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test failure in VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added #843

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nieder opened this issue Sep 1, 2019 · 2 comments

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@nieder
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nieder commented Sep 1, 2019

When running tests for pysam-py-0.15.3, tests fail like this. All tests passed on 0.15.2. This is macOS 10.13.6 with python-2.7.16 and htslib-1.9

tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED
tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED
tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added Assertion failed: (!fmt->p_free), function bcf_update_format, file vcf.c, line 3496.
/tmp/fink.7y4xf: line 6: 97317 Abort trap: 6           /sw/bin/pytest-2.7 tests
@jmarshall
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jmarshall commented Sep 2, 2019

This is the same problem as #640 and #734, caused by samtools/htslib#813 which has been fixed in HTSlib — the fix is on HTSlib develop and will appear in its next release.

@jmarshall
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This has been fixed since pysam 0.16.0 (when used with HTSlib 1.10 — which fixed the underlying problem — or later).

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