Change Log

[Unreleased]

[2.0.2] - 2017-07-06

Some new features:

the Fill module is now parallelized and can use several cores
additional information is output by the fill module:
- the abundance of each filled sequence is now computed and written in the fasta file
- a log file is output giving details about each gap-filling process

Bug fix:

some gap-filled sequences were incorrect (this happened only for multiple filled sequences in rare cases)

[2.0.1] - 2016-07-21

This is a bug-fix release :

fixed a compilation issue with old version of clang compilers (prior to clang 4.3 on mac), by updating the gatb-core version to 1.2.2.

[2.0.0] - 2016-06-29

Initial release after refactoring the whole code of MindTheGap to use the GATB library. Some of the benefits:
- faster (thanks to GATB improvements in kmer counting!);
- no longer need to recompile for changing the k parameter;
- automatic estimation of the paramater abundance-min;
- more user-friendly usage, with more readable help, progress bars, input-output summaries, etc.
- compatibility with other GATB tools: input-output graph in h5 format.
New features (with respect to the published version, August 2014):
- detection of homozygous SNPs and deletions (output in a separate VCF file); this should also improve the recall of insertion event detection;
- a quality score is now associated to each insertion prediction, this enables to filter out some predictions and to obtain a high-confidence subset.

Have a look at a comparison between the published and the 2.0.0 versions on simulated data here.