CHANGES

Revision history for MinCED

0.3.2 02-Mar-2019
        Fix a bug that was causing some string indexing errors where
        the bounds of the CRISPR was not being updated properly when
        a partial repeat was removed.

0.3.2 01-Oct-2018
        Modify searching behaviour so that parital repeats that are at
        the edges of contigs do not prevent the extension of other repeats
        in the array. This has the caveat that the repeat is lost in
        processing and the adjoining spacer is gone as well. However the
        remaining spacers and repeats should be more accurate.

0.3.1 31-Aug-2018
        update GFF format to include the rpt_family annotation

0.3.0 08-May-2018
        Updates to GFF format to be inline with NCBI naming.
        Fixed bug where a class wasn't included in the JAR file causing
        occasional errors.

0.2.0	13-Jul-2015
        New masking feature to skip over low complexity regions, such as
        runs of Ns, to increase speed with heavily scaffolded sequences

0.1.6	18-Jul-2014
        Fix off-by-one error in the gff output.

0.1.5   03-Apr-2014
        Changed the behaviour of the '-spacers' option. Without any
        output file given the behaviour is the same as before, creating
        a file with the input name's prefix and adding '_spacers.fa' to
        the end. Now when an output file is given the '_spacers.fa' will
        be appended to that name, not the input file's name

0.1.3   19-Nov-2013
        Fixed bug in gff output where the gff header was being printed 
        multiple times

0.1.2   18-Nov_2013
        Minor bug fixes to gff output format

0.1.1   19-Jul-2013
        Added in new output formats:
            * summary gff format
                - outputs the start and end of the whole CRISPR locus
            * full gff format
                - on top of what is written in the summary format, adds
                  in individual repeat_unit annotations for the direct repeats
            * output all spacers found in fasta format
                
        
0.1.0   15-Mar-2011
        Initial fork from CRT
        More robust parsing of FASTA files and support for multiFASTA files
        Support for finding CRISPRs in datasets with more than one sequence
        Fixed some compilation warnings