v0.4.2

Added

• gap(n): returns a string of n gap characters (-), useful for constructing MSA supermatrices from aligned FASTA files.
• longest_homopolymer(sequence): length of the longest homopolymer run in a sequence, case-insensitive.

Full Changelog: v0.4.1...v0.4.2

v0.4.1

Full Changelog: v0.4.0...v0.4.1

Added

• complement(sequence): generates complement of a DNA/RNA sequence.
• max_quality(quality): maximum Phred quality score of a FASTQ quality string.
• base_totals(sequence): aggregate that accumulates per-base counts (A, C, G, T, U) across all sequences in a result set, returned as JSON.
• bgzf seek support for FASTA and FASTQ. .gz files with a .fai alongside are now opened via noodles_bgzf and use block-level seeking for id = queries instead of full-file scanning.

Fixed

• Indexed .fai queries on .gz files no longer hang. The reader would attempt to seek into compressed binary data using the raw FAI offset, causing an infinite loop in the backward scan for the > record delimiter. .gz files now properly fall back to streaming.

v0.4.0

Full Changelog: v0.3.1...v0.4.0

Added

• .fai index support for FASTQ. Equality operators on ID columns will seek directly to record instead of scanning if a .fai file is alongside the fastq file.
• has_stop_codon(sequence): returns true if any stop codon (TAA, TAG, TGA / UAA, UAG, UGA) is present in the sequence. Reading frame agnostic.

Breaking Changes

• fasta and fastq modules are now registered as StandardModule only. Eponymous call syntax (FROM fasta('file.fa')) is no longer supported. All
  usage must go through CREATE VIRTUAL TABLE:

  -- before (no longer works)
  SELECT * FROM fasta('genome.fa') WHERE id = 'chr1';
  
  -- after
  CREATE VIRTUAL TABLE genome USING fasta('genome.fa');
  SELECT * FROM genome WHERE id = 'chr1';

v0.3.1

Full Changelog: v0.3.0...v0.3.1

v0.3.0

Full Changelog: https://github.com/arianfarid/sqlite-fastx/commits/v0.3.0