Merge pull request #541 from uclahs-cds/czhu-fix-vep-parser

Only read column 1-13 from VEP TSV
uclahs-cds · Jul 27, 2022 · b066c64 · b066c64
2 parents bc2f651 + 213fa35
commit b066c64
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,16 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Unreleased]
 
+## [0.9.1] - 2022-07-27
+
+### Added
+
+- UTIL command line tool `validateNoncodingCalling` added to validate the output of `callNoncoding` with `bruteForceNoncoding`. #524
+
+## Fixed
+
+- `parseVEP` updated to only parse the first 13 columns of the VEP TSV. #540
+
 ---
 
 ## [0.9.0] - 2022-07-18

diff --git a/moPepGen/__init__.py b/moPepGen/__init__.py
@@ -5,7 +5,7 @@
 from typing import Iterable, IO
 
 
-__version__ = '0.9.0'
+__version__ = '0.9.1'
 
 ## Error messages
 ERROR_INDEX_IN_INTRON = 'The genomic index seems to be in an intron'

diff --git a/moPepGen/parser/VEPParser.py b/moPepGen/parser/VEPParser.py
@@ -35,9 +35,6 @@ def parse(handle:IO) -> Iterable[VEPRecord]:
             codons = (codons[0], '')
 
         extra = {}
-        for field in fields[13].split(';'):
-            key, val = field.split('=')
-            extra[key] = val
 
         yield VEPRecord(
             uploaded_variation=fields[0],