Check the outputs from snpit. If the Species is not N/A, then make no changes.
If the Species is N/A then check the lineages in the tbprofiler full_report.json file. If the main_lin is lineage4 and the pct_reads_mapped is above 98% then:
Change Species to M. tuberculosis
Change Lineage to match the main_lin value from tbprofiler (should be Lineage 4)
Change Percentage to N/A (since the outputs are not directly based on SNP genotypes)
Fixes #18
This is the approach taken:
N/A, then make no changes.N/Athen check the lineages in the tbprofilerfull_report.jsonfile. If themain_linislineage4and thepct_reads_mappedis above 98% then:M. tuberculosismain_linvalue from tbprofiler (should beLineage 4)N/A(since the outputs are not directly based on SNP genotypes)