v2.4

minor: Update maf to gvcf
Handling gzipped fastq file names correctly now in read-mapping.
Add PHG version retrieval method
Create fasta from hvcf fix duplicate entries
verify AGC files bug fix
Removing the option to have map-kmers hit multiple reference ranges.
initdb warning, updated yml file
Remove optional parameters quick start
Add showDefaultValues=true to clikt help messages
Samples list command
Update export vcf
Resequencing haplotype vcf
Kmer mapping diagnostic
Haplotype graph efficiency improvements
Create fasta from hvcf oom
Changed data structure in contextToRange(). Was rangeSampleToChecksum…
Kmer mapping integration tests
Haplotype graph efficiency improvements
Hvcf2gvcf update export
fixed issue with hvcf2gvcf batched export command
added ref and chosen haplotype len to ImputationMetrics
Kmer mapping Update
Haplotype graph efficiency improvements
Prepare assembly fix tab and comment
Advanced imputation metrics
Whole graph checksum
Checksum for ref seq at range
added missing flag to CreateMafVcf:createASMHvcfs()
add graph hash to kmer processing
Add checksum column for reference range table
Paths to gff port
ref-range-fasta command
Log clikt parameters
Graph hapid seqlen
Update kmer index: Adding parameter and allowing large discard set

v2.3

chnages to include condaEnvPrefix for all ProcessBuilder calls
Refactor alignassemblies
Merge gvcfs clikt command
Multi ref range read mapping
Fixed pulling chrom name from fasta idLine
Gvcf from hvcf
added PrepareSlurmAlignFile to Phg.kt
Multiple file bug create fasta from hcvcf
Merge hvcf file hvcf dir create fasta from hvcf
Speedup map kmers
add condaEnvPrefix to Gvcf2hvcf and places it is called
Fixing Build Kmer Index Diagnostic Error.
Setup env file not exist
Hvcf2gvcf ref allele wrong
change CliktCommands to use required() for required parameters

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

v2.1

minor: Create fasta from hvcf

v2.0

Ci deployment
Create ranges
Unit test variant loading utils
Full integration test Skeleton
addition to the junit test
Add smallseq testdata
Initial commit of adding conda to the CI build.
Build ref hvcf
Load tiledb vcfs
Rework buildrefvcf
Anchorwave align
Create maf to vcf
Agc integration
align-assemblies unit tests
Agc retrieval
implemented additional AGC commands
Create maf to vcf
Export hvcf