updated Change log and version

cancerit · Sep 1, 2020 · d2fd362 · d2fd362
1 parent 8af3c89
commit d2fd362
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Showing 4 changed files with 8 additions and 5 deletions.
diff --git 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
@@ -3,7 +3,7 @@ USER root
 
 MAINTAINER  [email protected]
 
-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
@@ -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
@@ -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',