v.1.1.0

Changelog

• Update of resistance database: Included the 2022 WHO resistance catalogue and additional resistance conferring positions.

• --all_vars option removed, as it was anyway hardcoded for the neccessary steps.

• --snp_vars option is now working from non snp-only variant files in the TBjoin step.

• manual updates to reflect changes

v1.0.4

-added FAQ
-fix for samtools version check
-fix for java version check
-In all new miniconda installations GATK3 is now "gatk3" and not "gatk", while using "gatk3-register" instead of "gatk-register". MTBseq code has been changed accordingly.

v1.0.3

fix for conda

v1.0.2

checking dependencies
added --check option

v1.0.1

added --version option
relaxed fastq.gz to fq.gz
set to use environment version of perl
dies now on failed system calls
updated readme

Initial release v1.0.0

Fix for agglomarative clustering