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Add left normalization of INDELs as an RDD level primitive #1709

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fnothaft opened this issue Sep 5, 2017 · 1 comment
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Add left normalization of INDELs as an RDD level primitive #1709

fnothaft opened this issue Sep 5, 2017 · 1 comment
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enhancement
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0.23.0

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@fnothaft
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fnothaft commented Sep 5, 2017

Currently, to left normalize INDELs, you have to do full realignment. The raw normalization routines are private to ADAM.
@fnothaft fnothaft added this to the 0.23.0 milestone Sep 5, 2017
@fnothaft fnothaft self-assigned this Sep 5, 2017
@fnothaft fnothaft mentioned this issue Sep 5, 2017
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heuermh commented Sep 5, 2017

+1

fnothaft added a commit to fnothaft/adam that referenced this issue Sep 6, 2017
@fnothaft
[ADAM-1709] Add ability to left normalize reads containing INDELs.
8fcb03f 
Resolves bigdatagenomics#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 mentioned this issue Sep 6, 2017
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heuermh pushed a commit that referenced this issue Sep 6, 2017
@fnothaft @heuermh
[ADAM-1709] Add ability to left normalize reads containing INDELs.
28bbb48 
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.
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