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legumeinfo / gcv

Federating genomes with love (and synteny derived from functional annotations)
https://gcv.legumeinfo.org/
Apache License 2.0
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javascript error in console leading to perpetual wait for search results in alignment pipeline #420

Open adf-ncgr opened 2 years ago

adf-ncgr commented 2 years ago

A seemingly innocuous request: https://gcv.legumeinfo.org/gene;lis=cicar.CDCFrontier.gnm1.ann1.Ca_21954?algorithm=repeat&match=10&mismatch=-1&gap=-1&score=30&threshold=25&bmatched=20&bintermediate=10&bmask=10&linkage=average&cthreshold=20&neighbors=50&matched=4&intermediate=5&sources=lis&bregexp=&border=chromosome&regexp=&order=distance leads to console error: main.c67d416a58e79492.js:1 ERROR RangeError: Invalid array length and somewhat misleading pipeline status:

image

which leaves the user in some perplexity.

adf-ncgr commented 2 years ago

this may be a less innocuous request but leads to the same apparent behavior and derives from one of the example searches on the gcv.legumeinfo.org welcome page: https://gcv.legumeinfo.org/gene;lis=medtr.A17.gnm5.ann1_6.MtrunA17Chr3g0078741?q=medtr.A17.gnm5.MtrunA17Chr3:1000000-1500000&sources=lis&algorithm=repeat&match=10&mismatch=-1&gap=-1&score=30&threshold=25&bmatched=20&bintermediate=10&bmask=10&linkage=average&cthreshold=20&neighbors=70&matched=4&intermediate=5&bregexp=&border=chromosome&regexp=&order=distance

alancleary commented 2 years ago

Thanks for bumping this issue. It got buried among the other issues! Unless it's a high priority, this probably won't get fixed until June when I'm back from vacation. It's worth noting that switching the alignment algorithm to Smith-Waterman prevents the error: https://gcv.legumeinfo.org/gene;lis=medtr.A17.gnm5.ann1_6.MtrunA17Chr3g0078741?q=medtr.A17.gnm5.MtrunA17Chr3:1000000-1500000&sources=lis&algorithm=smith-waterman&match=10&mismatch=-1&gap=-1&score=30&threshold=25&bmatched=20&bintermediate=10&bmask=10&linkage=average&cthreshold=20&neighbors=70&matched=4&intermediate=5&bregexp=&border=chromosome&regexp=&order=distance

adf-ncgr commented 2 years ago

thanks, not urgent I just happened to run into again when doing something else. Good to know it is only an issue for the repeat algorithm, I guess that should help narrow down the cause later.

alancleary commented 2 years ago

Good to know it is only an issue for the repeat algorithm, I guess that should help narrow down the cause later.

Yeah, that's not at all surprising. Stitching together all the forward and reverse repeat alignment fragments is overly complicated at the moment. Hopefully addressing this issue helps simplify the code!