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 API for CRAM is 1.5–1.7x slower than BAM at decoding, but 1.8–2.6x faster at encoding. We see file size savings of 40–50%.
Availability Source code is available from http://sourceforge.net/projects/staden/files/io_lib/
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.