coinfinder-v1.2.1

Added functionality (issue 56); a raw csv version of the network heatmap is now output with suffix "heatmap-raw-data.csv"

coinfinder-v1.2.0

Fixed bug in the dissociation code that excluded gene pairs that never overlapped (issue 54).

coinfinder-v1.1.0

Adding functionality to the -q flag. It now takes a file name containing a list of genes of interest (i.e., only output associations/dissociations involving at least one gene in the list) instead of only taking in a single gene (file name instead of string). Potentially more testing required.

Also fixed the issue Gavin identified with CMakeLists.txt

coinfinder-v1.0.9

Includes a bug fix for the calculation of the Bonferroni correction.

coinfinder-v1.0.8

A few small things (e.g., check for newick formatted phylogeny at startup) & addition of a GML formatted output network file for input into Graphia and other network software.

coinfinder-v1.0.7

Bug fix to the display of data in the heatmaps for genomes whose names begin with a numeric character.

coinfinder-v1.0.6

Bug fix to treat "~"s as a special character; fails more gracefully if the gene_presence_absence table isn't a quoted CSV file.

coinfinder-v1.0.5

Bug fixes to -q usage.

coinfinder-v1.0.4

small bug fixes for conda install/R dependencies.

coinfinder-v1.0.3

small fixes to work with newer versions of R packages, and associated bug fixes.