Staden io_lib

Staden io_lib provides file input/output routines for trace files and Experiment Files and implements the C CRAM implementation "Scramble" to enable compressed sequence data storage and processing for genomic research.

Key Features:

• File I/O for trace and Experiment Files: Provides general-purpose reading and writing routines for trace files and Experiment Files used in genomic workflows.
• C CRAM implementation (Scramble): Implements the CRAM file format in C as 'Scramble'.
• Encoding performance: Encoding is 1.8–2.6× faster than BAM according to reported benchmarks.
• Decoding performance: Decoding is 1.5–1.6× slower compared to BAM according to reported benchmarks.
• Compression efficiency: Achieves CRAM file size reductions of 34–55% compared to BAM.

Scientific Applications:

• Compressed sequence storage: Reduces storage footprint for sequencing data by using CRAM compression via Scramble.
• High-throughput sequencing workflows: Faster encoding benefits processing and transmission of large-scale sequencing datasets.
• Trace data management: Supports reading and writing of trace files and Experiment Files for genomic analyses.

Methodology:

Implements the CRAM file format in C as 'Scramble' and reports measured encoding and decoding speed comparisons against BAM along with observed CRAM file size reductions of 34–55%.