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[AVOCADO-254] Open PrefilterReads up for external use.
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Resolves #254. Also drops the need to specify whether contig names follow GRCh
or UCSC conventions.
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@fnothaft
fnothaft committed Sep 4, 2017
1 parent e2a1b77 commit e3f4a3d
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Showing 2 changed files with 41 additions and 126 deletions.
21 changes: 7 additions & 14 deletions avocado-core/src/main/scala/org/bdgenomics/avocado/util/PrefilterReads.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -21,12 +21,7 @@ import org.bdgenomics.adam.models.SequenceDictionary
import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD
import org.bdgenomics.formats.avro.AlignmentRecord

private[avocado] trait PrefilterReadsArgs extends Serializable {

/**
* True if a genome build is not from the Genome Reference Consortium.
*/
var isNotGrc: Boolean
trait PrefilterReadsArgs extends Serializable {

/**
* True if we want to restrict our reads to the autosomal chromosomes.
Expand Down Expand Up @@ -58,7 +53,7 @@ private[avocado] trait PrefilterReadsArgs extends Serializable {
* Reifies an input AlignmentRecordRDD down to the contigs and reads we
* want to genotype.
*/
private[avocado] object PrefilterReads extends Serializable {
object PrefilterReads extends Serializable {

/**
* Filters out reads and contigs that should not be processed.
Expand Down Expand Up @@ -92,20 +87,18 @@ private[avocado] object PrefilterReads extends Serializable {
* should be kept.
*/
protected[util] def contigFilterFn(args: PrefilterReadsArgs): (String => Boolean) = {
val fns = if (args.isNotGrc) {
Iterable(filterNonGrcAutosome(_), filterNonGrcSex(_), filterNonGrcMitochondrial(_))
} else {
Iterable(filterGrcAutosome(_), filterGrcSex(_), filterGrcMitochondrial(_))
}
val filteredFns = Iterable(true, !args.autosomalOnly, args.keepMitochondrialChromosome)
val fns = Iterable(filterNonGrcAutosome(_), filterNonGrcSex(_), filterNonGrcMitochondrial(_),
filterGrcAutosome(_), filterGrcSex(_), filterGrcMitochondrial(_))
val filteredFns = Iterable(true, !args.autosomalOnly, args.keepMitochondrialChromosome,
true, !args.autosomalOnly, args.keepMitochondrialChromosome)
.zip(fns)
.filter(_._1)
.map(_._2)

assert(filteredFns.nonEmpty)

def filterFn(s: String): Boolean = {
filteredFns.map(fn => fn(s)).reduce(_ || _)
filteredFns.exists(fn => fn(s))
}

filterFn(_)
Expand Down
146 changes: 34 additions & 112 deletions avocado-core/src/test/scala/org/bdgenomics/avocado/util/PrefilterReadsSuite.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,7 @@ import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD
import org.bdgenomics.formats.avro.AlignmentRecord

case class TestPrefilterReadsArgs(var isNotGrc: Boolean = false,
var autosomalOnly: Boolean = false,
case class TestPrefilterReadsArgs(var autosomalOnly: Boolean = false,
var keepMitochondrialChromosome: Boolean = false,
var keepDuplicates: Boolean = true,
var minMappingQuality: Int = -1,
Expand Down Expand Up @@ -119,30 +118,18 @@ class PrefilterReadsSuite extends AvocadoFunSuite {
testChromosomeHelper(PrefilterReads.filterNonGrcMitochondrial, 7)
}

test("filter autosomal chromosomes with grc names from generator") {
testChromosomeHelper(PrefilterReads.contigFilterFn(TestPrefilterReadsArgs(autosomalOnly = true)), 0)
test("filter autosomal chromosomes from generator") {
testChromosomeHelperSet(PrefilterReads.contigFilterFn(TestPrefilterReadsArgs(autosomalOnly = true)), Set(0, 1))
}

test("filter autosomal + sex chromosomes with grc names from generator") {
testChromosomeHelperSet(PrefilterReads.contigFilterFn(TestPrefilterReadsArgs()), Set(0, 2, 4))
test("filter autosomal + sex chromosomes from generator") {
testChromosomeHelperSet(PrefilterReads.contigFilterFn(TestPrefilterReadsArgs()), Set(0, 1,
2, 3,
4, 5))
}

