update percentage limit for tngs

Dockerfile

@@ -3,7 +3,7 @@
 # Shelby Bennett, Erin Young, Curtis Kapsak, & Kutluhan Incekara
 
 ARG SAMTOOLS_VER="1.18"
-ARG TBP_PARSER_VER="1.5.8"
+ARG TBP_PARSER_VER="1.5.9"
 
 FROM ubuntu:jammy as builder
 
@@ -42,7 +42,7 @@ ARG TBP_PARSER_VER
 LABEL base.image="ubuntu:jammy"
 LABEL dockerfile.version="1"
 LABEL software="tbp-parser"
-LABEL software.version="1.5.8"
+LABEL software.version="1.5.9"
 LABEL description="tbp-parser and samtools"
 LABEL website="https://github.com/theiagen/tbp-parser"
 LABEL license="https://github.com/theiagen/tbp-parser/blob/main/LICENSE"

README.md

@@ -22,16 +22,16 @@ See also [this page](https://theiagen.notion.site/tbp-parser-b02bef0cbc814b12987
 We highly recommend using the following Docker image to run tbp-parser:
 
 ```markdown
-docker pull us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.5.8
+docker pull us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.5.9
 ```
 
 The entrypoint for this Docker image is the tbp-parser help message. To run this container interactively, use the following command:
 
 ```markdown
-docker run -it --entrypoint=/bin/bash us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.5.8
+docker run -it --entrypoint=/bin/bash us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.5.9
 # Once inside the container interactively, you can run the tbp-parser tool
 python3 /tbp-parser/tbp_parser/tbp_parser.py -v
-# v1.5.8
+# v1.5.9
 ```
 
 ### Locally with Python

tbp_parser/LIMS.py

@@ -33,14 +33,16 @@ def get_id(self):
     if self.tngs:
       number_of_lims_genes_above_coverage_threshold = sum(int(globals.COVERAGE_DICTIONARY[gene]) >= 90 for gene in globals.COVERAGE_DICTIONARY.keys())
       percentage_lims_genes_above = number_of_lims_genes_above_coverage_threshold / len(globals.COVERAGE_DICTIONARY.keys())
+      # if the percentage of genes above the coverage threshold is greater than 70%, then we can call the lineage
+      percentage_limit = 0.7
     else:
       number_of_lims_genes_above_coverage_threshold = sum(int(globals.COVERAGE_DICTIONARY[gene]) >= globals.COVERAGE_THRESHOLD for gene in globals.GENES_FOR_LIMS)
       percentage_lims_genes_above = number_of_lims_genes_above_coverage_threshold / len(globals.GENES_FOR_LIMS)
+      # if the percentage of genes above the coverage threshold is greater than 90%, then we can call the lineage
+      percentage_limit = 0.9
+
     self.logger.debug("LIMS:The percentage of LIMS genes above the coverage threshold is {}".format(percentage_lims_genes_above))
-
-    # if the percentage of genes above the coverage threshold is greater than 90%, then we can call the lineage
-    percentage_limit = 0.9
-
+
     with open(self.input_json) as json_fh:
       input_json = json.load(json_fh)
 

tbp_parser/__init__.py

@@ -1 +1 @@
-__VERSION__ = "v1.5.8"
+__VERSION__ = "v1.5.9"