diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index 6c36a4f0f4bb5bb24dc4fca1fbca78ad35936356..2671c05e531a2bc965c31eb92a940f68439051b8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -25,10 +25,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Contaminants", required = false)
- var contaminants: File = _
+ var contaminants: Option[File] = None
@Input(doc = "Adapters", required = false)
- var adapters: File = _
+ var adapters: Option[File] = None
@Input(doc = "Fastq file", shortName = "FQ")
var fastqfile: File = _
@@ -50,17 +50,19 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
override def afterGraph {
this.checkExecutable
- if (contaminants == null) {
- val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
- val defaultContams = getVersion match {
- case "v0.11.2" => new File(fastqcDir + "/Configuration/contaminant_list.txt")
- case _ => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
- }
- val defaultAdapters = getVersion match {
- case "v0.11.2" => new File(fastqcDir + "/Configuration/adapter_list.txt")
- case _ => null
- }
- contaminants = config("contaminants", default = defaultContams)
+ contaminants = contaminants match {
+ case None =>
+ val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
+ val defaultContams = getVersion match {
+ case "v0.11.2" => Option(new File(fastqcDir + "/Configuration/contaminant_list.txt"))
+ case _ => Option(new File(fastqcDir + "/Contaminants/contaminant_list.txt"))
+ }
+ val defaultAdapters = getVersion match {
+ case "v0.11.2" => Option(new File(fastqcDir + "/Configuration/adapter_list.txt"))
+ case _ => None
+ }
+ config("contaminants", default = defaultContams)
+ case wrapped @ Some(_) => wrapped
}
}
@@ -74,6 +76,6 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
conditional(noextract, "--noextract") +
conditional(extract, "--extract") +
conditional(quiet, "--quiet") +
- required("-o", output.getParent()) +
+ required("-o", output.getParent) +
required(fastqfile)
}
diff --git a/public/flexiprep/pom.xml b/public/flexiprep/pom.xml
index e9b58ab28a615ac8ce4e76063285b125f2b66b1b..86666db29645cd35f9d8f71c6b1aa775d0f22444 100644
--- a/public/flexiprep/pom.xml
+++ b/public/flexiprep/pom.xml
@@ -39,5 +39,17 @@
<artifactId>BiopetFramework</artifactId>
<version>${project.version}</version>
</dependency>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.scalatest</groupId>
+ <artifactId>scalatest_2.11</artifactId>
+ <version>2.2.1</version>
+ <scope>test</scope>
+ </dependency>
</dependencies>
</project>
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
index 1bd84bb36e21c8e577adaf5e9ad33d02b1db47fa..9aaca5f66336e38b16b215a9c175781fafc97fe0 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
@@ -33,14 +33,14 @@ class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutada
override def beforeCmd() {
super.beforeCmd
- val foundAdapters = fastqc.getFoundAdapters.map(_.seq)
+ val foundAdapters = fastqc.foundAdapters.map(_.seq)
if (default_clip_mode == "3") opt_adapter ++= foundAdapters
else if (default_clip_mode == "5") opt_front ++= foundAdapters
else if (default_clip_mode == "both") opt_anywhere ++= foundAdapters
}
override def cmdLine = {
- if (!opt_adapter.isEmpty || !opt_anywhere.isEmpty || !opt_front.isEmpty) {
+ if (opt_adapter.nonEmpty || opt_anywhere.nonEmpty || opt_front.nonEmpty) {
analysisName = getClass.getSimpleName
super.cmdLine
} else {
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index 4ee01c2605d5449dac33b19ac9c2ab360b383d45..dc5972ab488caf26cedc51f8362071d6e36cbd90 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -16,82 +16,154 @@
package nl.lumc.sasc.biopet.pipelines.flexiprep
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import java.io.{ File, FileNotFoundException }
+
import scala.io.Source
import argonaut._, Argonaut._
import scalaz._, Scalaz._
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+
+/**
+ * FastQC wrapper with added functionality for the Flexiprep pipeline
+ *
+ * This wrapper implements additional methods for parsing FastQC output files and aggregating everything in a summary
+ * object. The current implementation is based on FastQC v0.10.1.
+ */
class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(root) {
- def getDataBlock(name: String): Array[String] = { // Based on Fastqc v0.10.1
- val outputDir = output.getAbsolutePath.stripSuffix(".zip")
- val dataFile = new File(outputDir + "/fastqc_data.txt")
- if (!dataFile.exists) return null
- val data = Source.fromFile(dataFile).mkString
- for (block <- data.split(">>END_MODULE\n")) {
- val b = if (block.startsWith("##FastQC")) block.substring(block.indexOf("\n") + 1) else block
- if (b.startsWith(">>" + name))
- return for (line <- b.split("\n"))
- yield line
- }
- return null
- }
- def getEncoding: String = {
- val block = getDataBlock("Basic Statistics")
- if (block == null) return null
- for (
- line <- block if (line.startsWith("Encoding"))
- ) return line.stripPrefix("Encoding\t")
- return null // Could be default Sanger with a warning in the log
+ /** Class for storing a single FastQC module result */
+ protected case class FastQCModule(name: String, status: String, lines: Seq[String])
+
+ /** Default FastQC output directory containing actual results */
+ // this is a def instead of a val since the value depends on the variable `output`, which is null on class creation
+ def outputDir: File = new File(output.getAbsolutePath.stripSuffix(".zip"))
+
+ /** Default FastQC output data file */
+ // this is a def instead of a val since the value depends on the variable `output`, which is null on class creation
+ def dataFile: File = new File(outputDir, "fastqc_data.txt")
+
+ /**
+ * FastQC QC modules.
+ *
+ * @return Mapping of FastQC module names and its contents as array of strings (one item per line)
+ * @throws FileNotFoundException if the FastQC data file can not be found.
+ * @throws IllegalStateException if the module lines have no content or mapping is empty.
+ */
+ @throws(classOf[FileNotFoundException])
+ @throws(classOf[IllegalStateException])
+ def qcModules: Map[String, FastQCModule] = {
+
+ val fqModules = Source.fromFile(dataFile)
+ // drop all the characters before the first module delimiter (i.e. '>>')
+ .dropWhile(_ != '>')
+ // pull everything into a string
+ .mkString
+ // split into modules
+ .split(">>END_MODULE\n")
+ // make map of module name -> module lines
+ .map {
+ case (modString) =>
+ // module name is in the first line, without '>>' and before the tab character
+ val Array(firstLine, otherLines) = modString
+ // drop all '>>' character (start of module)
+ .dropWhile(_ == '>')
+ // split first line and others
+ .split("\n", 2)
+ // and slice them
+ .slice(0, 2)
+ // extract module name and module status
+ val Array(modName, modStatus) = firstLine
+ .split("\t", 2)
+ .slice(0, 2)
+ modName -> FastQCModule(modName, modStatus, otherLines.split("\n").toSeq)
+ }
+ .toMap
+
+ if (fqModules.isEmpty) throw new IllegalStateException("Empty FastQC data file " + dataFile.toString)
+ else fqModules
}
- protected case class Sequence(name: String, seq: String)
- def getFoundAdapters: List[Sequence] = {
- def getSeqs(file: File) = {
- if (file != null) {
- (for (
- line <- Source.fromFile(file).getLines(); if line.startsWith("#");
- values = line.split("\t*") if values.size >= 2
- ) yield Sequence(values(0), values(1))).toList
- } else Nil
- }
+ /**
+ * Retrieves the FASTQ file encoding as computed by FastQC.