test("filter all chromosomes with grc names from generator") {
testChromosomeHelperSet(PrefilterReads.contigFilterFn(TestPrefilterReadsArgs(keepMitochondrialChromosome = true)), Set(0, 2, 4, 6))
}

test("filter autosomal chromosomes with hg names from generator") {
testChromosomeHelper(PrefilterReads.contigFilterFn(TestPrefilterReadsArgs(isNotGrc = true,
autosomalOnly = true)), 1)
}

test("filter autosomal + sex chromosomes with hg names from generator") {
testChromosomeHelperSet(PrefilterReads.contigFilterFn(TestPrefilterReadsArgs(isNotGrc = true)), Set(1, 3, 5))
}

test("filter all chromosomes with hg names from generator") {
testChromosomeHelperSet(PrefilterReads.contigFilterFn(TestPrefilterReadsArgs(isNotGrc = true,
keepMitochondrialChromosome = true)), Set(1, 3, 5, 7))
test("filter all chromosomes from generator") {
testChromosomeHelperSet(PrefilterReads.contigFilterFn(TestPrefilterReadsArgs(keepMitochondrialChromosome = true)), Set(0, 1, 2, 3, 4, 5, 6, 7))
}

val reads = Seq(AlignmentRecord.newBuilder()
Expand Down Expand Up @@ -172,66 +159,34 @@ class PrefilterReadsSuite extends AvocadoFunSuite {
.foreach(p => assertIdx(p._2, p._1))
}

test("filter reads mapped to autosomal chromosomes with grc names from generator") {
testReadHelperSet(TestPrefilterReadsArgs(autosomalOnly = true), Set(8, 16))
test("filter reads mapped to autosomal chromosomes from generator") {
testReadHelperSet(TestPrefilterReadsArgs(autosomalOnly = true), Set(8, 9, 16, 17))
}

test("filter reads mapped to autosomal + sex chromosomes with grc names from generator") {
testReadHelperSet(TestPrefilterReadsArgs(), Set(8, 10, 12, 16, 18, 20))
test("filter reads mapped to autosomal + sex chromosomes from generator") {
testReadHelperSet(TestPrefilterReadsArgs(), Set(8, 9, 10, 11, 12, 13,
16, 17, 18, 19, 20, 21))
}

test("filter reads mapped to all chromosomes with grc names from generator") {
test("filter reads mapped to all chromosomes from generator") {
testReadHelperSet(TestPrefilterReadsArgs(keepMitochondrialChromosome = true),
Set(8, 10, 12, 14, 16, 18, 20, 22))
}

test("filter reads mapped to autosomal chromosomes with hg names from generator") {
testReadHelperSet(TestPrefilterReadsArgs(isNotGrc = true,
autosomalOnly = true), Set(9, 17))
}

test("filter reads mapped to autosomal + sex chromosomes with hg names from generator") {
testReadHelperSet(TestPrefilterReadsArgs(isNotGrc = true), Set(9, 11, 13, 17, 19, 21))
Set(8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23))
}

test("filter reads mapped to all chromosomes with hg names from generator") {
testReadHelperSet(TestPrefilterReadsArgs(isNotGrc = true,
keepMitochondrialChromosome = true),
Set(9, 11, 13, 15, 17, 19, 21, 23))
}

test("filter reads uniquely mapped to autosomal chromosomes with grc names from generator") {
test("filter reads uniquely mapped to autosomal chromosomes from generator") {
testReadHelperSet(TestPrefilterReadsArgs(keepDuplicates = false,
autosomalOnly = true), Set(16))
autosomalOnly = true), Set(16, 17))
}

test("filter reads uniquely mapped to autosomal + sex chromosomes with grc names from generator") {
test("filter reads uniquely mapped to autosomal + sex chromosomes from generator") {
testReadHelperSet(TestPrefilterReadsArgs(keepDuplicates = false),
Set(16, 18, 20))
}

test("filter reads uniquely mapped to all chromosomes with grc names from generator") {
testReadHelperSet(TestPrefilterReadsArgs(keepDuplicates = false,
keepMitochondrialChromosome = true),
Set(16, 18, 20, 22))
}

test("filter reads uniquely mapped to autosomal chromosomes with hg names from generator") {
testReadHelperSet(TestPrefilterReadsArgs(keepDuplicates = false,
isNotGrc = true,
autosomalOnly = true), Set(17))
Set(16, 17, 18, 19, 20, 21))
}

