Merge branch 'hotfix/1.2.1'

Updated README.md

.gitignore

@@ -29,6 +29,8 @@ MANIFEST
 out*
 test.txt
 tmpout
+tests/test_*/*.vcf
+*.log
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

CHANGES.md

@@ -1,4 +1,6 @@
 
+## 1.2.1
+* updated documentation and README
 ## 1.2.0
 * Added json config paramter to accept filtering paramaters
 * removed commandline paramaters that are now read from config file

Dockerfile

@@ -3,7 +3,7 @@ USER root
 
 MAINTAINER  [email protected]
 
-ENV ANNOTATEVCF_VER '1.2.0'
+ENV ANNOTATEVCF_VER '1.2.1'
 
 # install system tools
 RUN apt-get -yq update
@@ -40,7 +40,7 @@ RUN pip3 install --install-option="--prefix=$CGP_OPT/python-lib" dist/$(ls -1 di
 FROM ubuntu:20.04
 
 LABEL uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Sanger Institute" \
-      version="1.2.0" \
+      version="1.2.1" \
       description="Tool to perform vcf file annotation"
 
 ### security upgrades and cleanup

README.md

@@ -41,13 +41,13 @@ Various exceptions can occur for malformed input files.
  * ```input_vcf.gz```  snv or indel vcf file annotated using [VAGrENT]
  * ```normal_panel.vcf.gz```  normal panel to tag germline variants [VAGrENT]
  * ```lof_genes.txt ``` list of known loss of function [LoF] genes along with previous gene symbols ( to make sure all gene synonyms were matched with input vcf)
- * ```consequence types``` lof consequence types to restrict driver gene annotations  
+ * ```filters.json``` filters to be applied during driver annotations ( see default file ```filters.josn``` in config  folder)
  * ```driver_mutations.tsv.gz``` tab separated driver mutations along with consequence type 
  * ```info.header``` vcf header INFO line 
 
 ### outputFormat
 
- * ```<input>.drv.vcf.gz ``` output vcf file with DRV info field and consequence type if known, LoF in case annotated using LoF gene list.
+ * ```<input>_drv.vcf.gz ``` output vcf file with DRV info field and consequence type if known, LoF in case annotated using LoF gene list.
 
 ## INSTALL
 Installing via `pip install`. Simply execute with the path to the compiled 'whl' found on the [release page][annotateVcf-releases]:

annotate/commandline.py

@@ -29,16 +29,15 @@ def main():
                           default=None, help="vcf_file to annotate")
 
     optional.add_argument("-filters", "--vcf_filters", type=str, dest="vcf_filters", required=False,
-                          default=filters_json, help="Include vcf filters \
-                          configuration file in json (param:value) format \
+                          default=filters_json, help="Include vcf filters file in json format \
                           [please refer bcftools documentation for more details \
                            : http://samtools.github.io/bcftools/bcftools.html#expressions]")
 
     optional.add_argument("-np", "--normal_panel", type=str, dest="normal_panel", required=False,
                           default=None, help="normal panel file to flag germline variant sites")
 
     optional.add_argument("-g", "--lof_genes", type=str, dest="lof_genes", required=False,
-                          default=None, help="LoF gene name file to use annotations")
+                          default=None, help="Known LoF genes file to annotate LoF variants")
 
     optional.add_argument("-m", "--mutations", type=str, dest="mutations", required=False,
                           default=None, help="driver mutations file to use for driver variant annotations")
@@ -70,6 +69,5 @@ def main():
     with formatter.tempdir(outdir_path['outdir']) as base_dir:
         annotator.VcfAnnotator(my_formatter, base_dir)
 
-
 if __name__ == '__main__':
     main()

setup.py

@@ -3,7 +3,7 @@
 from setuptools import setup
 
 config = {
-    'version': '1.2.0',
+    'version': '1.2.1',
     'name': 'annotateVcf',
     'description': 'Tool to annotate and filter vcf files...',
     'author': 'Shriram Bhosle',