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Fix for CRAM regularizing failing #1367

merged 5 commits into from May 21, 2019


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commented May 21, 2019

Currently there are examples of CRAM name regularizing failing due to interaction with the sequence stores

  • We have a CRAM using nomenclature MT
  • The FASTA is using nomenclature MT
  • The system internal to CRAM uses name regularization and makes this chrm
  • Then it requests chrm from the seqFetch callback, at which point it fails

When it gets to the seq store, there is differing behavior depending on seqStore

  1. The IndexedFasta does not use the query name, it uses, so it actually works
  2. The SequenceChunks does something called compareReferenceSequence(, query.ref) and if this is 0, then it queries with there was a bug with this that resulted in MT getting double regularized though so it went from MT->chrm->chr
  3. The TwoBit only uses query name

The fix here is to avoid the regularization failure and make the behavior across sequence stores more consistent

@cmdcolin cmdcolin changed the base branch from master to dev May 21, 2019

@cmdcolin cmdcolin force-pushed the regularize_properly branch from 8ceefc1 to 7fb2ccc May 21, 2019


rbuels approved these changes May 21, 2019

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dude good catch. just the one question

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@cmdcolin cmdcolin merged commit 3ddd394 into dev May 21, 2019

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@cmdcolin cmdcolin deleted the regularize_properly branch Jun 13, 2019

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