test("filter reads uniquely mapped to autosomal + sex chromosomes with hg names from generator") {
test("filter reads uniquely mapped to all chromosomes from generator") {
testReadHelperSet(TestPrefilterReadsArgs(keepDuplicates = false,
isNotGrc = true), Set(17, 19, 21))
}

test("filter reads uniquely mapped to all chromosomes with hg names from generator") {
testReadHelperSet(TestPrefilterReadsArgs(keepDuplicates = false,
isNotGrc = true,
keepMitochondrialChromosome = true),
Set(17, 19, 21, 23))
Set(16, 17, 18, 19, 20, 21, 22, 23))
}

val sequences = new SequenceDictionary(contigNames.map(cn => SequenceRecord(cn, 10L))
Expand All @@ -246,64 +201,31 @@ class PrefilterReadsSuite extends AvocadoFunSuite {
assert(filteredRdd.sequences.records.size === numContigs)
}

sparkTest("filter rdd of reads mapped to autosomal chromosomes with grc names from generator") {
testRdd(TestPrefilterReadsArgs(autosomalOnly = true), 2, 1)
}

sparkTest("filter rdd of reads mapped to autosomal + sex chromosomes with grc names from generator") {
testRdd(TestPrefilterReadsArgs(), 6, 3)
sparkTest("filter rdd of reads mapped to autosomal chromosomes from generator") {
testRdd(TestPrefilterReadsArgs(autosomalOnly = true), 4, 2)
}

sparkTest("filter rdd of reads mapped to all chromosomes with grc names from generator") {
testRdd(TestPrefilterReadsArgs(keepMitochondrialChromosome = true), 8, 4)
sparkTest("filter rdd of reads mapped to autosomal + sex chromosomes from generator") {
testRdd(TestPrefilterReadsArgs(), 12, 6)
}

sparkTest("filter rdd of reads mapped to autosomal chromosomes with hg names from generator") {
testRdd(TestPrefilterReadsArgs(isNotGrc = true,
autosomalOnly = true), 2, 1)
}

sparkTest("filter rdd of reads mapped to autosomal + sex chromosomes with hg names from generator") {
testRdd(TestPrefilterReadsArgs(isNotGrc = true), 6, 3)
}

sparkTest("filter rdd of reads mapped to all chromosomes with hg names from generator") {
testRdd(TestPrefilterReadsArgs(isNotGrc = true,
keepMitochondrialChromosome = true),
8, 4)
sparkTest("filter rdd of reads mapped to all chromosomes from generator") {
testRdd(TestPrefilterReadsArgs(keepMitochondrialChromosome = true), 16, 8)
}

sparkTest("filter rdd of reads uniquely mapped to autosomal chromosomes with grc names from generator") {
sparkTest("filter rdd of reads uniquely mapped to autosomal chromosomes from generator") {
testRdd(TestPrefilterReadsArgs(keepDuplicates = false,
autosomalOnly = true), 1, 1)
autosomalOnly = true), 2, 2)
}

sparkTest("filter rdd of reads uniquely mapped to autosomal + sex chromosomes with grc names from generator") {
sparkTest("filter rdd of reads uniquely mapped to autosomal + sex chromosomes from generator") {
testRdd(TestPrefilterReadsArgs(keepDuplicates = false),
3, 3)
}

sparkTest("filter rdd of reads uniquely mapped to all chromosomes with grc names from generator") {
testRdd(TestPrefilterReadsArgs(keepDuplicates = false,
keepMitochondrialChromosome = true),
4, 4)
}

sparkTest("filter rdd of reads uniquely mapped to autosomal chromosomes with hg names from generator") {
testRdd(TestPrefilterReadsArgs(keepDuplicates = false,
isNotGrc = true,
autosomalOnly = true), 1, 1)
}

sparkTest("filter rdd of reads uniquely mapped to autosomal + sex chromosomes with hg names from generator") {
testRdd(TestPrefilterReadsArgs(keepDuplicates = false,
isNotGrc = true), 3, 3)
6, 6)
}

sparkTest("filter rdd of reads uniquely mapped to all chromosomes with hg names from generator") {
sparkTest("filter rdd of reads uniquely mapped to all chromosomes from generator") {
testRdd(TestPrefilterReadsArgs(keepDuplicates = false,
isNotGrc = true,
keepMitochondrialChromosome = true),
4, 4)
8, 8)
}
}

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