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Fix reading of CRAM headers on GCS #2463

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tomwhite opened this issue Mar 15, 2017 · 1 comment
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Fix reading of CRAM headers on GCS #2463

tomwhite opened this issue Mar 15, 2017 · 1 comment
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Currently CRAM files cannot be read from GCS since ReadsSparkSource#getHeader() does not set the reference, which is needed for reading CRAM.

To do this, provide a SamReaderFactory with a referenceSequence() set on it when you construct your ReadsDataSource. However, htsjdk does not support Path in this API, so that will need updating first.
@tomwhite tomwhite mentioned this issue Mar 15, 2017
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@droazen droazen added this to the beta milestone Mar 17, 2017
@droazen droazen changed the title Read CRAM headers on GCS Fix reading of CRAM headers on GCS Mar 17, 2017
@cmnbroad cmnbroad mentioned this issue Mar 23, 2017
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@droazen droazen modified the milestones: 4.0 release, beta May 30, 2017
@tomwhite tomwhite assigned cmnbroad and unassigned tomwhite Jun 13, 2017
@droazen droazen removed this from the Engine-4.0 milestone Oct 17, 2017
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Fixed in Disq

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