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feat: Additional interval joins implementations #169

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feat: Additional interval joins implementations #169

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274077e
interval join structures
Wychowany Jan 28, 2022
6fe33ef
add lacking files
Wychowany Jan 28, 2022
9c8c473
add tests for joins
Wychowany Feb 2, 2022
4361fa4
change invalidIndex condition
Wychowany Aug 22, 2022
298e641
add domains param
Wychowany Aug 22, 2022
fe41866
domainsNum + documentation
Wychowany Aug 25, 2022
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18 changes: 17 additions & 1 deletion page/content/en/docs/Algorithms/join.md
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Expand Up @@ -73,4 +73,20 @@ parameter. There are 2 prerequisites:

2. node class used for storing intervals must extend `org.biodatageeks.sequila.rangejoins.methods.base.BaseNode[V]`

Both Scala and Java classes are supported. Please use default interval tree implementation for reference.
Both Scala and Java classes are supported. Please use default interval tree implementation for reference.

---
title: "Available custom interval structures"
linkTitle: "Available custom interval structures"
weight: 3
description: >
Custom interval structures
---
| Structure | spark.biodatageeks.rangejoin.intervalHolderClass | Reference |
|-----------------------------------------|-----------------|------------------------------------------------------------------------------------|
| Nested Containment List | org.biodatageeks.sequila.rangejoins.exp.nclist.NCList | [link](https://academic.oup.com/bioinformatics/article/23/11/1386/199545) |
| Augmented Interval List | org.biodatageeks.sequila.rangejoins.exp.ailist.AIList | [link](https://academic.oup.com/bioinformatics/article/35/23/4907/5509521) |
| Implicit Interval Tree | org.biodatageeks.sequila.rangejoins.exp.iit.IITree | [link](https://pubmed.ncbi.nlm.nih.gov/32966548/)|
| Implicit Interval Tree With Interpolation Index | org.biodatageeks.sequila.rangejoins.exp.iitii.ImplicitIntervalTreeWithInterpolationIndex | [link](https://github.com/mlin/iitii) |


3 changes: 2 additions & 1 deletion page/content/en/docs/Configuration/join.md
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Expand Up @@ -12,4 +12,5 @@ description: >
|spark.biodatageeks.rangejoin.maxBroadcastSize| 0.1*spark.driver.memory| The maximum allowed size of the broadcasted intverval structure which is used by the SeQuiLa's optimizer to chose interval join [algorithm](http://biodatageeks.ii.pw.edu.pl/sequila/architecture/architecture.html#optimizations).|
|spark.biodatageeks.rangejoin.maxGap| 0 | The maximum gap between between regions |
|spark.biodatageeks.rangejoin.minOverlap| 1 | The minimal length of the overlap between regions |
|spark.biodatageeks.rangejoin.intervalHolderClass|[`IntervalTreeRedBlack`](https://github.com/biodatageeks/sequila/blob/master/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/IntervalTree/IntervalTreeRedBlack.java)| [Pluggable](/sequila/docs/algorithms/join/#custom-interval-structure) mechanism for implementing custom interval structures.|
|spark.biodatageeks.rangejoin.intervalHolderClass|[`IntervalTreeRedBlack`](https://github.com/biodatageeks/sequila/blob/master/src/main/scala/org/biodatageeks/sequila/rangejoins/methods/IntervalTree/IntervalTreeRedBlack.java)| [Pluggable](/sequila/docs/algorithms/join/#custom-interval-structure) mechanism for implementing custom interval structures.|
|spark.biodatageeks.rangejoin.iitii.domainsNum|floor(dataset.count/4880)| Parameter of the ImplicitIntervalTreeWithInterpolationIndex structure to explicitly provide number of domains that the dataset is divided into. It indicates the number of interpolation functions that are being used during intersection. |
4 changes: 2 additions & 2 deletions src/main/scala/org/biodatageeks/sequila/pileup/model/AlignmentsRDD.scala
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Expand Up @@ -200,7 +200,7 @@ case class AlignmentsRDD(rdd: RDD[SAMRecord]) {
.sqlContext
.setConf(InternalParams.AlignmentIntervals, "")
logger.info(s"Found ${boundsOverlappingReads.length} overlapping reads")
val tree = new IntervalHolderChromosome[TruncRead](boundsOverlappingReads, "org.biodatageeks.sequila.rangejoins.methods.IntervalTree.IntervalTreeRedBlack")
val tree = new IntervalHolderChromosome[TruncRead](boundsOverlappingReads, "org.biodatageeks.sequila.rangejoins.methods.IntervalTree.IntervalTreeRedBlack", Map[String,String]())
PartitionUtils.getAdjustedPartitionBounds(lowerBounds, tree, conf, contigs)
}

Expand Down Expand Up @@ -236,4 +236,4 @@ case class AlignmentsRDD(rdd: RDD[SAMRecord]) {
}
(adjustedAlignments, normBroadcastBounds)
}
}
}
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