Rename Seqstat -> SeqStat

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala → public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala

@@ -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

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqstatTest.scala → public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala

@@ -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

public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala

@@ -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)

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -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")

public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

@@ -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))

public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -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)