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Estimate contig lengths in SequenceDictionary for BED, GFF3, GTF, and NarrowPeak feature formats #1411

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heuermh commented Mar 1, 2017

Split from #1378 for easier review and merge. Fixes #1409, fixes #1410.

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Coverage Status

Coverage decreased (-0.1%) to 76.161% when pulling e74c392 on heuermh:feature-seq-dict into eb4aa6c on bigdatagenomics:master.

coveralls commented Mar 1, 2017

Coverage Status

Coverage decreased (-0.1%) to 76.161% when pulling e74c392 on heuermh:feature-seq-dict into eb4aa6c on bigdatagenomics:master.

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Coverage Status

Coverage decreased (-0.1%) to 76.161% when pulling e74c392 on heuermh:feature-seq-dict into eb4aa6c on bigdatagenomics:master.

Coverage Status

Coverage decreased (-0.1%) to 76.161% when pulling e74c392 on heuermh:feature-seq-dict into eb4aa6c on bigdatagenomics:master.

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Test PASSed.
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@fnothaft

Small nits; otherwise LGTM!

Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureRDD.scala
// create sequence records with length max(start, end) + 1L
val sequenceRecords = rdd
.keyBy(_.getContigName)
.map(kv => (kv._1, Math.max(kv._2.getStart, kv._2.getEnd) + 1L))

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fnothaft Mar 2, 2017

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Small preference, but I'd rather import scala.math.max and change Math.max -> max.

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fnothaft Mar 2, 2017

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Small preference, but I'd rather import scala.math.max and change Math.max -> max.

Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureRDD.scala
val sequenceRecords = rdd
.keyBy(_.getContigName)
.map(kv => (kv._1, Math.max(kv._2.getStart, kv._2.getEnd) + 1L))
.reduceByKey(math.max(_, _))

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fnothaft Mar 2, 2017

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Same here math.max(_, _) -> max

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fnothaft Mar 2, 2017

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Same here math.max(_, _) -> max

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Coverage Status

Coverage decreased (-0.1%) to 76.161% when pulling d77a184 on heuermh:feature-seq-dict into eb4aa6c on bigdatagenomics:master.

coveralls commented Mar 2, 2017

Coverage Status

Coverage decreased (-0.1%) to 76.161% when pulling d77a184 on heuermh:feature-seq-dict into eb4aa6c on bigdatagenomics:master.

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Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1824/
Test PASSed.

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1824/
Test PASSed.

@fnothaft fnothaft merged commit 6ee0b8b into bigdatagenomics:master Mar 3, 2017

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coverage/coveralls Coverage decreased (-0.1%) to 76.161%
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fnothaft Mar 3, 2017

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Merged! Thanks @heuermh!

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fnothaft commented Mar 3, 2017

Merged! Thanks @heuermh!

@heuermh heuermh deleted the heuermh:feature-seq-dict branch Mar 5, 2017

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