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Assertion `coverage_ends.empty()' failed. #11

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telatin opened this issue Jun 11, 2020 · 1 comment
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Assertion `coverage_ends.empty()' failed. #11

telatin opened this issue Jun 11, 2020 · 1 comment
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@telatin
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telatin commented Jun 11, 2020

Probably when --discard-invalid-alignments is enabled, some paired-ends could be broken and --physical-coverage needs a fix.

Running

covtobed --discard-invalid-alignments --min-cov=1 --physical-coverage mini.mapping.bam

Resulted in:

base.cpp:271: int main(int, char**): Assertion `coverage_ends.empty()' failed.
@telatin telatin added the bug Something isn't working label Jun 11, 2020
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telatin commented Sep 8, 2020 •
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samtools fixmate fixes this.

A new release will warn the user to use samtools, but program will not terminate.

@telatin telatin closed this as completed Sep 8, 2020
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