0.3.0

BREAKING

• the seed subcommand has been removed from the CLI (use nail search --only-seed instead)
• many CLI flag names have been changed

Features

• the CLI has been refactored, with several new options:
  • -s prints out pipeline summary statistics
  • -x prints alignments to stdout, doesn't write tabular output (useful for small scale experimentation)
  • --double-seed seeds alignments at two MRE targets (this was done by default in the last release) (note: this is not yet implemented for sequence to sequence search)
  • --only-seed does what nail seed used to do
  • --seeds-out <PATH> saves seeds produced during a normal run of nail search to <PATH>
  • --no-null2 turns off the null two (composition bias) score adjustment
• FASTA input files are now streamed from disk, enabling search of much larger target databases

Bug fixes

• fixed some subtle bugs relating to score calculations
• fixed some bugs relating to determining alignment boundaries
• fixed some bugs in the target/query positions shown in alignment output
• fixed some issues causing overallocation of memory