v1.5.0

v1.0.5:

1. variant_interpretation
2. add rrs gene condition
3. comment column -> warning column, fill with comment depending on %region > threshold
4. vcf->dataframe
5. filter information list as ; separated string
6. new input: bed file

v1.0.6:

1. add check that there is annotation for a variant at all, i.e. there is an ANN key
2. add option to filter variants if no PASS in filter vcf volumn
3. add verbose flag, message on stdout can be captured

v1.0.7:

1. change vcf_to_pandas_dataframe: choice of annotation from snpEff
2. choose 1st annotation if not modifier
3. if modifier variant, loop over all annotations and choose closest

v1.0.8:

1. add variant QC step for variants at end of variant_interpretation:
2. add QC failed to warning column
3. do not remove all large deletions, take all deletions for now

v1.0.9:

1. add new column mdl_LIMSfinal to lab report
2. copy mdl severity into mdl_LIMSfinal,
3. update that severity bases on variant QC and regions coverage QC

v1.1.0:

1. revamp filter_genes section: Gene_Name can be &-separated list of genes for large deletions
2. move this section to beginning, so genes with no antimicrobial get
3. antimicrobial set by using chemicals associated with region
4. remove Warning column,
5. set 'Insufficient Coverage' for mdl_LIMSfinal severity if 'Breadth_of_coverage_QC' == FAIL
6. except for variants with mdl severity R
7. go back to old 2.2.1 but with feature_ablation added
8. still check for upstream_gene_variant for is_notsynonymous
9. change to csv report

v1.2.0:

1. rename function 3_2 to 3_2_2 and update function:
2. 3.2.2: for non-synonymous variants introduce distinction: large deletions vs rest

v1.2.1:

1. changes to severity in 1.1, 2.1, 3.1
2. include has-deletion condition in region_coverage_qc
3. rename mdl_2_2 and looker_2_2 to mdl_2_1 and looker_2_1 to make naming more consistent
4. remove feature_ablation condition in region_coverage_QC, not needed anymore since has_deletion condition used now
5. change term has_large_deletion to has_deletion since we take all DELLY deletion which can be also smaller than 50bp, this need to be improved, use also mutect2 deletions
6. better get_deletions_in_region script: now get deletion interval and check for overlaps with array of regions of interest

v1.3.0:

1. split large deletion across several genes into several rows, one row per gene
2. revamp get deletions in region
3. add # bp deletion takes in region + gene length of lab report as debug option

v1.3.1:

1. create looker and mdl_prelim columns beforehand with defaults, just like the coverage columns, code just fills the new columns, those columns are the output produced

v1.4.0:

1. 2.2.2: change CDS to AA,
2. 2.2.1: use distance,
3. 3.2.2: split into 3.2.2.1/2/3, special treatment of gyrA and gyrB, use AA.pos, section 1: remove genes Rv0678, mmpL5, mmpS5 from gene_list_1 and create gene_list_4, special treatment of gene_list_4 in section 1

v1.5.0:

1. include vcf_to_pandas_dataframe_all_annotations