ChromImpute Version Log
Version 1.0.5 Released January 1, 2024
* Added the ability to have input files be present in different subdirectories, which can be
specified with fourth column entries to inputinfofile
* Added the ability for Apply to read predictors stored in a .tar.gz file through the -targz option
* Added to Eval outputting pearson correlations that clip outlier values to 500 or the value of clipthresh if the option -c clipthresh is specified
* Added throwing an error if an input DNA methylation data set has missing values for every entry
* Added throwing an error if an input signal file to convert does not end in .bedgraph, .bedgraph.gz, .wig, or .wig.gz
* Added throwing an error if -dnamethyl is a flag provided to Train specifying DNA methylation is the target, but 'mark' matches an input mark. 
'mark' should be the name to be given to DNA methylation
* Now compiled to target a minimum of Java 1.7 from 1.6

Version 1.0.4 Internal release only
*Added -coeffv and -t flags to Apply command for outputting coefficient of variation values

Version 1.0.3 Released December 31, 2017
*Added the ExportToChromHMM command

Version 1.0.2 Released August 19, 2017
*Fixed bug causing ChromImpute not to work with default Java locales that use commas
instead of periods for decimal marks. Now Locale.ENGLISH is used for all number formatting.

Version 1.0.1 Released October 16, 2016
*Fixed bug in Train command that caused it to reject commands with the '-k maxknn' option 

Version 1.0.0 Released September 4, 2015
*Fixed bugs in the Convert command that caused it to not
handle 'track' lines in wig files and also cases in which chromosome lengths
were evenly divisible by the bin resolution

Version 0.9.9 Released July 5, 2015
*Minor update to catch all Exceptions with the convert command in order to return 1 for all types of failures

Version 0.9.8 Released July 4, 2015
*Added return codes to ChromImpute so that 0 means succesful execution and 1 means some type of failure
*Fixed bug causing not all files to be closed when done being read when calling GenerateTrainData
on multiple chromosomes.
*Relaxed the checks on float point instability to be values less than -100 when expecting non-negative values
*Clarified in the manual when running wigToBigWig on wig files generated from ChromImpute
that the '-clip' option should be added


Version 0.9.6 Released March 29, 2015
*Fixed bug previously preventing mark names containing an underscore ('_')
from being processed properly
*Fixed inconsistencies with regard to the '-a mintotalensemble'
that could have the numbags be one off than intended
*Added additional error checking and more informative
error messages in places such as checking if the data to the Convert
is actually in wig or bedgraph command and checking if predictors
have been trained already before applying the Apply command.
*Minor internal code changes intended to improve performance

Version 0.9.5 Released February 18, 2015