Goby

- Fix SNP bug in realignment around read insertion.
- Add queryPosition field to SBI output.
- Prevent the writing of sbi entries when AddTrueGenotypeHelper indicated the entry should not be added.

- Fix frequency of bases when indels are also present. Now correctly removes bases that
support the flanking sequence of the indel and do not double count.
- Many changes to how we store varmaps introduced to support indels (vcf-to-varmap).
The serialization format is incompatible with previous versions, so make sure you regenerate
varmaps from VCF.
- Adjust VCF output for compatibility with REF/ALT conventions. This makes it possible to measure
performance with standard tools such as RTG vcfeval (http://realtimegenomics.com/products/rtg-tools/).
- Keep counts of indels separately for forward and reverse strand.
- vcf-to-varmap mode: improved semantic of --chromosome-prefix option allows removing (e.g., -chr)
or adding (+chr) prefix to chromosome name.

- fast-co-compact: fix a bug introduced on 10/6/2016 which created negative read entries.
- catch a number of exception that can be thrown by HTSJDK when processing BAM files. Exceptions
are caught so that an error on one alignment does not interrupt processing of an entire alignment.
Errors are shown in log.
- vcf-to-genotype-map mode now supports (b)gzipped vcf input.
- vcf-to-genotype-map: fix bug that manifested itself when the vcf had a single genotype field.
- vcf-to-genotype-map: add chromosome-prefix argument to help import VCF where the chr prefix is missing.

- Remove memory leak when reading SAM/BAM files. This was the likely cause for running out of memory error in
compression benchmarks (had nothing to do with compression but with the conversion of SAM/BAM to goby representation).
- Disabled tests that could not succeed anymore (because of choices we made in Goby 3, such as lack of auto-upgrade
for alignments produced with Goby 1 and 2.)
- BAM/CRAM support. Added an option to bypass the header check on SO:COORDINATE. Use
-x HTSJDKReaderImpl:force-sorted=true to force Goby to consider an alignment sorted.
- SBI format: add ability to add true labels while writing the file. Add support for downsampling sites without
variants.
- Genotype format: reorganization to support calling with deep learning models trained with variation analysis.

- Reorganize model prediction to facilitate installing new versions of the variationAnalysis jars.
Goby 3.1 is now compatible with variationanalysis 1.1.1.
- Replace models with versions trained with variationanalysis 1.1.1.
- Add somatic mutation models trained with whole genome data (ICGC GoldSet).

- Support reading BAM alignments directly with Goby APIs.
- Support probabilitic models for calling somatic variations, trained with deep learning.