+ *
+ * @return encoding name
+ * @throws NoSuchElementException when the "Basic Statistics" key does not exist in the mapping or
+ * when a line starting with "Encoding" does not exist.
+ */
+ @throws(classOf[NoSuchElementException])
+ def encoding: String =
+ qcModules("Basic Statistics")
+ .lines
+ .dropWhile(!_.startsWith("Encoding"))
+ .head
+ .stripPrefix("Encoding\t")
+ .stripSuffix("\t")
+
+ /** Case class representing a known adapter sequence */
+ protected case class AdapterSequence(name: String, seq: String)
- val seqs = getSeqs(adapters) ::: getSeqs(contaminants)
+ /**
+ * Retrieves overrepresented sequences found by FastQ.
+ *
+ * @return a [[Set]] of [[AdapterSequence]] objects.
+ */
+ def foundAdapters: Set[AdapterSequence] = {
- val block = getDataBlock("Overrepresented sequences")
- if (block == null) return Nil
+ /** Returns a list of adapter and/or contaminant sequences known to FastQC */
+ def getFastqcSeqs(file: Option[File]): Set[AdapterSequence] = file match {
+ case None => Set.empty[AdapterSequence]
+ case Some(f) =>
+ (for {
+ line <- Source.fromFile(f).getLines()
+ if !line.startsWith("#")
+ values = line.split("\t+")
+ if values.size >= 2
+ } yield AdapterSequence(values(0), values(1))).toSet
+ }
- val found = for (
- line <- block if !line.startsWith("#");
- values = line.split("\t") if values.size >= 4
- ) yield values(3)
+ val found = qcModules.get("Overrepresented sequences") match {
+ case None => Seq.empty[String]
+ case Some(qcModule) =>
+ for (
+ line <- qcModule.lines if !(line.startsWith("#") || line.startsWith(">"));
+ values = line.split("\t") if values.size >= 4
+ ) yield values(3)
+ }
- seqs.filter(x => found.exists(_.startsWith(x.name)))
+ // select full sequences from known adapters and contaminants
+ // based on overrepresented sequences results
+ (getFastqcSeqs(adapters) ++ getFastqcSeqs(contaminants))
+ .filter(x => found.exists(_.startsWith(x.name)))
}
- def getSummary: Json = {
- val subfixs = Map("plot_duplication_levels" -> "Images/duplication_levels.png",
- "plot_kmer_profiles" -> "Images/kmer_profiles.png",
- "plot_per_base_gc_content" -> "Images/per_base_gc_content.png",
- "plot_per_base_n_content" -> "Images/per_base_n_content.png",
- "plot_per_base_quality" -> "Images/per_base_quality.png",
- "plot_per_base_sequence_content" -> "Images/per_base_sequence_content.png",
- "plot_per_sequence_gc_content" -> "Images/per_sequence_gc_content.png",
- "plot_per_sequence_quality" -> "Images/per_sequence_quality.png",
- "plot_sequence_length_distribution" -> "Images/sequence_length_distribution.png",
- "fastqc_data" -> "fastqc_data.txt")
- val dir = output.getAbsolutePath.stripSuffix(".zip") + "/"
- var outputMap: Map[String, Map[String, String]] = Map()
- for ((k, v) <- subfixs) outputMap += (k -> Map("path" -> (dir + v)))
-
- val temp = ("" := outputMap) ->: jEmptyObject
- return temp.fieldOrEmptyObject("")
+ /** Summary of the FastQC run, stored in a [[Json]] object */
+ def summary: Json = {
+
+ val outputMap =
+ Map("plot_duplication_levels" -> "Images/duplication_levels.png",
+ "plot_kmer_profiles" -> "Images/kmer_profiles.png",
+ "plot_per_base_gc_content" -> "Images/per_base_gc_content.png",
+ "plot_per_base_n_content" -> "Images/per_base_n_content.png",
+ "plot_per_base_quality" -> "Images/per_base_quality.png",
+ "plot_per_base_sequence_content" -> "Images/per_base_sequence_content.png",
+ "plot_per_sequence_gc_content" -> "Images/per_sequence_gc_content.png",
+ "plot_per_sequence_quality" -> "Images/per_sequence_quality.png",
+ "plot_sequence_length_distribution" -> "Images/sequence_length_distribution.png",
+ "fastqc_data" -> "fastqc_data.txt")
+ .map {
+ case (name, relPath) =>
+ name -> Map("path" -> (outputDir + relPath))
+ }
+
+ ConfigUtils.mapToJson(outputMap)
}
}
object Fastqc {
+
def apply(root: Configurable, fastqfile: File, outDir: String): Fastqc = {
val fastqcCommand = new Fastqc(root)
fastqcCommand.fastqfile = fastqfile
@@ -102,6 +174,6 @@ object Fastqc {
//if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
fastqcCommand.output = new File(outDir + "/" + filename + "_fastqc.zip")
fastqcCommand.afterGraph
- return fastqcCommand
+ fastqcCommand
}
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
index 353fb1acb83c75fe121d064c1ab6b0149f87565d..4ff18fb7cc90d7c3a90255c3c9a49ffb0a191eda 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
@@ -201,7 +201,7 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
def fastqcSummary(fastqc: Fastqc): Option[Json] = {
if (fastqc == null) return None
- else return Option(fastqc.getSummary)
+ else return Option(fastqc.summary)
}
def clipstatSummary(): Option[Json] = {
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
index f6d6ac9d7c2727445723bd26c61d77398d081e95..0fdeee289de9672d917264e3e9dc2d556f6bc48b 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
@@ -25,7 +25,7 @@ class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.
override def beforeCmd {
super.beforeCmd
if (fastqc != null && Q == None) {
- val encoding = fastqc.getEncoding
+ val encoding = fastqc.encoding
Q = encoding match {
case null => None
case s if (s.contains("Sanger / Illumina 1.9")) => None
diff --git a/public/flexiprep/src/test/resources/fqc_contaminants_v0101.txt b/public/flexiprep/src/test/resources/fqc_contaminants_v0101.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13c6a999940201a402c3a7f9dd931ab9102de360
--- /dev/null
+++ b/public/flexiprep/src/test/resources/fqc_contaminants_v0101.txt
@@ -0,0 +1,170 @@
+# This file contains a list of potential contaminants which are
+# frequently found in high throughput sequencing reactions. These
+# are mostly sequences of adapters / primers used in the various
+# sequencing chemistries.
