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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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stringtie-2.0.6 GBitVec: index 45 out of bounds #259

Closed kylepalos closed 4 years ago

kylepalos commented 4 years ago

Hello,

Thank you for writing stringtie, it has been incredibly helpful in my research. I am assembling transcripts from Oxford Nanopore cDNA reads aligned using minimap2. For one of my assemblies, I receive the following error:

sudo /path/to/stringtie-2.0.6.Linux_x86_64/stringtie -L -G reference.gtf -o output.gtf input.bam Error at GBitVec: index 45 out of bounds (size 45)

I had other sequencing data assemble fine with the same reference annotation. I extracted the problem bundle and relevant reference annotation, suggested here.

Here is the problem alignment and the relevant annotation.

Please let me know if you need any other information regarding the issue.

Thank you very much for your assistance. Kyle Palos

gpertea commented 4 years ago

Thank you for the thorough report and for providing the perfect data for debugging, the bug is confirmed (reproduced it on the provided data) and debugging will start soon.