IRMA Changelog

v0.6.7 : 2017-04-14
- added parallelization for zipping files via pigz. If not compatible, defaults to gzip.
- updated the Ebola and CoV modules to use MERGE_SECONDARY=1


v0.6.6 : 2017-04-13
- added "MERGE_SECONDARY" option, puts secondary data into the unmatched read pool for round 2. Recommended if lineage references are close, and for non-segmented viruses where co-infection is unlikely.
- added "GENE_GROUP" variable for customizable two-stage sorting with BLAT performing rough sorting during MATCH step and before the SORT step. Example: influenza "LABEL-trio" in the paper

v0.6.5 : 2016-12-02
- added experimental configuration file "FLU-minion" for MinION R7/R9 chemistries
- fixed VCF bug that prevented correct VCF creation

v0.6.4 : 2016-11-04
- added plurality consensus script to IRMA_RES/scripts folder to aid in new module creation

v0.6.3 : 2016-08-12
- added failovers to local node computation when grid computation doesn't work

v0.6.2 : 2016-06-01
- optimized indel calling algorithm for performance
- added flexible segment numbering option for module init.sh (see SEG_NUMBERS in configuration, and SORT_GROUPS in primary vs. secondary)
- added NO_SORT_REFS option for custom reference sorting into LABEL classes
- added experimental MERS CoV module
- changed NextTera adapter masking back to adapter clipping but without length penalization (see ADAPTER in configuration)
- fixed bug with flexible parameter file naming

v0.6.1 : 2016-04-01
- added name + hashing to allow for multiple concurrent projects
- tweaked reference elongation algorithm
- changed ADAPTER clipping to masking

v0.6.0 : 2016-03-09  (test release)