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Can't load specific bigbed file from UCSC #1226

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cmdcolin opened this Issue Oct 5, 2018 · 1 comment

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cmdcolin commented Oct 5, 2018

The file http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/GCA_001632525.1_BALB_cJ_v1/maf/BALB_cJ.bigMafSummary.bb from http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/GCA_001632525.1_BALB_cJ_v1/maf/ isn't able to load and has infinite loading bar in JBrowse

I don't think there's anything particularly weird about this file, it just looks like this

chr1    0   3782    AKR_J   0.773556
chr1    0   3782    C3H_HeJ 0.771731
chr1    0   3782    CBA_J   0.775481
chr1    0   4790    A_J 0.677822
chr1    122 4790    C57BL_6NJ   0.653361
chr1    122 4790    NOD_ShiLtJ  0.630747
chr1    136 3782    DBA_2J  0.757485
chr1    158 2559    WSB_EiJ 0.464704
chr1    158 4790    129S1_SvImJ 0.578083
chr1    158 4790    CAST_EiJ    0.535326
chr1    158 4790    LP_J    0.578083
chr1    158 4790    NZO_HlLtJ   0.65974
chr1    158 4790    PWK_PhJ 0.557667

track config

[tracks.test]
urlTemplate=BALB_cJ.bigMafSummary.bb
type=CanvasFeatures
storeClass=JBrowse/Store/SeqFeature/BigBed
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cmdcolin commented Oct 5, 2018

If I re-encode the file using

table scores
"custom track types"
(
string  chrom;          "Reference sequence chromosome or scaffold"
uint    chromStart;     "Start position of feature on chromosome"
uint    chromEnd;       "End position of feature on chromosome"
string  name;           "Name of gene"
double    score;                "Score"
)

And run through bedToBigBed -type=bed3 -as=autosql.as data.bed chrom.sizes data.bb then the features do load. It is maybe an issue that I can't read the native bb file that is on their server though

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