Version 0.8.0

Remove some code which was preserving an old perl vcf file.

Version 0.7.0

Add nextflow parallelisation of build, in the multisample pipeline

Version 0.6.0

• add default filtering to final output VCF file (issue #68)
• speed up when splitting the reference into chunks, by not using unmapped reads on every chunk (issue #67)

Version 0.5.1

GT_CONF_PERCENTILE is added to the debug VCF file, which also means it ends up in the final VCF from the multi sample regenotyping pipeline

Version 0.5.0

• Rewrite of genotyping algorithm and code
• New GT_CONF_PERCENTILE in output VCF
• Numerous changes to check_with_ref
• Use latest gramtools version

Version 0.4.1

More robust checking that gramtools ran ok.

Version 0.4.0

• new functionality to chunk the genome and run gramtools on each chunk, to save RAM.
• new task make_split_gramtools_build to gramtools build a chunked genome
• expose gramtools kmer size option
• in check_with_ref, by default do not allow mismatches in mapped flanking regions

Version 0.3.0

• genotype ./. when no coverage
• new multi_sample_pipeline for calling across many samples

Version 0.2.0

Better logging

Version 0.1.0

• Better clustering. New option --max_alleles_per_cluster. Reduces RAM.
• Better TP/FP calling