+#
+# Please DO NOT rely on these sequences to design your own oligos, some
+# of them are truncated at ambiguous positions, and none of them are
+# definitive sequences from the manufacturers so don't blame us if you
+# try to use them and they don't work.
+#
+# You can add more sequences to the file by putting one line per entry
+# and specifying a name[tab]sequence. If the contaminant you add is
+# likely to be of use to others please consider sending it to the FastQ
+# authors, either via a bug report at www.bioinformatics.bbsrc.ac.uk/bugzilla/
+# or by directly emailing simon.andrews@bbsrc.ac.uk so other users of
+# the program can benefit.
+
+Illumina Single End Adapter 1 GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
+Illumina Single End Adapter 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+Illumina Single End PCR Primer 1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Single End PCR Primer 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+Illumina Single End Sequencing Primer ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+
+Illumina Paired End Adapter 1 ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End Adapter 2 GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
+Illumina Paried End PCR Primer 1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End PCR Primer 2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+Illumina Paried End Sequencing Primer 1 ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End Sequencing Primer 2 CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+
+Illumina DpnII expression Adapter 1 ACAGGTTCAGAGTTCTACAGTCCGAC
+Illumina DpnII expression Adapter 2 CAAGCAGAAGACGGCATACGA
+Illumina DpnII expression PCR Primer 1 CAAGCAGAAGACGGCATACGA
+Illumina DpnII expression PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina DpnII expression Sequencing Primer CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+Illumina NlaIII expression Adapter 1 ACAGGTTCAGAGTTCTACAGTCCGACATG
+Illumina NlaIII expression Adapter 2 CAAGCAGAAGACGGCATACGA
+Illumina NlaIII expression PCR Primer 1 CAAGCAGAAGACGGCATACGA
+Illumina NlaIII expression PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina NlaIII expression Sequencing Primer CCGACAGGTTCAGAGTTCTACAGTCCGACATG
+
+Illumina Small RNA Adapter 1 GTTCAGAGTTCTACAGTCCGACGATC
+Illumina Small RNA Adapter 2 TGGAATTCTCGGGTGCCAAGG
+Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA
+Illumina Small RNA PCR Primer 1 CAAGCAGAAGACGGCATACGA
+Illumina Small RNA PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina Small RNA Sequencing Primer CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+Illumina Multiplexing Adapter 1 GATCGGAAGAGCACACGTCT
+Illumina Multiplexing Adapter 2 ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Multiplexing PCR Primer 1.01 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Multiplexing PCR Primer 2.01 GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+Illumina Multiplexing Read1 Sequencing Primer ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Multiplexing Index Sequencing Primer GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+Illumina Multiplexing Read2 Sequencing Primer GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+
+Illumina PCR Primer Index 1 CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTC
+Illumina PCR Primer Index 2 CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTC
+Illumina PCR Primer Index 3 CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTC
+Illumina PCR Primer Index 4 CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTC
+Illumina PCR Primer Index 5 CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTC
+Illumina PCR Primer Index 6 CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTC
+Illumina PCR Primer Index 7 CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTC
+Illumina PCR Primer Index 8 CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTC
+Illumina PCR Primer Index 9 CAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTC
+Illumina PCR Primer Index 10 CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTC
+Illumina PCR Primer Index 11 CAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTC
+Illumina PCR Primer Index 12 CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTC
+
+Illumina DpnII Gex Adapter 1 GATCGTCGGACTGTAGAACTCTGAAC
+Illumina DpnII Gex Adapter 1.01 ACAGGTTCAGAGTTCTACAGTCCGAC
+Illumina DpnII Gex Adapter 2 CAAGCAGAAGACGGCATACGA
+Illumina DpnII Gex Adapter 2.01 TCGTATGCCGTCTTCTGCTTG
+Illumina DpnII Gex PCR Primer 1 CAAGCAGAAGACGGCATACGA
+Illumina DpnII Gex PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina DpnII Gex Sequencing Primer CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+Illumina NlaIII Gex Adapter 1.01 TCGGACTGTAGAACTCTGAAC
+Illumina NlaIII Gex Adapter 1.02 ACAGGTTCAGAGTTCTACAGTCCGACATG
+Illumina NlaIII Gex Adapter 2.01 CAAGCAGAAGACGGCATACGA
