- FDR mode: add ability to read groups from VCF file and adjust columns/fields marked as p-value. Mark adjusted columns with group q-value.
 - Somatic variation output format: annotate somatic p-value column with 'p-value' group. Fix the type of the p-value  column to be a number (was String in release 2.2).
 - Somatic variation output format: handle unrecognized sample-ids in the parents column.
 - Somatic variation output format: fix silly bug that produced false negative p-values when all somatic samples did not have the variation. The bug did not affect comparisons where only one somatic/germline pair was considered.
discover-sequence-variation mode: name the items, they are aligned reads, not genomic positions.
- discover-sequence-variants mode: list somatic_variations output format in help.
discover-sequence-variants mode: add assertion to give hint to user that syntax is incorrect in for -s and -e options.
- compact-file-stats mode: print progress when scanning reads files. Use a buffered reader to improve read file parsing performance.
- discover-sequence-variants: remove left-over filter for somatic variations output format.
discover-sequence-variants: Add a new filter to remove indels at a site where a sample shows lots of distinct
   possible indels. Indels at these sites are very likely to be artefactual. We count the number of samples where
   three distinct indel genotypes are seen. If more than 1/4 of the samples have likely indel artifacts, we remove
   all indel candidates at the site. This filter is added to the somatic variations output format.
Adust junit test results for fdr changes. Resolve bugs caught by junits.
more stringent filter on indels, keep indels at site when no more than one indel genotype detected.
Somatic variation output format: restore left-over filter, but with multiplier=1.
Somatic variation output format: do not consider genotypes that are also seen in germline (use 1 base as the cutoff).
Softer filter to remove candidates when the genotype exists in the germline.
Fix possible NPE.
Expose some parameters are dynamic options. Keep track of candidates screened in new filters.
Adjust changes.
Update version numbers for release.