v0.7.0 ncov-parser

• Added support for Pangolin v4 output changes as per issue #13
• General code cleanup

v0.6.9 ncov-parser

• supports changes to the primer name prefix in the scheme BED file

v0.6.8 ncov-parser

Lineage parser fix for Pangolin 3.1.3 related to issue ncov-tools #85

v0.6.7 ncov-parser

Added support for the scorpio_call field in the lineage report. Now included in the summary_qc.tsv file.

v0.6.6

Updated to support the latest version of Pangolin (3.0.3). The columns in the lineage report have been modified, this includes the content of the notes field. The Lineage.py parser now supports the changes to this.

v0.6.5 support for Freebayes

Merge pull request #6 from simpsonlab/support_freebayes

Support freebayes

v0.6.4: Added Pangolin lineage notes

Added field for Pangolin lineage notes to summary_qc.tsv report.

v0.6.3: Merge pull request #4 from simpsonlab/add_pangolin_lineage

Added lineage and watch mutations to the _summary_qc.tsv file. Replaced QC flag for POSSIBLE_FRAMESHIFT_INDELS with annotation from SNPEff.

v0.6.2

Removed EXCESS_VARIANTS flag from qc_flag

v0.6.1

Features includes:

• sorted summary QC summary file
• when the mixture report is included in get_qc.py, the qc_flag column includes samples identified as "POSSIBLE_MIXTURE"