dsrclib

Nim library for reading DSRC2 compressed FASTQ files. Returns readfx-compatible FQRecord objects.

Installation

nimble install dsrclib

Usage

Reading DSRC files

import dsrclib

for rec in readDSRC("reads.fastq.dsrc"):
  echo rec.name, "\t", rec.sequence.len

Writing DSRC files

Record-by-record (single-threaded):

var records: seq[FQRecord]
for rec in readDSRC("reads.fastq.dsrc"):
  records.add(rec)
writeDSRC("output.dsrc", records)

File-to-file (multi-threaded, fast)

compressDSRC and decompressDSRC use DsrcModule internally, which runs a multi-threaded pipeline (reader, N worker threads, writer) for maximum throughput:

compressDSRC("reads.fastq", "reads.dsrc")
decompressDSRC("reads.dsrc", "reads.fastq")

Optional parameters:

# Limit to 4 threads (default: all available cores)
compressDSRC("reads.fastq", "reads.dsrc", threads = 4)

# Read FASTQ from stdin
compressDSRC("", "reads.dsrc", useStdIo = true)

# Write FASTQ to stdout
decompressDSRC("reads.dsrc", "", useStdIo = true)

Reading FASTQ files (plain or gzipped)

A readFastq iterator is provided for reading FASTQ files, with gzip and stdin support:

for rec in readFastq("reads.fastq.gz"):
  echo rec.name

# Read from stdin
for rec in readFastq("-"):
  echo rec.name

CLI examples

The example/ directory contains two command-line tools:

• fastq2dsrc INPUT_FASTQ OUTPUT_DSRC — compress FASTQ to DSRC (supports plain, gzipped, and stdin via -)
• undsrc INPUT_DSRC [OUTPUT_FASTQ] — decompress DSRC to FASTQ (file or stdout)

License

GPL-2.0

(C) Quadram Institute Bioscience