+Illumina NlaIII Gex Adapter 2.02 TCGTATGCCGTCTTCTGCTTG
+Illumina NlaIII Gex PCR Primer 1 CAAGCAGAAGACGGCATACGA
+Illumina NlaIII Gex PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina NlaIII Gex Sequencing Primer CCGACAGGTTCAGAGTTCTACAGTCCGACATG
+
+Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA
+Illumina 5p RNA Adapter GTTCAGAGTTCTACAGTCCGACGATC
+Illumina RNA Adapter1 TGGAATTCTCGGGTGCCAAGG
+
+Illumina Small RNA 3p Adapter 1 ATCTCGTATGCCGTCTTCTGCTTG
+Illumina Small RNA PCR Primer 1 CAAGCAGAAGACGGCATACGA
+Illumina Small RNA PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina Small RNA Sequencing Primer CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+TruSeq Universal Adapter AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+TruSeq Adapter, Index 1 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 2 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 3 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 4 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 5 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 6 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 7 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 8 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 9 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 10 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 11 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 12 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG
+
+Illumina RNA RT Primer GCCTTGGCACCCGAGAATTCCA
+Illumina RNA PCR Primer AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA
+
+RNA PCR Primer, Index 1 CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 2 CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 3 CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 4 CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 5 CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 6 CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 7 CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 8 CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 9 CAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 10 CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 11 CAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 12 CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 13 CAAGCAGAAGACGGCATACGAGATTTGACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 14 CAAGCAGAAGACGGCATACGAGATGGAACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 15 CAAGCAGAAGACGGCATACGAGATTGACATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 16 CAAGCAGAAGACGGCATACGAGATGGACGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 17 CAAGCAGAAGACGGCATACGAGATCTCTACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 18 CAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 19 CAAGCAGAAGACGGCATACGAGATTTTCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 20 CAAGCAGAAGACGGCATACGAGATGGCCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 21 CAAGCAGAAGACGGCATACGAGATCGAAACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 22 CAAGCAGAAGACGGCATACGAGATCGTACGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 23 CAAGCAGAAGACGGCATACGAGATCCACTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 24 CAAGCAGAAGACGGCATACGAGATGCTACCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 25 CAAGCAGAAGACGGCATACGAGATATCAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 26 CAAGCAGAAGACGGCATACGAGATGCTCATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 27 CAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 28 CAAGCAGAAGACGGCATACGAGATCTTTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 29 CAAGCAGAAGACGGCATACGAGATTAGTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 30 CAAGCAGAAGACGGCATACGAGATCCGGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 31 CAAGCAGAAGACGGCATACGAGATATCGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 32 CAAGCAGAAGACGGCATACGAGATTGAGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 33 CAAGCAGAAGACGGCATACGAGATCGCCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 34 CAAGCAGAAGACGGCATACGAGATGCCATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 35 CAAGCAGAAGACGGCATACGAGATAAAATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 36 CAAGCAGAAGACGGCATACGAGATTGTTGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 37 CAAGCAGAAGACGGCATACGAGATATTCCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 38 CAAGCAGAAGACGGCATACGAGATAGCTAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 39 CAAGCAGAAGACGGCATACGAGATGTATAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 40 CAAGCAGAAGACGGCATACGAGATTCTGAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 41 CAAGCAGAAGACGGCATACGAGATGTCGTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 42 CAAGCAGAAGACGGCATACGAGATCGATTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 43 CAAGCAGAAGACGGCATACGAGATGCTGTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 44 CAAGCAGAAGACGGCATACGAGATATTATAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 45 CAAGCAGAAGACGGCATACGAGATGAATGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 46 CAAGCAGAAGACGGCATACGAGATTCGGGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 47 CAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 48 CAAGCAGAAGACGGCATACGAGATTGCCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+
