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NEW FEATURES:
* A user friendly database GUI replaces the old database functions. The four main functions are 1) New database creation, 2) Adding samples to a database, 3) Extracting subsets of a database, 4) Searching a database for specific variants.
Importantly, the database formats are slightly changed from the previous version. The simple format has 6 columns: CHROM, POS, OBS = number of samples with the variant, HET = heterozygous observations, HOM = homozygous observations, AFREQ = allele frequency = (HET + 2*HOM) / total number of samples
The extended format has the same 6 columns, succeeded by one column for each sample, indicating the alternative allele count (0, 1 or 2) for each variant.
* General column splits: In the Input settings dialog, one can now indicate up to 2 columns with associated separators. For example, if the AD field in a VCF file is split on "," (comma), it will be replaced by columns AD_1, AD_2, ... .
OTHER:
* The layout of the "Input settings dialog" is slightly changed, to reflect some necessary changes in the internal file reading process. The most significant change is the Genotype format choice. The "VCF format" should be checked if the file has a VCF-like genotype format (i.e. a format column followed by individual sample columns) even if the file itself is not a vcf file. Examples of this include typical output from the Annovar annotation software.
* Toggle between long and short display of loaded sample names.
* Removed the automatic naming in VCF-like files lacking sample names. Instead the filename itself is used as sample name, and an error is raised if the file appear to have more than one sample.
* GUI appearance: Replaced the word "file" by "sample" many places, e.g. "Loaded samples".
BUG FIXES:
* Gene files with non-Windows end-of-line characters caused crashes.
* The VCF preamble reader was too simplistic, hindering files from loading in some cases.