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Bump htsjdk to 3.0.3 #884

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Bump htsjdk to 3.0.3 #884

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c810117
chore: bump htsjdk to 3.0.3
clintval Nov 16, 2022
585db08
fix: update JointVariantContextIterator to use locatable ordering
clintval Nov 16, 2022
ade04c6
fix!: remove VariantContextComparator entrypoint to JointVariantConte…
clintval Nov 16, 2022
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2 changes: 1 addition & 1 deletion build.sbt
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Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,7 @@ lazy val root = Project(id="fgbio", base=file("."))
"org.scala-lang.modules" %% "scala-xml" % "2.1.0",
"com.fulcrumgenomics" %% "commons" % "1.4.0",
"com.fulcrumgenomics" %% "sopt" % "1.1.0",
"com.github.samtools" % "htsjdk" % "2.24.1-26-ga38c78d-SNAPSHOT" excludeAll(htsjdkExcludes: _*),
"com.github.samtools" % "htsjdk" % "3.0.3" excludeAll(htsjdkExcludes: _*),
"org.apache.commons" % "commons-math3" % "3.6.1",
"com.beachape" %% "enumeratum" % "1.7.0",
"com.intel.gkl" % "gkl" % "0.8.8",
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28 changes: 9 additions & 19 deletions src/main/scala/com/fulcrumgenomics/vcf/JointVariantContextIterator.scala
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Expand Up @@ -24,57 +24,47 @@

package com.fulcrumgenomics.vcf

import com.fulcrumgenomics.coord.LocatableOrdering
import com.fulcrumgenomics.fasta.SequenceDictionary
import htsjdk.variant.variantcontext.{VariantContext, VariantContextComparator}

object JointVariantContextIterator {
def apply(iters: Seq[Iterator[VariantContext]],
dict: SequenceDictionary
): JointVariantContextIterator = {
new JointVariantContextIterator(
iters=iters,
dictOrComp = Left(dict)
)
new JointVariantContextIterator(iters = iters, dict = dict)
}

@deprecated("VariantContextComparator will no longer compare variant contexts on location alone.")
def apply(iters: Seq[Iterator[VariantContext]],
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@clintval clintval Nov 16, 2022 •
edited
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This entrypoint was never used in this codebase. And it is no longer possible to use VariantContextComparator since it compares variants beyond location alone (source). Seems like my only option is deprecation and raising an exception.

comp: VariantContextComparator
): JointVariantContextIterator = {
new JointVariantContextIterator(
iters=iters,
dictOrComp = Right(comp)
)
throw new NotImplementedError("VariantContextComparator class can no longer order variant contexts on location alone.")
}
}

/**
* Iterates over multiple variant context iterators such that we return a list of contexts for the union of sites
* across the iterators. If samples is given, we subset each variant context to just that sample.
*/
class JointVariantContextIterator private(iters: Seq[Iterator[VariantContext]],
dictOrComp: Either[SequenceDictionary, VariantContextComparator]
)
class JointVariantContextIterator private(iters: Seq[Iterator[VariantContext]], dict: SequenceDictionary)
extends Iterator[Seq[Option[VariantContext]]] {
import com.fulcrumgenomics.fasta.Converters.ToSAMSequenceDictionary

if (iters.isEmpty) throw new IllegalArgumentException("No iterators given")

private val iterators = iters.map(_.buffered)
private val comparator = dictOrComp match {
case Left(dict) => new VariantContextComparator(dict.asSam)
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@clintval clintval Nov 16, 2022 •
edited
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The class VariantContextComparator now compares more than just on location (source)

Searching the codebase, this was the only improper use of the new class (and unit tests were failing).

case Right(comp) => comp
}
private val ordering = LocatableOrdering(dict)

def hasNext: Boolean = iterators.exists(_.nonEmpty)

def next(): Seq[Option[VariantContext]] = {
val minCtx = iterators.filter(_.nonEmpty).map(_.head).sortWith {
case (left: VariantContext, right: VariantContext) => comparator.compare(left, right) < 0
case (left: VariantContext, right: VariantContext) => ordering.compare(left, right) < 0
}.head
// TODO: could use a TreeSet to store the iterators, examine the head of each iterator, then pop the iterator with the min,
// and add that iterator back in.
iterators.zipWithIndex.map { case(iter, idx) =>
if (iter.isEmpty || this.comparator.compare(minCtx, iter.head) != 0) None
iterators.map { iter =>
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The variable idx wasn't used and zipWithIndex is slower than mapping.

if (iter.isEmpty || ordering.compare(minCtx, iter.head) != 0) None
else Some(iter.next())
}
}
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