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Segfault when writing uncompressed BAM #1617

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tijyojwad opened this issue May 5, 2023 · 2 comments
Closed

Segfault when writing uncompressed BAM #1617

tijyojwad opened this issue May 5, 2023 · 2 comments
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@vasudeva8

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@tijyojwad
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Hi,

I am running into a segfault when I attempt to write a header into an uncompressed BAM. I'm opening the file using hts_open(fname, "wbu"). I tried with the commit 6143086502567c5c4bb5cacb2951f664ba28ed6e (release 1.17) but still see that issue.

The same code runs if I just change the mode to "wb".

Could that be looked into?
Thanks!
@tijyojwad
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thanks to a tip from @cjw85 I learnt that wb0 did the trick for generating uncompressed BAMs. Could the API documentation be updated for that?

@daviesrob
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u should work, and certainly shouldn't segfault. We'll look into it.

@vasudeva8 vasudeva8 mentioned this issue Jun 5, 2023
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vasudeva8 added a commit to vasudeva8/htslib that referenced this issue Aug 17, 2023
@vasudeva8
Changes to avoid segfault with uncompressed bam (PR samtools#1632)
0e29bf2 
Avoids segfault when writing bam/bcf with mode "wbu" by
changing "wbu" to "wb0".  The ensures the output file will
be properly wrapped in BGZF blocks, even though it's not
been compressed.

Fixes samtools#1617
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@tijyojwad @daviesrob @vasudeva8