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[ADAM-1362] Fixing issue where FromKnowns consensus model fails if no reads hit a target. #1363

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merged 1 commit into from Jan 23, 2017
Merged

[ADAM-1362] Fixing issue where FromKnowns consensus model fails if no reads hit a target. #1363

merged 1 commit into from Jan 23, 2017

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fnothaft
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Fixes #1362:

  • Adding ConsensusGeneratorFromKnownsSuite.
  • ConsensusGeneratorFromKnowns drops any targets that did not get hit with any reads, instead of trying to identify the full reference region overlapped by reads. While this case (target with no reads) cannot happen in the FromReads consensus model, it can happen in the FromKnowns model (e.g., use all known INDELs from 1000G with a WES dataset).
  • Additionally, tracked down a minor off by one bug in RealignIndels that caused one index in the consensus sequence to not get tested. This could cause reads that aligned to the end of the target to not get realigned.
  • To improve legibility, broke up a set of long lines in RealignIndels.

@fnothaft
[ADAM-1362] Fixing issue where FromKnowns consensus model fails if no…
43c56d1 
… reads hit a target.

Fixes bigdatagenomics#1362:

* Adding ConsensusGeneratorFromKnownsSuite.
* ConsensusGeneratorFromKnowns drops any targets that did not get hit with any
  reads, instead of trying to identify the full reference region overlapped by
  reads. While this case (target with no reads) cannot happen in the FromReads
  consensus model, it can happen in the FromKnowns model (e.g., use all known
  INDELs from 1000G with a WES dataset).
* Additionally, tracked down a minor off by one bug in RealignIndels that caused
  one index in the consensus sequence to not get tested. This could cause reads
  that aligned to the end of the target to not get realigned.
* To improve legibility, broke up a set of long lines in RealignIndels.
@fnothaft fnothaft added this to the 0.21.1 milestone Jan 23, 2017
@fnothaft fnothaft requested a review from heuermh January 23, 2017 06:25
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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1748/
Test PASSed.

fnothaft added a commit to fnothaft/avocado that referenced this pull request Jan 23, 2017
@fnothaft
[AVOCADO-200] Feed assembled variants to INDEL realigner.
9c7094c 
Resolves bigdatagenomics#200. Depends on bigdatagenomics/adam#1363.

* Adds a ConsensusRealigner that uses the main Realigner to realign reads,
  which are then fed into the variant discovery engine with loose filters. Any
  INDEL variants that are discovered are then fed in to ADAM's INDEL realignment
  engine as known INDELs.
* Uses this realignment mode in the BiallelicGenotyperSuite to clean up a
  previously failing test.
* Adds this to the Reassemble CLI as a `-use_consensus_realigner` switch.
@heuermh heuermh merged commit 00dc230 into bigdatagenomics:master Jan 23, 2017
@heuermh
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heuermh commented Jan 23, 2017

Thank you, @fnothaft!

fnothaft added a commit to fnothaft/avocado that referenced this pull request Jan 25, 2017
@fnothaft
[AVOCADO-200] Feed assembled variants to INDEL realigner.
908349d 
Resolves bigdatagenomics#200. Depends on bigdatagenomics/adam#1363.

* Adds a ConsensusRealigner that uses the main Realigner to realign reads,
  which are then fed into the variant discovery engine with loose filters. Any
  INDEL variants that are discovered are then fed in to ADAM's INDEL realignment
  engine as known INDELs.
* Uses this realignment mode in the BiallelicGenotyperSuite to clean up a
  previously failing test.
* Adds this to the Reassemble CLI as a `-use_consensus_realigner` switch.
fnothaft added a commit to fnothaft/avocado that referenced this pull request Feb 28, 2017
@fnothaft
[AVOCADO-200] Feed assembled variants to INDEL realigner.
57a7e64 
Resolves bigdatagenomics#200. Depends on bigdatagenomics/adam#1363.

* Adds a ConsensusRealigner that uses the main Realigner to realign reads,
  which are then fed into the variant discovery engine with loose filters. Any
  INDEL variants that are discovered are then fed in to ADAM's INDEL realignment
  engine as known INDELs.
* Uses this realignment mode in the BiallelicGenotyperSuite to clean up a
  previously failing test.
* Adds this to the Reassemble CLI as a `-use_consensus_realigner` switch.
fnothaft added a commit to fnothaft/avocado that referenced this pull request Mar 1, 2017
@fnothaft
[AVOCADO-200] Feed assembled variants to INDEL realigner.
e96ddea 
Resolves bigdatagenomics#200. Depends on bigdatagenomics/adam#1363.

* Adds a ConsensusRealigner that uses the main Realigner to realign reads,
  which are then fed into the variant discovery engine with loose filters. Any
  INDEL variants that are discovered are then fed in to ADAM's INDEL realignment
  engine as known INDELs.
* Uses this realignment mode in the BiallelicGenotyperSuite to clean up a
  previously failing test.
* Adds this to the Reassemble CLI as a `-use_consensus_realigner` switch.
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@heuermh heuermh heuermh approved these changes

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