Commit 58102415 authored by bow's avatar bow
Browse files

Rename Seqstat -> SeqStat

parent e4b0834e
......@@ -38,7 +38,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils
*
* @param root Configuration object for the pipeline
*/
class Seqstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
javaMainClass = getClass.getName
@Input(doc = "Input FASTQ", shortName = "input", required = true)
......@@ -76,16 +76,16 @@ object FqEncoding extends Enumeration {
val Unknown = Value(0, "Unknown")
}
object Seqstat extends ToolCommand {
def apply(root: Configurable, input: File, output: File): Seqstat = {
val seqstat = new Seqstat(root)
object SeqStat extends ToolCommand {
def apply(root: Configurable, input: File, output: File): SeqStat = {
val seqstat = new SeqStat(root)
seqstat.input = input
seqstat.output = new File(output, input.getName.substring(0, input.getName.lastIndexOf(".")) + ".seqstats.json")
seqstat
}
def apply(root: Configurable, fastqfile: File, outDir: String): Seqstat = {
val seqstat = new Seqstat(root)
def apply(root: Configurable, fastqfile: File, outDir: String): SeqStat = {
val seqstat = new SeqStat(root)
seqstat.input = fastqfile
seqstat.output = new File(outDir, fastqfile.getName.substring(0, fastqfile.getName.lastIndexOf(".")) + ".seqstats.json")
seqstat
......
......@@ -27,9 +27,9 @@ import org.testng.annotations.{ DataProvider, Test }
import scala.collection.JavaConverters._
class SeqstatTest extends TestNGSuite with MockitoSugar with Matchers {
class SeqStatTest extends TestNGSuite with MockitoSugar with Matchers {
import nl.lumc.sasc.biopet.tools.Seqstat._
import nl.lumc.sasc.biopet.tools.SeqStat._
import nl.lumc.sasc.biopet.tools.FqEncoding._
private def resourceFile(p: String): File =
......@@ -59,7 +59,7 @@ class SeqstatTest extends TestNGSuite with MockitoSugar with Matchers {
def testSeqCountReads(fqMock: FastqReader) = {
when(fqMock.iterator) thenReturn recordsOver("1", "2", "3", "4", "5")
val seqstat = Seqstat
val seqstat = SeqStat
val numReads = seqstat.seqStat(fqMock)
numReads shouldBe 5
}
......@@ -67,7 +67,7 @@ class SeqstatTest extends TestNGSuite with MockitoSugar with Matchers {
@Test(dataProvider = "mockReaderProvider", groups = Array("phredscore"), singleThreaded = true, dependsOnGroups = Array("read"))
def testEncodingDetectionSanger(fqMock: FastqReader) = {
val seqstat = Seqstat
val seqstat = SeqStat
seqstat.summarize()
seqstat.phredEncoding shouldBe Sanger
......@@ -76,7 +76,7 @@ class SeqstatTest extends TestNGSuite with MockitoSugar with Matchers {
@Test(dataProvider = "mockReaderProvider", groups = Array("nucleocount"), singleThreaded = true, dependsOnGroups = Array("phredscore"))
def testEncodingNucleotideCount(fqMock: FastqReader) = {
val seqstat = Seqstat
val seqstat = SeqStat
nucleotideHistoMap('N') shouldEqual 5
nucleotideHistoMap('A') shouldEqual 5
nucleotideHistoMap('C') shouldEqual 5
......@@ -87,7 +87,7 @@ class SeqstatTest extends TestNGSuite with MockitoSugar with Matchers {
@Test(dataProvider = "mockReaderProvider", groups = Array("basehistogram"), singleThreaded = true, dependsOnGroups = Array("nucleocount"))
def testEncodingBaseHistogram(fqMock: FastqReader) = {
val seqstat = Seqstat
val seqstat = SeqStat
baseHistogram(40) shouldEqual 5
baseHistogram(39) shouldEqual 10
baseHistogram(34) shouldEqual 15
......
......@@ -54,7 +54,7 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl.lumc.sasc.biopet.tools.BastyGenerateFasta,
nl.lumc.sasc.biopet.tools.MergeAlleles,
nl.lumc.sasc.biopet.tools.SamplesTsvToJson,
nl.lumc.sasc.biopet.tools.Seqstat,
nl.lumc.sasc.biopet.tools.SeqStat,
nl.lumc.sasc.biopet.tools.VepNormalizer,
nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed,
nl.lumc.sasc.biopet.tools.VcfWithVcf)
......