+ABI Dynabead EcoP Oligo CTGATCTAGAGGTACCGGATCCCAGCAGT
+ABI Solid3 Adapter A CTGCCCCGGGTTCCTCATTCTCTCAGCAGCATG
+ABI Solid3 Adapter B CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT
+ABI Solid3 5' AMP Primer CCACTACGCCTCCGCTTTCCTCTCTATG
+ABI Solid3 3' AMP Primer CTGCCCCGGGTTCCTCATTCT
+ABI Solid3 EF1 alpha Sense Primer CATGTGTGTTGAGAGCTTC
+ABI Solid3 EF1 alpha Antisense Primer GAAAACCAAAGTGGTCCAC
+ABI Solid3 GAPDH Forward Primer TTAGCACCCCTGGCCAAGG
+ABI Solid3 GAPDH Reverse Primer CTTACTCCTTGGAGGCCATG
diff --git a/public/flexiprep/src/test/resources/v0101.fq_fastqc/fastqc_data.txt b/public/flexiprep/src/test/resources/v0101.fq_fastqc/fastqc_data.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d44bfae6fa962cd5d3e88084107b22efed3b025
--- /dev/null
+++ b/public/flexiprep/src/test/resources/v0101.fq_fastqc/fastqc_data.txt
@@ -0,0 +1,838 @@
+##FastQC 0.10.1
+>>Basic Statistics pass
+#Measure Value
+Filename ct_r1.fq
+File type Conventional base calls
+Encoding Sanger / Illumina 1.9
+Total Sequences 1000
+Filtered Sequences 0
+Sequence length 100
+%GC 53
+>>END_MODULE
+>>Per base sequence quality fail
+#Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile
+1 32.244 33.0 31.0 34.0 30.0 34.0
+2 32.589 34.0 31.0 34.0 31.0 34.0
+3 32.814 34.0 31.0 34.0 31.0 34.0
+4 36.231 37.0 35.0 37.0 35.0 37.0
+5 35.907 37.0 35.0 37.0 35.0 37.0
+6 35.934 37.0 35.0 37.0 35.0 37.0
+7 35.783 37.0 35.0 37.0 35.0 37.0
+8 36.008 37.0 35.0 37.0 35.0 37.0
+9 37.706 39.0 37.0 39.0 35.0 39.0
+10-14 37.857600000000005 39.2 37.2 39.4 34.8 39.4
+15-19 38.9788 40.2 38.0 41.0 35.0 41.0
+20-24 38.8246 40.0 38.0 41.0 34.8 41.0
+25-29 38.589600000000004 40.0 38.0 41.0 34.4 41.0
+30-34 38.3568 40.0 38.0 41.0 33.8 41.0
+35-39 38.1592 40.0 37.4 41.0 33.6 41.0
+40-44 37.4808 39.8 36.0 41.0 32.6 41.0
+45-49 36.9478 39.0 35.0 40.8 31.2 41.0
+50-54 35.845600000000005 37.8 34.6 40.0 29.4 41.0
+55-59 34.739 36.6 33.6 40.0 27.4 41.0
+60-64 34.1336 35.4 33.4 38.6 27.2 40.2
+65-69 32.7464 35.0 32.6 37.2 24.6 39.6
+70-74 29.3478 34.0 29.6 35.6 2.0 38.6
+75-79 27.4908 33.2 26.4 35.0 2.0 36.6
+80-84 25.893000000000008 33.0 21.8 35.0 2.0 35.4
+85-89 25.031799999999997 32.4 16.2 34.6 2.0 35.0
+90-94 23.9446 31.4 6.4 34.0 2.0 35.0
+95-99 22.9358 30.4 2.0 34.0 2.0 35.0
+100 21.984 30.0 2.0 34.0 2.0 35.0
+>>END_MODULE
+>>Per sequence quality scores pass
+#Quality Count
+11 1.0
+12 4.0
+13 3.0
+14 1.0
+15 4.0
+16 4.0
+17 6.0
+18 7.0
+19 4.0
+20 2.0
+21 7.0
+22 9.0
+23 9.0
+24 17.0
+25 23.0
+26 30.0
+27 52.0
+28 39.0
+29 28.0
+30 23.0
+31 33.0
+32 43.0
+33 47.0
+34 74.0
+35 88.0
+36 148.0
+37 202.0
+38 89.0
+39 3.0
+>>END_MODULE
+>>Per base sequence content fail
+#Base G A T C
+1 52.35707121364093 17.251755265797392 11.735205616850552 18.655967903711137
+2 34.300000000000004 11.1 24.8 29.799999999999997
+3 41.0 6.5 20.200000000000003 32.300000000000004
+4 37.5 8.7 26.0 27.800000000000004
+5 35.4 12.4 31.8 20.4
+6 57.3 11.1 1.6 30.0
+7 20.9 24.7 32.6 21.8
+8 20.0 27.200000000000003 30.0 22.8
+9 24.5 21.5 27.800000000000004 26.200000000000003
+10-14 25.22 23.28 26.26 25.240000000000002
+15-19 26.44 21.34 26.1 26.119999999999997
+20-24 25.240000000000002 22.1 24.6 28.060000000000002
+25-29 24.62 22.06 25.119999999999997 28.199999999999996
+30-34 26.240000000000002 21.44 24.279999999999998 28.04
+35-39 24.8 22.439999999999998 24.34 28.42
+40-44 25.8 22.84 23.9 27.46
+45-49 26.26 22.64 23.66 27.439999999999998
+50-54 26.72 22.58 23.18 27.52
+55-59 25.019999999999996 22.58 24.38 28.02
+60-64 26.251501802162597 22.00640768922707 23.28794553464157 28.454144973968766
+65-69 25.683829444891394 23.873692679002414 23.049074818986323 27.39340305711987
+70-74 25.554134697357206 25.44757033248082 21.717817561807333 27.28047740835465
+75-79 25.818501428257523 23.643155350472423 23.071852340145025 27.466490881125026
+80-84 26.973532796317606 23.95857307249712 21.74913693901036 27.318757192174914
+85-89 25.452016689847014 24.849327770050998 22.624014835419565 27.07464070468243
+90-94 24.547101449275363 22.35054347826087 24.139492753623188 28.962862318840582
+95-99 25.318837549655026 24.231653773782146 23.186284758519758 27.263223918043067
+100 24.0 26.0 21.9 28.1
+>>END_MODULE
+>>Per base GC content fail
+#Base %GC
+1 71.01303911735206
+2 64.1
+3 73.3
+4 65.3
+5 55.800000000000004
+6 87.3
+7 42.699999999999996
+8 42.8
+9 50.7
+10-14 50.46000000000001
+15-19 52.559999999999995
+20-24 53.300000000000004
+25-29 52.82
+30-34 54.279999999999994
+35-39 53.22
+40-44 53.26
+45-49 53.7
