CHANGELOG

v1.1.0-rc1:
    * Support for read groups:
        * Support ‘pool’ read groups taken from BED file, e.g.:
            * nCoV2019_1
            * nCoV2019_2
        * These can be helpfully viewed in the Tablet viewer.
        * Do variant calling separately on each group, permits detection of incongruent mutations e.g. from contamination
    * Update to nanopolish 0.12.5 fo more informative VCF output
    * Change nanopore filtering to support new VCF output (e.g. strand-bias)
    * Support indels with bcftools consensus
    * Longshot added to Medaka to permit filter VCF on depth
    * New workflow model - all commands run "one per sample", script nanopolish index
    * Add 'artic gupplyplex' for support for demultiplexed Guppy output to replace 'artic gather'
    * Fix for align_trim to remove erroneous CIGAR strains that can cause medaka to fail
    * Support for amplicons v3 format file (Will Rowe)
    * Test suite (Will Rowe)
    * Documentation (Will Rowe)
    * Remove old deprecated code (Will Rowe)

v0.13:
    * ARTIC fork

v0.12: 
    * Update to nanopolish v0.8.4 for Albacore 2.0+ support:
        * run nanopolish -d /path/to/fast5 input.fasta before zibra.py minion

v0.11-dev:
    * Add stringent pipeline

v0.11 (25th July 2017):
    * Revert back to Ryan Wick's porechop repo as --untrimmed now implemented
    * New script: align_trim_fasta.py and reconstitute.py as basis for more principled demultiplexing (align first, then trim to known amplicon end points +/- 40 bases) to help prevent chimeric reads resulting in incorrect barcode identification

v0.10 (15th July 2017):
    * Better handling of confident deletions (previously ignored, now N-masked)
    * Update to nanopolish HEAD
    * Fixes to support latest nanopolish VCF format changes
    * Ability to choose higher values of max-haplotypes to support more divergent references

v0.9:
    * New command line interface zibra.py to ease extraction and demultiplexing with Albacore and multiple groups

v0.8:
    * Track latest Porechop with better adaptor trimming

v0.7:
    * Add Illumina wrapper scripts

v0.6:
    * Update poretools

v0.5:
    * Update nanopolish to latest HEAD - to fix Albacore 1.1 support (7de633d01cc35a58e5537af5dd1024ae0040d15c)
    * Add Lassa virus scheme

v0.4:
    * Update nanopolish to latest HEAD - aaaf90beb4efe37243c651e62fcfd11374fe2176 for Albacore 1 support
    * Initial support for Yellow Fever (500 and 1000 bp schemes)
        * Move to poretools for extraction with named basecaller

v0.3:
    * add Porechop

v0.2:
    * update nanopolish to 0.6 - adds default support for various nanopore models
    * update samtools to 1.4