The Scramble conversion tool

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%. Av...

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Detalles Bibliográficos
Autor principal: Bonfield, James K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173023/
https://www.ncbi.nlm.nih.gov/pubmed/24930138
http://dx.doi.org/10.1093/bioinformatics/btu390
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author Bonfield, James K.
author_facet Bonfield, James K.
author_sort Bonfield, James K.
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description 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. Contact: jkb@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-41730232014-09-25 The Scramble conversion tool Bonfield, James K. Bioinformatics Applications Notes 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. Contact: jkb@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2014-10 2014-06-14 /pmc/articles/PMC4173023/ /pubmed/24930138 http://dx.doi.org/10.1093/bioinformatics/btu390 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Bonfield, James K.
The Scramble conversion tool
title The Scramble conversion tool
title_full The Scramble conversion tool
title_fullStr The Scramble conversion tool
title_full_unstemmed The Scramble conversion tool
title_short The Scramble conversion tool
title_sort scramble conversion tool
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173023/
https://www.ncbi.nlm.nih.gov/pubmed/24930138
http://dx.doi.org/10.1093/bioinformatics/btu390
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