+50-54 54.24
+55-59 53.04
+60-64 54.70564677613135
+65-69 53.07723250201126
+70-74 52.834612105711855
+75-79 53.28499230938255
+80-84 54.29228998849251
+85-89 52.526657394529444
+90-94 53.509963768115945
+95-99 52.5820614676981
+100 52.1
+>>END_MODULE
+>>Per sequence GC content fail
+#GC Content Count
+0 0.0
+1 0.0
+2 0.0
+3 0.0
+4 0.0
+5 0.0
+6 0.0
+7 0.0
+8 0.0
+9 0.0
+10 0.0
+11 0.0
+12 0.0
+13 0.0
+14 0.0
+15 0.0
+16 0.0
+17 0.0
+18 0.0
+19 0.0
+20 0.0
+21 0.0
+22 0.0
+23 0.5
+24 0.5
+25 0.5
+26 1.0
+27 1.5
+28 2.0
+29 3.5
+30 5.5
+31 6.0
+32 6.5
+33 6.0
+34 4.5
+35 6.0
+36 11.0
+37 17.0
+38 21.0
+39 16.5
+40 15.0
+41 24.0
+42 28.5
+43 33.0
+44 35.5
+45 32.5
+46 32.0
+47 32.0
+48 29.5
+49 30.5
+50 30.0
+51 29.5
+52 30.0
+53 27.5
+54 26.5
+55 27.0
+56 29.5
+57 34.0
+58 36.0
+59 36.0
+60 37.0
+61 31.5
+62 24.0
+63 22.5
+64 27.0
+65 28.5
+66 20.5
+67 15.0
+68 17.0
+69 13.5
+70 8.0
+71 7.0
+72 9.0
+73 8.0
+74 5.5
+75 4.5
+76 2.0
+77 2.0
+78 3.0
+79 2.0
+80 1.5
+81 1.0
+82 0.0
+83 0.5
+84 1.0
+85 0.5
+86 0.0
+87 0.0
+88 0.0
+89 0.0
+90 0.0
+91 0.0
+92 0.0
+93 0.0
+94 0.0
+95 0.0
+96 0.0
+97 0.0
+98 0.0
+99 0.0
+100 0.0
+>>END_MODULE
+>>Per base N content warn
+#Base N-Count
+1 0.3
+2 0.0
+3 0.0
+4 0.0
+5 0.0
+6 0.0
+7 0.0
+8 0.0
+9 0.0
+10-14 0.0
+15-19 0.0
+20-24 0.0
+25-29 0.0
+30-34 0.0
+35-39 0.0
+40-44 0.0
+45-49 0.0
+50-54 0.0
+55-59 0.0
+60-64 0.12
+65-69 0.5599999999999999
+70-74 6.16
+75-79 8.98
+80-84 13.100000000000001
+85-89 13.719999999999999
+90-94 11.68
+95-99 4.34
+100 0.0
+>>END_MODULE
+>>Sequence Length Distribution pass
+#Length Count
+100 1000.0
+>>END_MODULE
+>>Sequence Duplication Levels pass
+#Total Duplicate Percentage 3.4
+#Duplication Level Relative count
+1 100.0
+2 0.4140786749482402
+3 0.0
+4 0.0
+5 0.0
+6 0.0
+7 0.0
+8 0.0
+9 0.0
+10++ 0.2070393374741201
+>>END_MODULE
+>>Overrepresented sequences fail
+#Sequence Count Percentage Possible Source
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCCAAGATCTCGTAT 14 1.4000000000000001 TruSeq Adapter, Index 1 (97% over 36bp)
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCCAAGATCTCGTATG 12 1.2 TruSeq Adapter, Index 1 (97% over 36bp)
+AGGGGGAATGATGGTTGTCTTTGGATATACTACAGCGATGGCTATTGAGG 2 0.2 No Hit
+GGCTTGTTTTATTTTAATGGCTGATCTATGTAATCACAGAGGCCAGTATG 2 0.2 No Hit
+GTGGGGTGGTGTTTGTGGGGGACTTCATCATCTCAGGCTTCCCAGGGTCC 2 0.2 No Hit
+CGGAAGAGCACACGTCTGAACTCCAGTCACTTCCAAGATCTCGTATGCCG 2 0.2 TruSeq Adapter, Index 1 (96% over 33bp)
+>>END_MODULE
+>>Kmer Content fail
+#Sequence Count Obs/Exp Overall Obs/Exp Max Max Obs/Exp Position
+AAAAA 385 7.3597403 68.038994 65-69
+AGATC 435 5.4375157 23.135067 1
+GAAGA 375 5.258809 32.443344 6
+GGAAG 420 5.044668 33.345257 5
+TCCAG 475 4.8355613 14.131038 2
+AAGAG 320 4.487517 25.954676 7
+CCAGG 475 4.4180827 17.21471 3
+GAGCA 380 4.3399205 21.1377 9
+AGCAC 395 4.2895336 15.0741825 7
+CTCCA 415 4.0171337 12.105032 95-96
+AGAGC 340 3.883087 21.137697 8
+TTTTT 280 3.8749053 8.964593 10-14
+CTTCT 370 3.8646336 11.598914 55-59
+CTGAA 305 3.812511 13.130004 90-94
+CGGAA 320 3.65467 26.422123 5
+ACCAG 335 3.6379597 10.049457 7
+TCTGA 310 3.6325634 12.308498 90-94
+CACAC 340 3.5108058 14.806036 85-89
+ATCGG 325 3.4795394 24.768969 3
+TCGGA 320 3.426008 19.815174 3
+GATCG 320 3.426008 19.815174 1
+CGTCT 355 3.387832 11.578538 85-89
+CTGCT 355 3.387832 17.662533 3
+GCACA 310 3.3664696 15.0741825 8
+TCTTC 320 3.3423858 7.7326093 50-54
+CAGCA 305 3.3121717 10.049455 6
+GAACT 260 3.2500093 13.130004 90-94
+GTCTG 320 3.2116532 12.65067 90-94
+CAGGA 280 3.197836 15.8532715 3
+AACTC 265 3.1497202 23.781752 95-96
+TGAAC 250 3.125009 13.130004 90-94
+CCAGC 350 3.0954454 6.6359653 95-96
+AGTCA 240 3.0000086 10.41078 25-29
+CACCA 290 2.9945107 6.079907 70-74
+TGCTG 295 2.960743 9.2877 2
+CAGAT 230 2.875008 11.040063 70-74
+CTTCC 315 2.8583732 10.916445 30-34
+CACGT 280 2.8504362 12.351324 85-89
+CAGGG 290 2.8367646 22.630535 9
+ACACG 260 2.8234906 13.175687 85-89
+TTCCA 250 2.7855206 9.279795 30-34
+TTCTT 230 2.765239 6.6755276 50-54
+AGCAG 240 2.7410026 15.853272 2
+TTCTG 240 2.6363494 10.165324 55-59
+ACTCC 270 2.6135564 14.526036 95-96
+GCCAG 280 2.6043434 8.607355 1
+ACGTC 255 2.595933 10.105629 85-89
+GATCT 220 2.5779483 8.675031 40-44
+TCTGC 265 2.5289452 13.2469015 2
+AAGAT 160 2.4557784 12.783248 35-39
+ATCTC 220 2.4512577 9.279794 40-44
+CAGTC 240 2.4432309 8.554544 90-94
+TCCAA 205 2.4365761 10.999062 7
+CTTTT 200 2.4045558 16.688818 6
+TTCCT 230 2.40234 9.665762 7
+CCAGT 235 2.3923304 9.4206915 25-29
+TTTCT 195 2.3444414 16.688818 8
+CTGGG 255 2.3383298 6.004135 80-84
+TGCTT 210 2.3068056 10.165323 4
+TCTTT 190 2.284328 5.5629396 15-19
+TTTTC 190 2.2843277 11.125878 7
+GGGGG 255 2.2468696 16.307867 2
+AGGAA 160 2.2437584 19.466007 5
+GTCAC 220 2.2396283 10.184532 95-96
+TCACT 200 2.2284167 8.360176 95-96
+CACTT 200 2.2284167 10.3108835 30-34
+GAAAA 135 2.2103586 10.606119 60-64
+ACTTC 195 2.172706 9.279794 30-34
