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Add gzip support to VCF.read #1

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Add gzip support to VCF.read #1

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826d0ac
Add gzip support to VCF.read
lucacozzuto Aug 11, 2026
9b713e5
Import gzip module in formats.py
lucacozzuto Aug 11, 2026
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6 changes: 5 additions & 1 deletion formats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import time
import re
import multiprocessing as mp
import gzip

# Internal
from GAPI import log
Expand Down Expand Up @@ -851,7 +852,10 @@ def read(self, filePath):
'''
Read VCF file
'''
vcfFile = open(filePath)
if str(filePath).endswith('.gz'):
vcfFile = gzip.open(filePath, 'rt')
else:
vcfFile = open(filePath)

## 1. Read VCF and differenciate between header and variant entries
header = []
Expand Down