......@@ -22,7 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
import nl.lumc.sasc.biopet.core.{ SampleLibraryTag, BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.tools.Seqstat
import nl.lumc.sasc.biopet.tools.SeqStat
import nl.lumc.sasc.biopet.tools.FastqSync
class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
......@@ -186,14 +186,14 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
deps_R2 ::= R2.get
}
val seqstat_R1 = Seqstat(this, R1, outDir)
val seqstat_R1 = SeqStat(this, R1, outDir)
seqstat_R1.isIntermediate = true
seqstat_R1.deps = deps_R1
add(seqstat_R1)
addSummarizable(seqstat_R1, "seqstat_R1")
if (paired) {
val seqstat_R2 = Seqstat(this, R2.get, outDir)
val seqstat_R2 = SeqStat(this, R2.get, outDir)
seqstat_R2.isIntermediate = true
seqstat_R2.deps = deps_R2
add(seqstat_R2)
......@@ -259,13 +259,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
if (paired) R2 = Some(sickle.output_R2)
}
val seqstat_R1_after = Seqstat(this, R1, outDir)
val seqstat_R1_after = SeqStat(this, R1, outDir)
seqstat_R1_after.deps = deps_R1
add(seqstat_R1_after)
addSummarizable(seqstat_R1_after, "seqstat_R1_after")
if (paired) {
val seqstat_R2_after = Seqstat(this, R2.get, outDir)
val seqstat_R2_after = SeqStat(this, R2.get, outDir)
seqstat_R2_after.deps = deps_R2
add(seqstat_R2_after)
addSummarizable(seqstat_R2_after, "seqstat_R2_after")
......
......@@ -26,7 +26,7 @@ import org.testng.annotations.{ AfterClass, DataProvider, Test }
import nl.lumc.sasc.biopet.core.config.Config
import nl.lumc.sasc.biopet.extensions.{ Sickle, Gzip, Zcat }
import nl.lumc.sasc.biopet.tools.Seqstat
import nl.lumc.sasc.biopet.tools.SeqStat
import nl.lumc.sasc.biopet.tools.FastqSync
import nl.lumc.sasc.biopet.utils.ConfigUtils
......@@ -78,7 +78,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
else if (!paired && (skipClip && skipTrim)) 1
else if (paired && !(skipClip && skipTrim)) 4
else if (!paired && !(skipClip && skipTrim)) 2)
flexiprep.functions.count(_.isInstanceOf[Seqstat]) shouldBe (if (paired) 4 else 2)
flexiprep.functions.count(_.isInstanceOf[SeqStat]) shouldBe (if (paired) 4 else 2)
flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe (if (zipped) (if (paired) 2 else 1) else 0)
flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe (if (paired) 2 else 1)
flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe (if (skipClip) 0 else (if (paired) 2 else 1))
......
......@@ -29,7 +29,7 @@ import nl.lumc.sasc.biopet.core.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaSamse, BwaSampe, BwaAln, BwaMem }
import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, AddOrReplaceReadGroups, MarkDuplicates, SortSam }
import nl.lumc.sasc.biopet.pipelines.flexiprep.{ SeqtkSeq, Cutadapt, Fastqc }
import nl.lumc.sasc.biopet.tools.{ Seqstat, FastqSync }
import nl.lumc.sasc.biopet.tools.{ SeqStat, FastqSync }
import nl.lumc.sasc.biopet.utils.ConfigUtils
/**
......@@ -91,7 +91,7 @@ class MappingTest extends TestNGSuite with Matchers {
//Flexiprep
mapping.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (skipFlexiprep) 0 else if (paired) 4 else 2)
mapping.functions.count(_.isInstanceOf[Zcat]) shouldBe (if (!zipped || (chunks > 1 && skipFlexiprep)) 0 else if (paired) 2 else 1)
mapping.functions.count(_.isInstanceOf[Seqstat]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 4 else 2) * chunks)
mapping.functions.count(_.isInstanceOf[SeqStat]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 4 else 2) * chunks)
mapping.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * chunks)
mapping.functions.count(_.isInstanceOf[Cutadapt]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * chunks)
mapping.functions.count(_.isInstanceOf[FastqSync]) shouldBe ((if (skipFlexiprep) 0 else if (paired && !skipFlexiprep) 1 else 0) * chunks)
......
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