+TTGAA 150 2.1582448 11.9834385 60-64
+CTCCT 235 2.1324375 16.794533 4
+TCCTC 235 2.1324372 8.397265 5
+ATCTT 165 2.11616 7.1210704 10-14
+GGGGA 205 2.1089406 14.2801 3
+ACACA 165 2.092039 11.7331705 8
+TGCAG 195 2.0877237 9.907587 5
+GACCA 190 2.0633202 10.049455 6
+AGGGG 200 2.057503 9.520067 1
+CCTCC 260 2.049668 14.590484 5
+AGGAG 170 2.0418897 5.557543 2
+TCCTT 195 2.0367663 14.498643 4
+GTCTT 185 2.032186 15.247986 7
+GCTGG 220 2.0173824 8.485845 1
+CCAGA 185 2.0090222 5.3284492 70-74
+CCTGG 230 2.0054333 8.068818 3
+GCAGG 205 2.005299 9.052214 3
+GGACC 215 1.9997637 8.607355 5
+TTCAT 155 1.987908 5.934226 2
+CCTTT 190 1.9845415 14.498643 5
+TTTCC 190 1.9845415 5.799457 15-19
+TGGCA 185 1.980661 14.861383 2
+TCTTG 180 1.977262 10.165323 5
+CCAAG 180 1.9547247 9.044511 35-39
+CTTCA 175 1.9498644 10.310883 6
+CAAGA 145 1.933477 12.339583 35-39
+CTGGA 180 1.9271295 9.907587 6
+GGCTG 210 1.9256833 16.97169 2
+AATGA 125 1.918577 7.677627 95-96
+TGAAA 125 1.918577 15.623971 60-64
+GCTTC 200 1.9086379 13.2469015 2
+GTCCA 185 1.8833237 14.131036 1
+AGAAA 115 1.882898 7.5757995 7
+TGGGG 195 1.8805519 13.386638 1
+TTCTC 180 1.880092 5.799457 25-29
+CTTGA 160 1.8748715 8.675031 60-64
+ACAAA 120 1.8682072 5.762797 40-44
+TCTCG 195 1.8609219 8.831266 5
+GGGAC 190 1.8585701 9.052216 5
+TGAGG 165 1.8578365 5.209824 2
+TGAAG 140 1.8404517 6.082693 2
+CATCT 165 1.8384434 5.155441 4
+CACTG 180 1.8324232 9.4206915 6
+CTGCA 180 1.8324231 5.3465896 90-94
+GCTGC 210 1.8310483 8.068819 1
+GCAGA 160 1.8273348 10.568848 3
+CCTTC 200 1.8148402 8.397265 9
+AGGGA 150 1.8016673 6.0081544 95-96
+TTTCA 140 1.7955297 7.1210704 15-19
+CACAG 165 1.7918309 5.432139 95-96
+AAACA 115 1.7903653 7.6389136 70-74
+ATTTT 120 1.7715117 13.661307 6
+TTTTG 140 1.7701824 17.551357 7
+GGGGC 210 1.7594293 11.629828 3
+GATTT 130 1.7534488 12.481857 6
+CAAAT 120 1.7513192 6.7527947 50-54
+GAGGG 170 1.7488776 9.520067 1
+GAAGG 145 1.7416117 6.0081544 95-96
+CATTT 135 1.7314036 5.9342256 5
+ATTTC 135 1.7314036 5.9342256 7
+CCTCT 190 1.7240983 8.397266 1
+ATCCA 145 1.7234317 5.49953 4
+GCAGC 185 1.7207267 6.9789357 95-96
+TCCTG 180 1.717774 13.2469 2
+CTCTG 180 1.717774 13.2469 2
+AAAAC 110 1.7125233 7.6389136 70-74
+CTTGG 170 1.7061908 9.2877 2
+AAAAT 95 1.7024158 8.291661 9
+TCACC 175 1.693972 8.957724 8
+TCCAC 175 1.693972 8.957724 5
+GAGAA 120 1.6828189 6.488669 6
+TCTCC 185 1.6787271 5.038359 55-59
+GAGCC 180 1.6742208 8.607355 9
+TCATC 150 1.6713123 5.1554413 2
+AGACA 125 1.6667906 6.169792 2
+TGATG 135 1.6636823 11.404236 9
+GGGAG 160 1.6460025 9.520067 1
+AGCCA 150 1.6289369 6.029673 10-14
+ATGCC 160 1.6288207 8.478622 45-49
+CTCGT 170 1.6223421 8.831266 3
+GAGGA 135 1.6215005 11.115086 3
+TGTTG 140 1.6173534 10.690706 2
+CTCAT 145 1.6156021 5.1554418 2
+CAGGT 150 1.6059413 9.907587 4
+GCTTG 160 1.6058266 9.2877 60-64
+GGGTC 175 1.6047363 12.728768 2
+TCATT 125 1.6031516 5.934226 9
+GTTGA 130 1.6020645 5.702118 1
+ACAGA 120 1.6001189 10.005068 95-96
+GGAGG 155 1.5945649 9.520067 2
+GGGGT 165 1.5912362 13.386638 1
+TGGGA 140 1.5763463 10.419649 2
+GGATG 140 1.5763462 15.629472 6
+GCCTC 190 1.575248 7.672287 2
+CCTGC 190 1.5752479 11.508429 2
+GCTCC 190 1.5752479 11.508429 6
+TCTCT 150 1.5667434 5.224736 95-96
+GGGAA 130 1.561445 11.115086 4
+TCCAT 140 1.5598917 10.3108835 8
+GGCTT 155 1.5556445 13.93155 1
+TTGAT 115 1.5511277 6.240928 4
+CATCA 130 1.5451456 5.49953 2
+AGAGA 110 1.542584 6.488669 9
+AGGAC 135 1.541814 6.341309 55-59
+GTATG 125 1.5404466 9.123388 45-49
+AACAT 105 1.5324043 13.5055895 9
+AGCTC 150 1.5270194 9.4206915 5
+TTTGT 120 1.5172992 17.551357 8
+GATGA 115 1.5117996 6.082693 5
+GAGAT 115 1.5117996 6.082693 4
+AGGAT 115 1.5117996 12.165386 4
+TGAGA 115 1.5117996 6.082693 5
+CTGGT 150 1.5054625 9.2877 4
+GCTGT 150 1.5054625 18.5754 3
+TTCAC 135 1.504181 10.310883 7
+CCCAG 170 1.5035021 12.276537 2
+CAGTG 140 1.4988785 9.907587 5
+CTCCC 190 1.4978343 7.295242 1
+CCCTG 180 1.4923402 11.5084305 2
+CAGAG 130 1.4847097 7.398194 20-24
+CTTTG 135 1.4829465 10.165323 2
+CAAAA 95 1.4789973 7.203496 9
+TCTCA 130 1.4484707 5.1554413 8
+GAATG 110 1.4460692 12.165386 7
+GGAAT 110 1.4460692 12.165386 5
+TTTGG 125 1.4440656 5.345353 7
+GGCCT 165 1.4386805 12.103227 1
+GCTCT 150 1.4314783 6.1818867 20-24
+TCTGT 130 1.4280226 15.247986 3
+CTGTT 130 1.4280226 15.247986 4
+AGGTT 115 1.4172109 11.404235 8
+TTGAG 115 1.4172107 5.702117 4
+TTTGA 105 1.416247 7.4891143 10-14
+ATCTG 120 1.4061534 5.4218936 2
+GGTCT 140 1.4050984 9.287701 6
+TTTTA 95 1.4024467 7.384491 95-96
+GGGTG 145 1.3983592 13.386638 2
+GGCAC 150 1.3951839 8.607355 4
+AAAGA 85 1.3917071 7.5757985 8
+AAGAA 85 1.3917071 5.254889 75-79
+TTGTT 110 1.3908576 5.850453 4
+GGAGA 115 1.3812783 5.557543 3
+ATGAC 110 1.3750039 6.252721 95-96
+TGTTC 125 1.3730987 10.165325 5
+GGGCA 140 1.3694727 9.052216 4
+ATGAT 95 1.3668885 6.6574664 6
+CCACT 140 1.3551775 5.3746343 30-34
+TGGCT 135 1.3549163 13.931552 3
