# The Scramble Conversion Tool

## TL;DR

Scramble is a new C-based tool for working with genomic data file formats, offering faster encoding and smaller file sizes.

## Contribution

A new C implementation of SAM, BAM, and CRAM file I/O with performance and compression improvements.

## Key findings

- The C API for CRAM is 1.8–2.6x faster at encoding compared to BAM.
- CRAM files are 40–50% smaller than BAM files.
- The C implementation is slower than BAM at decoding but offers significant encoding benefits.

## 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 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%.

Source code is available from http://sourceforge.net/projects/staden/files/io_lib/