Version 0.4.2

There is no difference between 0.4.1 and 0.4.2 except that the version is now output correctly.

Version 0.4.1

Support using environments by honoring JAVA_HOME environment variable.

Download both the minced wrapper and the minced.jar files and keep them in the same directory. Note that this jar file was compiled using Java 12, if you have an older version of java please download the source and compile yourself using make

Version 0.4.0

Version 0.4.0

Version 0.3.3

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.

Please Download both minced and minced.jar and keep them in the same folder. Usage is:

minced -gff <file.fasta>

Version 0.3.2

Sometimes repeats can run off the very beginning or end of a
contig, which causes all of the repeats to be truncated. The change
checks for repeats that are at the edges of sequences and removes
them if there are enough additional repeats.

This method has two downsides:

1. The partial repeat at the very end is lost and therefore that
   spacer will also be lost
2. There is an edge case where a full length repeat could end at
   the beginning or end and therefore be dropped erroneously

However, the repeats and spacers that remain should be accurate.

Version 0.3.1

• update GFF format to include the rpt_family annotation

Version 0.3.0

• 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
• Jar file now be compiled against JVM 1.5 (should work on older systems by default)

Version 0.2.1

Version 0.2.1

Version 0.2.0

This version introduces a masking feature to skip over low complexity regions, such as runs of Ns, which can greatly increase program speed with heavily scaffolded sequences.

Download both minced and minced.jar and make sure to keep them in the same directory.
Basic Usage:

cd <download_folder>
chmod +x minced
./minced -h
./minced -gff <file.fasta>

Version 0.1.6

This is a bug fix release that fixes problems with the GFF file reporting. In both the 'gff' and 'gffFull' options the end positions of the CRISPR/repeat sequences was one nucleotide greater than what it should have been that could cause other programs to crash (as well as being just wrong).