ISSUE: Navigation black hole

[Malcolm Cook]

When I load the bed file below, and use control-b control-f to navigate, it ONLY visits the following regions and will not advance past either end.

[ Super-Scaffold_10 > Super-Scaffold_19 > Super-Scaffold_117 > Super-Scaffold_219 > Super-Scaffold_300 > Super-Scaffold_1049 ]

Looking for a pattern, I first guess that it is only visiting "Super-Scaffold.*" but then I notice that it skipped Super-Scaffold_493

Also, if I type the region into the search box (i.e. "scaffold2439 74898 81532"), it navigates correctly as expected and I do see the feature.

But, I can not navigate away from it using control-{b,f}

I am at a loss.  I've upgraded to 2.3.75 and tried on old version (2.3.66).

This is new data so I can't say it ever "worked" as expected with this data.

Any insights?

Thanks,

Malcolm

Super-Scaffold_10 3059895 3382433 hoxa1_HOXB4_hoxb7-b_HOXD8_hoxd9a_HOXA10_hoxa11b 0 .

Super-Scaffold_1049 735507 742905 hoxc13b 0 .

Super-Scaffold_117 1832795 1840086 Hoxc4 0 .

Super-Scaffold_19 12872672 13310984 HOXA13_HOXA9_HOXA9_HOXD8_HOXD8_HOXA7_Hoxa6_hoxc4a_HOXA3_HOXA2 0 .

Super-Scaffold_219 659676 667987 HOXC11 0 .

Super-Scaffold_300 39990 385606 HOXA11_hoxb8a_Hoxa4_hoxd3_Hoxb2 0 .

Super-Scaffold_493 43566 47340 HOXD13 0 .

scaffold13125 2280 3534 hoxc13b 0 .

scaffold1596 610 143466 hoxc9a_HOXA10_Hoxa11 0 .

scaffold1898 40727 64671 hoxb5b 0 .

scaffold19866 3045 3718 hoxb1a 0 .

scaffold2439 74898 81532 HOXA3 0 .

scaffold2852 16236 19051 hoxa11b 0 .

scaffold2859 12194 18828 HOXA4 0 .

scaffold3143 6490 12015 HOXD12 0 .

scaffold3608 8853 26553 HOXD8 0 .

scaffold3644 15232 17354 HOXC4 0 .

scaffold3965 24836 28059 HOXA5 0 .

scaffold4136 19079 27324 HOXB13 0 .

scaffold4428 4837 22535 HOXB1 0 .

scaffold5401 6939 21753 HOXA4 0 .

scaffold5673 21576 27751 hoxa13b 0 .

scaffold5708 11345 15852 HOXD4 0 .

scaffold6122 21071 21764 Hoxa3 0 .

scaffold7040 10113 19341 HOXC8 0 .

scaffold8443 7067 9378 HOXC9 0 .

scaffold8794 3953 4190 HOXD8 0 .

[Jim Robinson]

Malcolm, is it possible to share the fasta,  or at least a portion of the fasta containing the scaffolds referenced?  

Also the bed file,  cutting and pasting does funny things to the whitespace.

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[Malcolm Cook]

Sure, thanks for offering to take a squiz, here is the whole thing:

http://research.stowers.org/mec/jim.tar

untar into new empty directory and launch igv like:

 igv.sh -g scaffolds.fa  $(ls -m *.gff3.gz *.bed | perl -pe 's/, /,/g')  &

The track that  navigates funny is hoxCluster.bed

[Jim Robinson]

OK, I found the problem.  In what must have seemed like a good idea at the time,  "small" chromosomes were skipped in the ctrl-f / ctrl-b jumps.  This was probably added to filter the "random" contings in human, but is the wrong thing to do in any event.  I've pushed a fix.  If you can't wait for the next release you can try the nightly snapshot tomorrow.   The nightly builds from here out require Java 1.8.   

Let me know if you need this fix released quickly.

Jim

[Malcolm Cook]

Hooray.

Thanks so much - sorry for sending such a huge package - at least it was a working example though.

I can use nightly snapshot tomorrow no problem and I can direct my "users" to similarly do so (but it would be 'nice' not to have to)

Thanks again for following up on this.... I know you must have a zillion things going...

Cheers,

Malcolm

~ Malcolm Cook
h: 913.642.5257
m: 913.226.1542
w: 816.926.4449

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[Jim Robinson]

Fixed in 2.3.76

[Malcolm Cook]

Great - agreed - confirmed - thanks!

On Thursday, June 9, 2016 at 4:09:57 PM UTC-5, Jim Robinson wrote:

Fixed in 2.3.76