v1.3.1

Version 1.3.1 is a patch to 1.3.0:

• fixes a bug occurring when variants are too close to the reference sequence ends
• the genotype quality for variants that are not covered is now 0 (instead of 100)

v1.3.0

This release:

• adds support for haploid organisms (see -1 argument)
• replaces gt likelihood with gt log-likelihood (now malva should work correctly with any coverage)
• improves call quality with high coverages
• allows to use uniform a priori probabilities (see -u argument)
• minor code fixes

v1.2.0

This release:

• Adds a new flag to strip "chr" from sequences names (-p), set to false by default. Note that this version changes the default behavior of MALVA.

v1.1.1

Version 1.1.1 is a patch to 1.1.0:

• minor fixes to log output

v1.1.0

This release:

• solves a bug occurring with missing alleles in the GT field (thanks gmagoon for catching this)
• adds support for unphased genotypes
• adds -s argument: it is now possible to select the subset of samples to use when building alleles' signatures (this will improve efficiency but it may reduce accuracy)
• adds -f argument: it is now possible to select the key of the INFO field to use as a priori frequency

v1.0.1

Version 1.0.1 is a patch to 1.0.0:

• renames malva executable as malva-geno
• solves compilation errors occurring when compiling with g++-8
• adds license
• small other fixes

v1.0.0

Updates BF sizes