adf-ncgr

don't throw error about csi indexing needed when csi indexing has been specified

1

## PR checklist - [x] This comment contains a description of changes (with reason). digging into #855 more on our side, we found that the .nextflow.log contained the error: >...

eutils rate limits exceeded (with relatively small input set of accessions)

4

### Description of the bug looks like #102 may have had some unintended side effects, although I am not %100 sure that I'm interpreting the situation correctly. Basically I returned...

CNV-induced inversions

7

despite #262 we are still seeing some false inversions in regions of CNV, e.g.: https://legumeinfo.org/gcv2/gene;lis=phavu.Phvul.003G002400?algorithm=repeat&match=10&mismatch=-1&gap=-1&score=30&threshold=25&bmatched=20&bintermediate=10&bmask=10&linkage=average&cthreshold=20&neighbors=10&matched=4&intermediate=5&sources=lis&bregexp=&border=chromosome&regexp=&order=distance per @alancleary : > Yeah, it's an inversion issue. Unfortunately the inversion algorithm is optimizing...

currently, we have some brute force filtering implemented client side with regex matching applied to track names (micro and macro). While this has given us a lot of bang for...

would be helpful to know when you've hit the end of a sequence in the view

3

a nice-to-have, especially for dealing with fragmented genomes; sometimes it's not completely obvious whether a track has ended because synteny has been disrupted by a genomic rearrangement event or simply...

Should have functionality similar to the synteny dot plots. [LEGUME-602] created by alancleary

add scrolling to multi view?

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not sure this is a good idea, but I got the urge to try scrolling over just now and felt the lack. It seems like it would be possible to...

need to think of a better way to determine track boundaries in pan-view

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currently, the pan-view uses the old strategy from basic view whereby every track extent is determined exclusively by "num neighbors"; when some tracks have internal gene PAVs (as is typically...

investigate conditions under which inversions not represented in macrosynteny blocks

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from earlier email exchanges: adf : > One thing while it's on my mind, you had mentioned inversions in the context of the chord view and > I think I...

extend query track(s) when genes "just outside" neighborhood belong to families of genes within neighborhood(s)

2

Currently, there's a bit of asymmetry in terms of the way that query and result tracks behave with respect to their bounds. A result track extent is "greedy" in the...