v0.17.0

Log of changes:

• Added the intersect module to perform intersections/removals with the output files of two runs (similar to bedtools)
• Added the chimeric module to find genes harboring chimeras between two different haplotypes
• Added the junctions module to calculate statistics on neighboring blocks from different origins (REF, ALT, or simply from two different calls)
• Fixed a small bug in the default mode, that was not producing the heterozygous BED file.
• Modified the density module to produce more values. Specifically, besides the mean snp density, it calculates a distribution and extracts the quantiles. It does the same for SNP distances. These values are useful to set as thresholds in JLOH extract, so it produces an estimation of which parameters would fit the best. Module has been renamed as jloh stats.
• modified the --min-snps and the --snp-distance parameter in a way that two values have to be passed, one for heterozygous and one for homozygous SNPs. These values can be estimated with jloh stats, or passed by the user.
• All heterozygous blocks within --min-length - 1 from each other are now merged before the generation of REF and ALT LOH blocks.