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pysam 0.16.0 halts with malformed VCF file #613

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samanvp opened this issue Jun 11, 2020 · 0 comments
Open

pysam 0.16.0 halts with malformed VCF file #613

samanvp opened this issue Jun 11, 2020 · 0 comments
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good first issue P1

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samanvp commented Jun 11, 2020

One of our integration tests timed out after pysam was updated to 0.16.0.

test_allow_malformed_records tries to parse a malformed VCF file with missing start_position values in one its lines. We need to investigate this problem and remove the pinned pysam version introduced in #612
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