xlavir v0.6.2 (2022-03-18) - nf-core/viralrecon Medaka VCF sample name fix

Fixes sample name extraction from viralrecon Medaka VCF filename with ".merged" to get sample name that matches SnpSift filename extracted sample name.

xlavir v0.6.1 (2022-02-02) - low/no coverage Medaka VCF fix

• Added more checks for Medaka VCFs from low coverage samples which may produce ValueError and ZeroDivisionError errors

xlavir v0.6.0 (2022-01-05) - annotated Medaka VCF support

• Add support for reading annotated Medaka VCF files (medaka_variant VCF annotated with medaka tools annotate)
• Changed mutation string format to {gene}:{AA change} ({NT change}{extra}) if there is a AA change
• Added low coverage filtering of variants for Medaka VCF
• "Variants Summary" table now sorted by nucleotide position

xlavir v0.5.3 (2021-11-09) - consensus output fix

• Fixed shorter consensus sequences not being written to report
• Improve nf-virontus VCF compatibility

xlavir v0.5.2 (2021-11-09) - bugfix patch release

Fixes and changes from PR #15

Fixes:

• low coverage coordinate output off by one (xlavir.tools.mosdepth.get_interval_coords_bed)
• error on no Pangolin reports found (e.g. non-SARS-CoV-2 report) (xlavir.tools.pangolin.get_info)
• user QC thresholds not being used (xlavir.xlavir.run)
• not showing all QC fail comments (xlavir.qc.create_qc_stats_dataframe)
• consensus sequences being too long for Excel cell character limit (32,767 characters); longer sequences are chunked into 80 character segments with one segment per line in consensus sheet (xlavir.tools.consensus.read_fasta)

Changes:

• Ignore and skip unsupported VCFs instead of throwing NotImplementedError (xlavir.tools.variants.get_info)
• In consensus sheet, only add QC comments on FASTA header rows if necessary (xlavir.io.xl.add_comments)

xlavir v0.5.1 (2021-08-04) - bugfix patch release

• Fixed issue (#12) where iVar ref allele depth corresponds to depth of base before deletion. For indels, ref allele depth is taken from the total depth minus the alt allele depth.
• Fixed issue (#14) where the total number of reads from samtools flagstat may not be the true number of reads. The unmapped reads may be excluded from the BAM file so the samtools flagstat total number of reads may be equal to the number of mapped reads. There is now a search for fastp JSON files to get the true total number of reads.

xlavir v0.5.0 (2021-07-30) - nf-core/viralrecon v2.1/v2.2 Nanopore Nanopolish support

• Added support for Nanopolish VCF parsing as generated by the ARTIC pipeline
• Added deduplication of VCF and SnpSift entries since the ARTIC pipeline may produce VCF files with duplicate variant calls due to overlap between amplicons.
• Added VCF and SnpSift test data for CLI test to generate Excel report.

xlavir v0.4.3 (2021-07-29) bugfix patch release

Fix an issue where single base positions are being reported as 0-based when all other ranges are 1-based for reporting of low/no coverage regions from Mosdepth per-base BED files (#10).

xlavir v0.4.2 (2021-05-21) - nf-core/viralrecon v2.0 support

• Add support for nf-core/viralrecon version 2.0 (requires Mosdepth bed.gz files be output; needs custom modules.config like this one)
• Nextclade CLI per sample results parsed into sheet showing useful info like Nextstrain clade, # of mutations, # of PCR primer changes
• Added check that input directory exists and is a directory
• Added sheet with xlavir info
• Added Gene, Variant Effect, Variant Impact, Amino Acid Change to Variant Summary table

xlavir v0.4.1 (2021-05-14)

• Add reference sequence length to QC stats table. Get ref seq length from max mosdepth per base BED coverage value.
• Add more conditional formatting
• Fix execution_report.html finding
• Fix version printing; add to help
• Add epilog with usage info