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Add CSI index support for BAM and VCF #1086

merged 21 commits into from Jul 5, 2018


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cmdcolin commented Jul 2, 2018

This adds support for using CSI indexes on BAM and VCF

This allows doing coordinates of over a gigabase (or specifically 2^30 which is 1073741824)

It seems effective! The 64-bit bit manipulations are done using some floating point math specifically multiplying by two and dividing by two. A proper 64 bit math library could potentially be implemented.

Ref #926

@wafflebot wafflebot bot added the in progress label Jul 2, 2018

cmdcolin added some commits Jul 2, 2018

@rbuels rbuels merged commit 34bbb6c into dev Jul 5, 2018

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@wafflebot wafflebot bot removed the in progress label Jul 5, 2018


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rbuels commented Jul 5, 2018

This looks good! My only gripe is that it's implemented in the old dojo style, so we are going to have to put in some extra work later to move it out into a node module.


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thomasvangurp commented Jul 10, 2018

Would it be possible to support this for GFF3Tabix as well? this might allow for more informative feature density plots as you can set the step size for the index...


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nathanhaigh commented Jul 10, 2018

@thomasvangurp Hopefully #1105 delivers support for CSI indexed GFF3Tabix.

@rbuels rbuels added this to the 1.15.0 milestone Jul 10, 2018

@cmdcolin cmdcolin deleted the csi_index branch Jul 11, 2018

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