https://github.com/ctSkennerton/minced
CHANGES
Revision history for MinCED
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