Troubles with GTF files

[lietai]

I am currently working on human data mapped with hisat2 using Gencode fasta files and annotations

ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.annotation.gtf.gz
ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/GRCh38.primary_assembly.genome.fa.gz

And I have some troubles with the GTF option.
It crash with this error

Inspecting sample......
strawberry: /home/ruolin/git/strawberry/src/alignments.cpp:1789: double compute_doc(uint, uint, const std::vector&, std::vector&, IntronMap&, uint): Assertion `gf.right() > gf.left()' failed.
Abandon (core dumped)

I tried with the example, it crashed also.

I tried with other GTF files without any more luck.
Any idea?

Or may be you could indicate from where you take your GTF file.

[ruolin]

@47Lies Did you use the zipped file gz? Please unzip first if so.

[lietai]

I used the unzipped file.

[ruolin]

@47Lies Thank you for reporting! I can reproduce your error. Will get back to you shortly.

[ruolin]

@47Lies Thanks again. This bug is triggered by a one bp intron in the gff file. This has been fixed in 0.9.3. https://github.com/ruolin/strawberry/tree/0.9.3

chr1 ENSEMBL exon 6457184 6457264 . + . gene_id "ENSG00000187017.16";
chr1 ENSEMBL exon 6457266 6457274 . + . gene_id "ENSG00000187017.16";

[lietai]

@ruolin Thank you for your reactivity. Indeed I succeded with your example bam geuvadis_300/sample_01.sorted.bam

But it failed with my bam file.

Inspecting sample......
strawberry: /home/ruolin/git/strawberry/src/alignments.cpp:1939: void filter_intron(const string&, uint, uint, const std::vector&, IntronMap&): Assertion `end > start' failed.

I suspect the same kind of issue as before.

Should I open a new issue?

Do you need one of my .bam?

[ruolin]

@47Lies Thank you for testing it! No, you don't need to open a new issue. I think it is still something related. If you can share me your bam, it will be very helpful.

[lietai]

@ruolin I manage to extract a few reads that make strawberry crash with the genecode.v28 gtf

CRASH.bam.gz

I just gzip the file so that github accept it.

Best regards

[ruolin]

@47Lies thank you very much for providing the test case. It helped me a lot! I have fixed the bug and tested it on your bam and it seems to work now. https://github.com/ruolin/strawberry/releases/tag/0.9.3.
Please test 0.9.3 on your whole bam and let me know how it goes.

[lietai]

@ruolin It works, thank you.

Best regards.

[ruolin]

@47Lies Thank you for your help and patients. I will close it now.