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gt1 / biobambam2

Tools for early stage alignment file processing
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bamsormadup v2.0.79: assertion failed #77

Closed fgvieira closed 5 years ago

fgvieira commented 5 years ago

Dear all,

I've just tried running bamsormadup with STAR, but got this error:

bamsormadup: include/libmaus2/bambam/SamInfo.hpp:323: void libmaus2::bambam::SamInfo::parseSamLine(const char*, const char*): Assertion `pa != pe' failed.
bamsormadup: include/libmaus2/bambam/SamInfo.hpp:323: void libmaus2::bambam::SamInfo::parseSamLine(const char*, const char*): Assertion `pa != pe' failed.

Not sure if it helps, but I am piping output from STAR into 

STAR --runThreadN 10 [...] | bamsormadup inputformat=sam threads=10 tmpfile=/tmp SO=coordinate indexfilename=output.bai > output.bam

Any idea of what it means? thanks,

gt1 commented 5 years ago

Could you provide a short example triggering this?

fgvieira commented 5 years ago

It seems it was an upstream issue, that I managed to fix. thanks anyway.