diff --git a/CHANGES.md b/CHANGES.md index dffdf01..e7e5f82 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,3 +1,5 @@ +## 1.1.4 +* updated regex to get genename ## 1.1.3 * fixed bug in gene name comparison with hyphen(-) * corrected typo in default directory name diff --git a/Dockerfile b/Dockerfile index cda4cdc..c3dc72b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,7 +3,7 @@ USER root MAINTAINER cgphelp@sanger.ac.uk -ENV ANNOTATEVCF_VER '1.1.3' +ENV ANNOTATEVCF_VER '1.1.4' # install system tools RUN apt-get -yq update diff --git a/annotate/commandline.py b/annotate/commandline.py index 28f9ef7..2f38e71 100644 --- a/annotate/commandline.py +++ b/annotate/commandline.py @@ -17,7 +17,7 @@ def main(): - usage = "\n %prog [options] -vcf input.vcf [-drv_json test.json -drv_data test_dir] " + usage = "\n %prog [options] -vcf input.vcf [-filter -np -gt -g -m -lof -hl -o ]" optParser = argparse.ArgumentParser(prog='annotateVcf', formatter_class=argparse.ArgumentDefaultsHelpFormatter) @@ -27,7 +27,7 @@ def main(): required.add_argument("-vcf", "--vcf_file", type=str, dest="vcf_file", required=True, default=None, help="vcf_file to annotate") - required.add_argument("-filter", "--vcf_filter", type=str, dest="vcf_filter", nargs='+', + optional.add_argument("-filter", "--vcf_filter", type=str, dest="vcf_filter", nargs='+', required=False, default=['PASS'], help="Include variant sites \ matching vcf FILTER flag(s), multiple flags can be specified \ with space separator") @@ -36,7 +36,8 @@ def main(): default=None, help="normal panel file to flag germline variant sites") optional.add_argument("-gt", "--germline_tag", type=str, dest="germline_tag", required=False, - default="NPGL", help="tag to mark normal panel filtered variants in vcf INFO field") + default="NPGL", help="tag to mark normal panel filtered variants in \ + vcf INFO field, only applicable when -np is set") optional.add_argument("-g", "--lof_genes", type=str, dest="lof_genes", required=False, default=None, help="LoF gene name file to use annotations") diff --git a/setup.py b/setup.py index 5297938..986a553 100644 --- a/setup.py +++ b/setup.py @@ -3,7 +3,7 @@ from setuptools import setup config = { - 'version': '1.1.3', + 'version': '1.1.4', 'name': 'annotateVcf', 'description': 'Tool to annotate and filter vcf files...', 'author': 'Shriram Bhosle',