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