1.4.0

phredsort v1.4.0

• [new] new subcommand headersort for sorting sequences using pre-computed quality scores from headers
• [upd] refactoring code (splitting into subcommands)
• [upd] tests updated

1.3.0

phredsort v1.3.0

Updates:

• [new] two new quality metrics added (--metric):
  • lqcount - number of bases below quality threshold ("unqualified" bases)
  • lqpercent - percentage of bases below quality threshold
  • in addition, the --minphred flag is added to specify the quality threshold for these metrics
• [new] quality-based filtering of reads (flags --minqual and --maxqual)
• [new] option to add multiple quality scores to sequence headers (--header flag)
• [upd] code refactoring and cleanup
• [fix] bug with writing compressed data to output file

0.5.0

phredsort v0.5.0 - initial release

phredsort is a high-performance tool for sorting FASTQ files based on sequence quality metrics.

Features

• Multiple quality metrics:

  • avgphred: Average Phred quality score
  • maxee: Maximum expected error (absolute number)
  • meep: Maximum expected error percentage (per sequence length)

• Flexible input/output:

  • Supports both file-based and stdin/stdout streaming
  • Handles compressed (gzip, bzip2, xz, zstd) and uncompressed FASTQ files
  • (Optionally) utilizes memory compression for stdin-based processing mode (to reduce memory footprint)