TODO.md

DONE

• Remove predefined primers
• Generalise use of generic unassigned-scaffold prefix to compress reporting (use --unassigned-prefix STRING)
• The --primers option may be used to load primer sequences from a Fasta file
• The --pf and --pr options may be used to specify primer sequences on the command line
• Added --allow-overlap option to allow primer hits to overlap
• Assure that searches for hits restart at the proper location when using --optimise
• Implemented --show-mismatches to count mismatches when --mismatch-simple is in effect
• Searches can be limited to specific regions of the reference genome with the --focal-sites and --focal-bounds options
• Found a way to nicely check for module availability (the whole re::engine::RE2 issue), need to end the eval with 1: eval 'use re::engine::RE2; 1';
• using re::engine::RE2 for much faster regex matching
• simply reverse-complement the calculated pattern
• Primer pairs delineating each amplicon are indicated. An amplicon marked F,R is produced from the + strand, with the forward and reverse primers in native orientation. An amplicon marked r,f is produced from the - strand, with both forward and reverse primers in reverse-complement orientation. An amplicon marked F,f was produced from forward primers in native and reverse-complement orientations, and r,R was produced from reverse primers.
• Primer hits may be output with --primer-seq and --primer-bed
• Amplicon hits may be output with --seq and --bed
• Interior (amplicon minus primers) hits may be output with --interior-seq and --interior-bed
• The number of unique concrete primer sequences produced with each degenerate primer, including mismatches if specified, is calculated prior to finding matches. This procedure may be lengthy and can be suppressed with --skip-count.
• The --mismatch-simple option is provided for specifying mismatches in the 5' end of the primer and optionally in the 3' remainder