bigdatagenomics / adam / 2964

DEFAULT BRANCH: master
Ran
Jobs 8
Files 140
Run time 2min
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jenkins

heuermh 
[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.

10 of 10 new or added lines in 1 file covered. (100.0%)

6241 of 7470 relevant lines covered (83.55%)

6.64 hits per line

Coverage Regressions

Lines Coverage ∆ File
6
100.0
 adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/Features.scala
5
100.0
 adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
3
100.0
 adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala
3
100.0
 adam-cli/src/main/scala/org/bdgenomics/adam/cli/View.scala
2
100.0
 adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
1
100.0
 adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtils.scala
1
100.0
 adam-core/src/main/scala/org/bdgenomics/adam/models/MdTag.scala
1
100.0
 adam-core/src/main/scala/org/bdgenomics/adam/models/RecordGroupDictionary.scala
1
100.0
 adam-core/src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala
1
100.0
 adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureParser.scala
1
100.0
 adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala
1
100.0
 adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala
1
100.0
 adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala
1
100.0
 adam-core/src/main/scala/org/bdgenomics/adam/util/IndexedFastaFile.scala
Jobs
ID Job ID Ran Files Coverage
1 2964.1 0
83.04
2 2964.2 0
83.05
3 2964.3 0
83.04
4 2964.4 0
83.05
5 2964.5 0
83.05
6 2964.6 0
83.05
7 2964.7 0
83.04
8 2964.8 0
83.04
Source Files on build 2964
Detailed source file information is not available for this build.