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taffy view with a --region SEGVs when stdin as input #62
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It should not seg fault, but this behavior would not be trivial to
implement given the current design. I'd vote to "fix" by just printing a
warning and exiting.
…On Tue, Jul 16, 2024 at 4:46 PM Mark Diekhans ***@***.***> wrote:
% ./bin/taffy view --region=Anc0refChr0:10-100 < tests/dupe_test.maf
#taf version:1 scoring:N/A
Segmentation fault (core dumped)
It would be useful to be able to select regions from a stream rather than
an indexed
taf.
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yes, really two different issues.
The use case pipeline for a stream is:
- python program pulls blocks for a region from a bigMaf using pyBigWig
- convert to taffy
- taffy norm
- taffy view of region to trim blocks to desired region
BTW, there now a Rust library to read bigBed files:
https://github.com/jackh726/bigtools
which could be use to have taffy directly access bigMaf without the
huge weight of the kent library.
Benedict Paten ***@***.***> writes:
… It should not seg fault, but this behavior would not be trivial to
implement given the current design. I'd vote to "fix" by just printing a
warning and exiting.
On Tue, Jul 16, 2024 at 4:46 PM Mark Diekhans ***@***.***>
wrote:
> % ./bin/taffy view --region=Anc0refChr0:10-100 < tests/dupe_test.maf
> #taf version:1 scoring:N/A
> Segmentation fault (core dumped)
>
> It would be useful to be able to select regions from a stream rather than
> an indexed
> taf.
>
> —
> Reply to this email directly, view it on GitHub
> <#62>, or
> unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AAEQ4ICHEYBE3RP2R3XIULTZMWWEJAVCNFSM6AAAAABK7Q3VZGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQYTEMRTGEYDGNI>
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#62 (comment)
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The crash is fixed in #62. Thanks for reporting it. I guess the other issue is that you want region queries without the index. This is certainly possible and would be analogous to |
thanks
bigMafToMaf pull blocks, not regions. I wanted this trimmed to
simplify down-stream analysis. In this case miRNAs.
I just wrote tmp taffy files, indexed then and then extract the
region.
taffy did a beautiful job of creating single blocks.
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It would be useful to be able to select regions from a stream rather than an indexed
taf.
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