonfield

    PMID: 24930138

    DOI: 10.1093/bioinformatics/btu390

    Abstract

    The reference CRAM file format implementation is in Java. We present 'Scramble': a new C implementation of SAM, BAM and CRAM file I/O. 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%. Source cod...read more

    Mentioned in this Paper

    CCRL2 gene
    Computers, Digital
    Genome, Bacterial
    Information Extraction
    Programming Languages
    14
    1
    34
    Paper Details
    References
    • References4
    • Citations11
    • References4
    • Citations11
  • Get paper from

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