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Remove the IterableThreadLocal class and use the one in commons #730

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Oct 19, 2021
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Remove the IterableThreadLocal class and use the one in commons #730

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19 changes: 1 addition & 18 deletions src/main/scala/com/fulcrumgenomics/umi/ConsensusCallingIterator.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -24,12 +24,11 @@

package com.fulcrumgenomics.umi

import java.util.concurrent.ForkJoinPool

import com.fulcrumgenomics.FgBioDef._
import com.fulcrumgenomics.bam.api.SamRecord
import com.fulcrumgenomics.commons.async.AsyncIterator
import com.fulcrumgenomics.commons.util.LazyLogging
import com.fulcrumgenomics.commons.util.Threads.IterableThreadLocal
import com.fulcrumgenomics.umi.UmiConsensusCaller.SimpleRead
import com.fulcrumgenomics.util.ProgressLogger

Expand Down Expand Up @@ -105,22 +104,6 @@ class ConsensusCallingIterator[ConsensusRead <: SimpleRead](sourceIterator: Iter
override def next(): SamRecord = this.iter.next
}

// TODO: migrate to the commons version of this class after the next commons release
// TODO: https://github.com/fulcrumgenomics/commons/pull/51
private class IterableThreadLocal[A](factory: () => A) extends ThreadLocal[A] with Iterable[A] {
private val all = new java.util.concurrent.ConcurrentLinkedQueue[A]()

override def initialValue(): A = {
val a = factory()
all.add(a)
a
}

/** Care should be taken accessing the iterator since objects may be in use by other threads. */
def iterator: Iterator[A] = all.iterator
}


/** Groups consecutive records based on a method to group records. */
private class SamRecordGroupedIterator[Key](sourceIterator: Iterator[SamRecord],
toKey: SamRecord => Key) extends Iterator[Seq[SamRecord]] {
Expand Down