periscope-v0.1.2

New features:

• Added gRNA count per ORF for Illumina datasets

Minor changes:

• Changed mapped reads to display only primary reads and exclude secondary and supplementary mappings
• Added mapping_threads command line argument to uncouple mapping and parallel processing

Bug fixes:

• Fixed PyVCF install error

periscope-v0.1.0

• Added Vanguard optimisation using parallel processing to speed up sgRNA counting
• Added feature allowing to use custom primers and amplicons
• Added more primer scheme choices (ARTIC V4 and midnight)
• Fixed a bug where ORF1 is being called as an sgRNA
• Fixed a bug where default resources folder wasn't working
• Fixed a bug where incorrect normalisaton was applied to illumina reads

periscope-v0.0.11

Realised detection of compressed fastq files was not working. Fixed.

periscope-v0.0.10

• Fix to ARTIC Field Bioinformatics Package Version

periscope-v0.0.8a

• Fixed bug introduced by new arguments for logging in 0.0.8

periscope-v0.0.8

Addressing some issues with Illumina analysis:

• non-canonical sub-genomic RNA sometimes listed with evidence of 0
• over calling of non-canonical sub-genomic RNA caused by poor leader match (increased stringency slightly)
• all sgRNA counts off by 1