v1.5.2

• Refactoring of CLIP_merge_bed_files.pl to reduce memory footprint by a factor of 10x (Fixes #174)
• Refactoring of Piranha run to support multithreading (Fixes #177)
• Fixing copy process of final files (Fixes #184)
• Setting default bin size for Piranha to 30 (Fixes #178)
• This version is archived as .

v1.5.1 Performance improvements

Added optimized pre-binning step for Piranha (Fixes #132)

This version is archived as .

v1.5.0 Accepted version of microPIECE (including some improvements)

• Removing additional length cutoff during CLIP transfer (Fixes #153)
• Add command line options --CLIPminProcessLength, --CLIPmaxProcessLength, and --CLIPminlength for length limits used in run_CLIP_process and run_CLIP_clip_mapper steps enabling
  processing of peaks with user defined widths (Fixes #145)
• Dynamic naming of output files based on minlength variable in run_CLIP_clip_mapper (Fixes #146)
• Correct calculation of length of a bed feature and moving scripts/CLIP_bedtool_discard_sizes.pl into lib/microPIECE.pm (Fixes #147)
• Add an optimized pre-binning step with pseudocounts for bins covered by an exon as preparation for Piranha (Fixes #132 and #155)
• This version is archived as .
• This version was accepted by The Journal of Open Source Software (Review issue #616)

v1.4.0 Pseudo mirBASE files and structures

• Copying pseudo mirBASE dat file final_mirbase_pseudofile.dat into output folder (Fixes #131)
• Corrected RNA::HairpinFigure output (Fixes #137)
• Fix the requirement of an accession inside mirBASE dat file (Fixes #134)
• Avoiding error message while copying the out file for genomic location into base folder (Fixes #117)

v1.3.0 mirBase dat-file as source for mature/precursor sequences

• Creating all structures on the fly using pseudo-mirBASE-dat as input.
• Using miRNA.dat from mirBASE as source for mature/precursor sequence and relationship (Fixes #127)
• Fix of division-by-zero bug for empty mapping files (Fixes #118)
• Fix of typo in --piranhabinsize option (Fixes #116)

v1.2.3 Single matures for precursor

• Fix transformation of precursor sequences based on mirbase #22 precursor sequences with a single mature (Fixes L<#109|https://github.com/microPIECE-team/microPIECE/issues/109>)

Improved collision handling for newly miRNAs stable IDs

Improved collision detection for newly identified miRNAs avoiding crashed caused by genomic copies. (Fixes #105)

Stable IDs for newly identified miRNAs

Enables stable numbering for newly identified miRNAs based on their precursor and mature sequences

Fixes #101

Reenable miraligner

Downgrades java inside docker container to version 1.7.*, due to miraligner requirement.

Fixes #97 and #98

v1.1.0 isomirs and genomic location

Add isomir detection and copy the final genomic location file to the output filter

Fixes #34