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[ADAM-1709] Add ability to left normalize reads containing INDELs. #1711

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merged 1 commit into from Sep 6, 2017

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fnothaft commented Sep 6, 2017

Resolves #1709. Opens protection on main method in NormalizationUtils to be package-private to org.bdgenomics.adam. Adds code to AlignmentRecordRDD exposing INDEL normalization as a transformation.

[ADAM-1709] Add ability to left normalize reads containing INDELs.
Resolves #1709. Opens protection on main method in NormalizationUtils to be
package-private to org.bdgenomics.adam. Adds code to AlignmentRecordRDD
exposing INDEL normalization as a transformation.

@fnothaft fnothaft added this to the 0.23.0 milestone Sep 6, 2017

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Coverage Status

Coverage increased (+0.08%) to 83.548% when pulling 8fcb03f on fnothaft:issues/1709-left-normalize-indels into 51efbaf on bigdatagenomics:master.

coveralls commented Sep 6, 2017

Coverage Status

Coverage increased (+0.08%) to 83.548% when pulling 8fcb03f on fnothaft:issues/1709-left-normalize-indels into 51efbaf on bigdatagenomics:master.

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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/2354/
Test PASSed.

AmplabJenkins commented Sep 6, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2354/
Test PASSed.

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heuermh approved these changes Sep 6, 2017

@heuermh heuermh merged commit 28bbb48 into bigdatagenomics:master Sep 6, 2017

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codacy/pr Not so good... This pull request quality could be better.
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coverage/coveralls Coverage increased (+0.08%) to 83.548%
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heuermh Sep 6, 2017

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Thank you, @fnothaft

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heuermh commented Sep 6, 2017

Thank you, @fnothaft

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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