This is gunzip except that there is a new -t [int] parameter that controls the number of threads, and you can only use it to decompress FASTQ files ¯\_(ツ)_/¯

Installing

Type make

Usage

Exactly same as gunzip. Two new parameters:

• -t [n] use n threads

• -s [p] skip p bytes in the compressed file and start decompression as soon as a unambiguous block is found.

Those two parameters are mutually exclusive, -s can only decompress at a location using 1 thread.

Limitations

Cannot compress, only decompress. In some files with normal/high compression levels, the program will not return all sequences, but will also tell you how many sequences were not returned.

Citation

Random access to sequences in gzip-compressed FASTQ files, submitted

Reproducibility

We have included a few scripts that were used to create the results from the paper.

• paper/list_files: list of 100 ENA files
• scripts/test_random_access.sh: script that runs fqgz to obtain data for Table 1
• scripts/parse_random_access.py: script that creates Table 1 from the output of the above script