taffy view with a --region SEGVs when stdin as input

[diekhans]

% ./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.

[benedictpaten]

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> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[diekhans]

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> > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > -- Reply to this email directly or view it on GitHub: #62 (comment) You are receiving this because you authored the thread. Message ID: ***@***.***>

[glennhickey]

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 bcftools view -t (where the current taffy view -r matches bcftools view -r), but I don't personally have any plans to implement it anytime soon. In your use case, why not just pull the exact region out of the bigMaf?

[diekhans]

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.