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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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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 the enhancement label Sep 5, 2017

@fnothaft fnothaft added this to the 0.23.0 milestone Sep 5, 2017

@fnothaft fnothaft self-assigned this Sep 5, 2017

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heuermh 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

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

@heuermh heuermh closed this in #1711 Sep 6, 2017

heuermh added a commit that referenced this issue Sep 6, 2017

[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.

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

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