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CRAM should validate the SAM header against the reference being used #1244

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cmnbroad opened this issue Dec 19, 2018 · 0 comments
Open

CRAM should validate the SAM header against the reference being used #1244

cmnbroad opened this issue Dec 19, 2018 · 0 comments
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cmnbroad commented Dec 19, 2018 •
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When creating a CRAM file, the SAM header from the input is propagated to the output, but I don't think there is any checking to validate that the reference being used matches the sequence dictionary in the header. At a minimum we should issue a warning when this happens.

Somewhat related to #506.
@cmnbroad cmnbroad added the cram label Dec 19, 2018
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