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Build up reference information during cigar processing #233

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merged 1 commit into from May 6, 2014

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arahuja commented Apr 28, 2014

This PR is to track more reference information during the cigar processing.

Currently, RichADAMRecord parses the Cigar string to extract the reference position (as a Long).
This:

  • Also captures the reference base, cigar element, and cigar offset (which will allow for us to not reparse the cigar string when building pileups)
  • Change reference position to be an instance of ReferencePosition (and changes the overlaps function to check other ReferencePosition ensuring a contigName check (resolving #113))

Also, this removes ReferenceLocation in favor of ReferencePosition as they had duplicate functionality

Noted issues:

  • This has overlaps with #230 slightly
  • This still uses the current Cigar processing from samtools, there was some talk of removing this dependency
  • DecadentRead vs RichAdamRecord do we want to merge or distinguish these more?
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fnothaft Apr 28, 2014

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+1, looks good!

  • This still uses the current Cigar processing from samtools, there was some talk of removing this dependency

I've been speaking with the UCSC folks about this. I'm hoping to have a design document/writeup for this approach by the end of the week.

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fnothaft commented Apr 28, 2014

+1, looks good!

  • This still uses the current Cigar processing from samtools, there was some talk of removing this dependency

I've been speaking with the UCSC folks about this. I'm hoping to have a design document/writeup for this approach by the end of the week.

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AmplabJenkins Apr 28, 2014

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/306/

AmplabJenkins commented Apr 28, 2014

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/306/

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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/307/

AmplabJenkins commented Apr 28, 2014

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/307/

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nealsid Apr 28, 2014

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Sorry to be a commit history nag but can you move some of the PR description over to the git commit message?

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nealsid commented Apr 28, 2014

Sorry to be a commit history nag but can you move some of the PR description over to the git commit message?

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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/308/

AmplabJenkins commented Apr 28, 2014

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/308/

capture reference base, cigar element, and cigar offset during cigar …
…processing; remove reference location in favor of reference position
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arahuja May 6, 2014

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Rebased after #230 merged in.

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arahuja commented May 6, 2014

Rebased after #230 merged in.

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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/317/

AmplabJenkins commented May 6, 2014

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/317/

massie added a commit that referenced this pull request May 6, 2014

Merge pull request #233 from hammerlab/refpos-reconcile
Build up reference information during cigar processing

@massie massie merged commit aca27a4 into bigdatagenomics:master May 6, 2014

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massie May 6, 2014

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Thanks, Arun!

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massie commented May 6, 2014

Thanks, Arun!

@arahuja arahuja deleted the hammerlab:refpos-reconcile branch May 6, 2014

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