3.4.1 - bugfix explizit seeds and seed order check

IntaRNA

• BUGFIX : seed order check was buggy
• BUGFIX : explizit seed : wrong direction of query base pair parsing (thanks to @Tim15-tech, fixes #220 )

3.4.0 - pfscale + bugfix accessibility constraints

IntaRNA

• new arguments t|qPfScale for sequence-specific ViennaRNA pf_scale parameter used
  to scale partition functions for ED value computation to avoid overflows
• BUGFIX : when using sequence subset selection in combination with precomputed
  accessibilities from file, wrong accessibilities were loaded for the selected
  sequences
• BUGFIX : seed-extension-based predictions (default prediction mode) were not
  heeding accessibility constraints
• BUGFIX : query accessibility constraints were applied in reversed indexing

3.3.2 - bugfix IntaRNAhelix

IntaRNA

• compilation fix: correcting shared variables for parallelization
• BUGFIX debug check
• BUGFIX IntaRNAhelix traceback of helices where seed is not at right end

3.3.1 - bugfix FASTA parsing

IntaRNA

• BUGFIX: empty lines with white spaces within FASTA input were causing parsing
  errors

3.3.0 - pairwise sequence processing

IntaRNA

• --outPairwise enables pairwise sequence processing instead of all-vs-all
• input range for --q|tIdxPos0 is now +-2,000,000,000 (was +-9,999,999) to enable genomic position settings

3.2.2 - bugfix release

IntaRNA

• BUGFIX: maximal interaction length correction for precomputed accessibility
  data was one to large (wrong dangling end computation for maximally long RRIs)
  (thanks to Sabine Reisser)
• BUGFIX: explicit seed encodings within last 7 nucleotides (seedBP) were
  ignored (thanks to Sebastian Holler)
• BUGFIX: outNoLP option was not correctly implemented (missing recursion cases)
  and was thus missing interactions
• BUGFIX: osx: configure adaptation to old grep version in osx

3.2.1 - bugfix release

IntaRNA

• support for multi-seq input when seedQ|TRange given
• BUGFIX: Andronescu07 energy parameter set was not loaded by name without file
• BUGFIX: outMinPu was not fully implemented
• BUILDFIX: non-global import of boost::bind to avoid warnings/problems with recent boost library version

CopomuS :

• exit value 0 if no favorable interaction was found

3.2.0 - CopomuS + fixed accessibility constraints

IntaRNA

• BUGFIX: accessibility blocking constraints were only applied to seed location
• improved Zall estimate (and depending values) for --model=X (default)
• new arguments:
  • qId|tId : optional id (FASTA prefix) setup for sequence naming
  • acc|accW|accL : meta accessibility setup for both query and target
  • intLenMax|intLoopMax : meta interaction and interior loop length setup

CopomuS

• Compensatory mutation selector to support interaction validation experiments

3.1.5 - bugfix bulged seeds with noLP

IntaRNA :

• bugfix traceback of interactions with seed on right-boundary
• bugfix traceback of seeds with bulges when outNoLP present

3.1.4 - bugfix and extend bulged seed handling + `IntaRNA_CSV_p-value.R`

IntaRNA

• bugfix generation and tracing of seeds with bulges and no GU ends (combination of seedNoGUend and seed?MaxUP > 0)
• bugfix seed-extension prediction for seeds with bulges (seed?MaxUP > 0)
• outNoLP for seeds with bulges enabled (seed?MaxUP > 0)

auxiliary R scripts

• IntaRNA_CSV_p-value.R script to estimate p-values based on energy values
• IntaRNA_plotRegions.R = renaming of former plotRegions.R