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BwaSpark does inappropriate validation of bam sequence dictionary against reference #2121

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lbergelson opened this issue Aug 25, 2016 · 1 comment
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BwaSpark does inappropriate validation of bam sequence dictionary against reference #2121

lbergelson opened this issue Aug 25, 2016 · 1 comment
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bug BWA Spark
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Engine-2Q2018

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@lbergelson
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Since it's realigning the bam, it shouldn't validate that the file to be aligned already matches the header. This makes it impossible to realign to a different reference or align a headerless file.

This can currently be worked around using --disableSequenceDictionaryValidation
@lbergelson lbergelson added the bug label Aug 25, 2016
@droazen droazen added this to the 4.0 release milestone Mar 22, 2017
@droazen droazen modified the milestones: Engine-4.0, Engine-4.0.1.0, Engine-4.1 Jan 16, 2018
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This was closed by #4308

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bug BWA Spark
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