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Controlled access BAM not working; BlobFilehandleWrapper copy not needed & contains buggy typo #101

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GFJHogue opened this issue Sep 10, 2020 · 0 comments · Fixed by #102
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@GFJHogue
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BlobFilehandleWrapper module code was copied from JBrowse in #98 along with others to modify file retrieval code to support GDC authentication token.

As I pointed out in the PR, BlobFilehandleWrapper seemed unnecessary to copy since it appeared to be unchanged from the original.

It turns out the return statement here was changed (probably for some local testing?) and breaks BAM retrieval in the @gmod/bam code:
https://github.com/LincolnSteinLab/gdc-viewer/blob/develop/gdc-viewer/js/Model/BlobFilehandleWrapper.js#L14
https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Model/BlobFilehandleWrapper.js#L14
https://github.com/GMOD/bam-js/blob/master/src/bamFile.ts#L114

Best fix is to delete BlobFilehandleWrapper copy and use the JBrowse version.

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