v2.2

minor: Bumping up the version to 2.2 so I can trigger a pre-release.
Export hvcf
Remove temp dir from load to vcf
update test REf.h.vcf with ASM_ fields in ALT header
Integrate age maf to vcf
added check that bed file and ref fasta chrom names match
added envFile param, code to use default env file if no param
Update integration test
initial commit checking for duplicate sample names
Rename alignassemblies params
Initial logging utils
Handle range overlaps
Change reference flag to "reference-file"
Initdb update use minus n
Haplotypegraph
Handle inversions by using list of Regions in HVCF
Agc fasta updates
Agc query update
Handle inversions
Handle inversions
Altheader samplenames update
Coded PHGv2 to return correct version
Chrom batching create fasta from hvcf
Haplotypegraph
Kmer Index Migration
Align assemblies autothreading
Buffered Reader and Writer
Initial Merge of Read mappings
Application conf to phg tar
Most likely parent migration
Added unit test for samples Endpoint with sampleDbId specified
Cleanup CLI help output
Variants endpoint
Add port to start server
Update maf vcf
bug fix creating intergenic regions between nearby genic regions
Migrate diploid path finding
Export multi sample hvcf
Adding in Kmer based read mappings
Separate hvcf creation
Brapi variantsets
Tiledb apijava
fixed annotateFastas to rename files
made dbPath parameter optional, couple document updates
Add data class and return methods for efficient rPHG2 JVM evaluation
Refactor path finding
ensure no duplicate seqHashs in Ref h.vcf ALT headers
adds documentation for FindPaths
fixes printing of alt headers
Fixing relative path issue we noticed during scale testing.
Imputation for full pipeline it
Minimum refrange size
Adding in docs for kmer index and read mapping.
Implemented option for human-readable symbolic alleles when exporting…
Export from samples file
uses map of Pair(sample,region) to hapid to process data returned fro…
trim assembly name from align-assemblies assembly list
Annotate fastas remove bgzip step
Improve imputation workflow
Add fastq extension check to MapReads
Agc compress clarify parameters
set anchorwave version in phg_environment.yml
Rename annotate fasta fix
Faster build kmer index
Merge hvcfs cli
Add faster R retrieval methods
Unit test phg clikt
add sorting after BioKotlin getVariantContextfromMAF()
allow blank hapids in CreateFastaFromHvcf
Anchorwave dotplot
Vcf metrics
Fix null haplotype emission probability
Export vcf extensions
fixed ggsave() relative path problem.
added path parameter to ggplot call
Opening up optional parameters for map kmers so users can change them
rPHG2 - add ID to reference range data object
Kmer Diagnostics
Export path as sample gametes
Fix build kmer index contig name bug
Bedfile for export vcf
BuildKmerIndex test for empty sampleContigList and map hapids to multiple ReferenceRanges
Fixes to BuildKmerIndex and emission probability calculation
Fix build kmer index chromosome naming