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Another error with particular TBI file #17

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cmdcolin opened this issue Mar 1, 2019 · 3 comments
Closed

Another error with particular TBI file #17

cmdcolin opened this issue Mar 1, 2019 · 3 comments
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@cmdcolin
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cmdcolin commented Mar 1, 2019

Here is a snippet of a vcf with a failing tabix file

failing_tabix.tar.gz

Ends up getting a negative chunkCount

@cmdcolin
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cmdcolin commented Mar 1, 2019

@garrettjstevens i'll go ahead and take a look at this

@cmdcolin cmdcolin added this to To do in JBrowse team board via automation Mar 1, 2019
@cmdcolin cmdcolin moved this from To do to In progress in JBrowse team board Mar 1, 2019
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cmdcolin commented Mar 5, 2019

The reason this was happening was due to chromosomes of length greater than 2^29 being indexed which is technically a tabix limit but older versions of tabix allowed it

Tabix 1.2.1 allows it but tabix 1.9 gives a proper error

[E::hts_idx_push] Region 536930580..536930581 cannot be stored in a tbi index. Try using a csi index with min_shift = 14, n_lvls >= 6
tbx_index_build failed: G3116.vcf.gz

@cmdcolin cmdcolin mentioned this issue Mar 5, 2019
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cmdcolin commented Mar 5, 2019

Possible fix in #18

@cmdcolin cmdcolin closed this as completed Mar 5, 2019
JBrowse team board automation moved this from In progress to Done Mar 5, 2019
@cmdcolin cmdcolin moved this from Done to In progress in JBrowse team board Mar 6, 2019
@cmdcolin cmdcolin moved this from In progress to Done in JBrowse team board Mar 6, 2019
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