feat: Expose bcf_hdr_remove via remove_header#323
feat: Expose bcf_hdr_remove via remove_header#323fxwiegand wants to merge 2 commits intobrentp:mainfrom
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Summary of ChangesHello @fxwiegand, I'm Gemini Code Assist1! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed! This pull request introduces a significant enhancement to the Highlights
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Code Review
This pull request introduces a new remove_header method to the VCF class, exposing the bcf_hdr_remove function from htslib. This is a useful addition for manipulating VCF headers. The implementation looks correct, and it's great that you've included a test for the new functionality. I have one suggestion to make the test more comprehensive by covering all header types that remove_header is designed to handle (INFO, FORMAT, and FILTER). This will increase confidence in the new feature.
| def test_bcf_hdr_remove(): | ||
| """Test that remove_header works to remove INFO and FORMAT fields from header""" | ||
| v = VCF(VCF_PATH) | ||
| v.add_info_to_header({'ID': 'TESTINFO', 'Description': 'Test INFO field', | ||
| 'Type': 'String', 'Number': '1'}) | ||
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| assert v.get_header_type("TESTINFO") | ||
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| v.remove_header('TESTINFO') | ||
| with pytest.raises(KeyError): | ||
| v.get_header_type('TESTINFO') |
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The added test is a great start and covers the removal of an INFO field. To make the test more robust, I suggest expanding it to also cover the removal of FORMAT and FILTER fields, as remove_header supports these types as well. This will ensure all aspects of the new function are tested.
def test_bcf_hdr_remove():
"""Test that remove_header works to remove INFO, FORMAT and FILTER fields from header"""
# Test INFO
v = VCF(VCF_PATH)
v.add_info_to_header({'ID': 'TESTINFO', 'Description': 'Test INFO field',
'Type': 'String', 'Number': '1'})
assert v.get_header_type("TESTINFO")
v.remove_header('TESTINFO')
with pytest.raises(KeyError):
v.get_header_type('TESTINFO')
v.close()
# Test FORMAT
v = VCF(VCF_PATH)
v.add_format_to_header({'ID': 'TESTFORMAT', 'Description': 'Test FORMAT field',
'Type': 'String', 'Number': '1'})
assert v.get_header_type("TESTFORMAT")
v.remove_header('TESTFORMAT')
with pytest.raises(KeyError):
v.get_header_type('TESTFORMAT')
v.close()
# Test FILTER
v = VCF(VCF_PATH)
v.add_filter_to_header({'ID': 'TESTFILTER', 'Description': 'Test FILTER field'})
def filter_exists(vcf, flt_id):
for h in vcf.header_iter():
if h.type == 'FILTER' and h.info().get('ID') == flt_id:
return True
return False
assert filter_exists(v, 'TESTFILTER')
v.remove_header('TESTFILTER')
assert not filter_exists(v, 'TESTFILTER')
v.close()1 participant
We are trying to modify some headers in a project of ours and would love to keep using cyvcf2 for that. I hope this fixes #237 and allows removing and then re-adding a header record.
I have tried to make the new
remove_headerfunction as similar toget_header_typeand the newly added test runs fine on my machine so i can at least say it works. Still, would appreciate a careful look to make sure I didn't screw up somewhere.