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
Refactoring, fixing build and adding in functionality to ropebwt3 index
Graph constructor dir
Graph dir constructor
Rope bwt to read mapping
Updating docs to match the code.
Adding in initial support for Positional Support for Gamete files.
Read mapping target counts QC
Rope bwt chr index
Add missing commands to documentation
Update spline interpolation to use the Akima algorithm (1970)
Fix merge hvcfs
Add fix to Conda "-p" parameter variable
Updated dependency BioKotlin from version 0.22 to 0.25
Update test hvcfs spec
Tiledb separate conda env
Remove ehcache depend
Create maf vcf ram updates
Change documentation to make RopeBWT Imputation the preferred method
Contigs missing from hvcfs
fixed overflow error in full-assembly reference lengths
Hvcf to gvcf performance
Change sorting of positions. Contigs will try to be sorting numerical…
Update ps4g
In Hvcf2Gvcf, parsing filename to get sample name using ".h.vcf" inst…
Update VCF to ps4g
Adding back in ImputationMetrics
Add checks for empty sets
Biokotlin version 1
Spline speed changes
Spline speed changes. Writing out files to directory instead of single file.
Spline speed changes
Update spline code to use a linear lookup instead of the existing spline.
Initial commit of bed file to read mapping code
Remove encoding splines
ropebwt3 mem wrapper
Added option to filter reads by max range when converting ropebwt output to ps4g, changed default ps4g file extension to .ps4g