Switch to using neural net trained from data.
Add repeat pattern length as feature.
Fix potential NPE.
Latest model (r=0.27 on validation).
Fix expected indel frequency model.
Fix expected indel frequency model. When reverting indel counts to avoid thresholding effect, remove indel from failed indel list.
Fix thresholding effect for indels.
Mode suggest-position-slices: add option number-of-bytes to suggest slices with a uniform number of compressed bytes. This option aims to provide more balanced slices in bases where the genome as very non uniform coverage by position. With this option, the number of slices is determined to yield slices that need to decompress about the amount of bytes indicated on the command line.
Merge branch 'locations-by-bytes' into somatic
prepare for 2.2 release
updated version numbers for python and c++ APIs
 - 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.