+GATGG 120 1.3511539 10.419648 9
+TCGTA 115 1.3475639 5.421894 40-44
+TGTCA 115 1.3475639 5.421894 5
+GCTGA 125 1.3382844 9.907587 6
+CAGAA 100 1.3334324 5.6025352 90-94
+CCAAA 105 1.3312978 5.8665853 8
+GGGCT 145 1.3296387 12.728768 1
+TAGGA 100 1.3146083 12.165386 4
+GACAG 115 1.313397 5.2844243 1
+GGTCC 150 1.3078917 8.068819 6
+CCATC 135 1.3067783 8.957724 9
+AAATG 85 1.3046323 7.101804 6
+TTCAA 95 1.2997144 6.330293 9
+CGTAT 110 1.2889742 8.675031 45-49
+TGACT 110 1.2889742 5.421894 3
+TATGC 110 1.2889739 8.67503 45-49
+GCCCT 155 1.2850707 7.672287 3
+TGGGC 140 1.283789 8.485846 7
+ACTTT 100 1.2825212 5.9342256 1
+ATGTT 95 1.2813665 6.2409286 1
+ATTTG 95 1.2813663 12.481856 9
+TGGTT 110 1.2707777 5.345353 5
+TGGTG 120 1.2666163 9.767722 7
+GTTTT 100 1.2644161 5.8504534 6
+GCCTG 145 1.2642952 12.103229 1
+TTGCT 115 1.2632507 6.0991945 50-54
+CCACC 150 1.2614243 7.7821474 5
+GGACA 110 1.2562928 15.853274 6
+GAAGC 110 1.2562928 10.568849 9
+TGACA 100 1.2500036 5.7837667 9
+GACAT 100 1.2500035 11.567533 7
+TGGAA 95 1.248878 6.082693 5
+ACAGC 115 1.2488517 10.049455 5
+AATCC 105 1.2480024 5.499531 7
+TGCCT 130 1.2406145 8.831266 3
+AGGTG 110 1.2385577 5.209824 4
+GTGGC 135 1.2379395 12.728768 1
+CATGT 105 1.2303842 5.4218936 1
+TAGAT 85 1.2230055 6.0453725 90-94
+CCCTC 155 1.2219174 7.295242 4
+GCCGT 140 1.2206988 8.068819 3
+AGTTT 90 1.2139261 6.2409286 7
+TTTAG 90 1.213926 6.240928 8
+TTGGG 115 1.2138406 9.767722 2
+ACCTC 125 1.20998 8.957724 1
+AGCAA 90 1.2000892 6.169792 9
+CAAAG 90 1.2000891 6.169791 5
+AAAGC 90 1.2000891 6.169791 6
+ACAGG 105 1.1991886 10.568849 8
+AGGCA 105 1.1991886 5.712891 95-96
+ATCAG 95 1.1875033 5.7837663 6
+ATGAG 90 1.1831475 6.082693 25-29
+CAGTT 100 1.1717947 5.1698627 85-89
+ATGCT 100 1.1717947 5.421894 8
+TCAAT 85 1.1629024 6.3302937 10-14
+TGTGT 100 1.1552525 10.690706 3
+GCCCA 130 1.1497369 12.276536 1
+TGATT 85 1.1464858 12.481857 5
+TGCTC 120 1.1451827 8.831267 4
+TGTCC 120 1.1451827 13.2469015 2
+TCCCC 145 1.143084 7.295242 2
+AAGGC 100 1.1420842 5.493164 65-69
+CAACA 90 1.1411123 5.8665853 8
+CACAA 90 1.1411123 11.7331705 9
+ACATC 95 1.129145 5.4995303 8
+AAGCT 90 1.1250031 6.2527194 95-96
+GAAAG 80 1.1218792 12.977338 7
+AAGGA 80 1.1218792 6.488669 3
+GCACT 110 1.1198142 9.4206915 5
+CCTGA 110 1.119814 9.420691 9
+ACCTT 100 1.1142083 5.1554418 7
+GTCAT 95 1.113205 5.421894 1
+TGATC 95 1.113205 10.843788 5
+TCATG 95 1.113205 5.421894 3
+TGGAT 90 1.1091216 5.702118 9
+GTGGG 115 1.1090435 8.924425 1
+CTGTG 110 1.1040058 9.2877 4
+GCTTT 100 1.0984789 5.4947696 95-96
+TGTCT 100 1.0984789 10.165323 5
+TTGGT 95 1.0974898 5.345353 4
+CTGTC 115 1.0974668 17.662535 4
+CAGAC 100 1.0859579 5.0247273 5
+GGAAC 95 1.0849801 5.2844243 6
+CCTCG 130 1.0778012 7.672287 6
+GCGGC 135 1.075477 7.372196 1
+ATAAA 60 1.0752101 8.291662 7
+GGGAT 95 1.0696635 10.419649 3
+CATCC 110 1.0647823 8.957723 3
+ACAGT 85 1.062503 5.7837663 4
+ACTGA 85 1.062503 11.567533 7
+GTTGG 100 1.0555136 9.767722 1
+TGTGG 100 1.0555136 9.767722 5
+GGAAA 75 1.0517617 19.466007 6
+GTGAA 80 1.0516868 6.082693 1
+GAAGT 80 1.0516866 6.082693 5
+GTCTC 110 1.0497508 8.831267 1
+CGGCT 120 1.046313 8.068818 1
+TTTAT 70 1.0333818 5.4645233 10-14
+GACAC 95 1.0316601 10.049455 7
+GGCAA 90 1.0278759 10.56885 3
+TCATA 75 1.0260904 6.330293 5
+ATTCA 75 1.0260903 6.3302927 7
+TAACA 70 1.0216029 6.7527957 8
+GGTCA 95 1.0170963 9.907589 3
+ATGGC 95 1.0170962 9.907587 1
+TCAGG 95 1.0170962 9.907587 8
+GGTGA 90 1.0133655 15.629474 3
+TGTTT 80 1.0115329 5.8504534 5
+TGAAT 70 1.007181 6.6574664 5
+ATTGA 70 1.0071809 6.6574664 7
+AAGTT 70 1.0071809 6.6574664 6
+TTGCC 105 1.0020349 8.831267 2
+CTTGC 105 1.0020349 8.831267 6
+GCAAA 75 1.0000744 6.169792 4
+CATAG 80 1.0000029 6.2527204 95-96
+GACTT 85 0.99602544 5.421894 1
+CTGAT 85 0.99602544 5.421894 4
+CTTGT 90 0.988631 10.165323 3
+AATGG 75 0.98595625 6.082693 8
+AAGGT 75 0.9859562 6.0826926 4
+GATGT 80 0.98588586 5.7021174 7
+GGATT 80 0.98588586 11.404235 5
+GGCGG 115 0.96349704 7.753219 1
+AGAGG 80 0.9608892 5.557543 8
+GAGGT 85 0.95706743 5.2098246 3
+ATGGG 85 0.9570673 5.209824 1
+CCGTC 115 0.95343953 7.672287 4
+TAGCA 75 0.9375027 5.7837667 1
+ACATG 75 0.9375026 5.7837663 2
+TTGCA 80 0.93743575 5.421894 4
+GTTCA 80 0.93743575 5.421894 6
+ATGTC 80 0.93743575 5.421894 5
+TTCAG 80 0.93743575 5.421894 8
+TTGAC 80 0.9374356 5.4218936 2
+GTTCT 85 0.93370706 5.0826616 1
+TTGTC 85 0.93370706 5.0826616 9
+TTTGC 85 0.93370706 5.0826616 3
+ATGGT 75 0.924268 5.7021174 4
+ATGAA 60 0.920917 7.1018047 9
+AGATG 70 0.92022586 6.082693 5
+GCTCA 90 0.91621155 5.092265 95-96
+AGTGC 85 0.9100334 9.907587 2
+AGGGT 80 0.90076935 10.419649 1
+GTAGG 80 0.90076923 10.419648 6
+AGTGG 80 0.90076923 5.209824 2
+TAAAA 50 0.89600843 8.291662 8
+CACAT 75 0.89143026 5.499531 6
+CCATT 80 0.89136666 10.3108835 9
+ATACT 65 0.8892783 6.330293 9
+ACATT 65 0.88927823 6.3302927 7
+GCGGG 105 0.87971467 7.753219 2
+ACACC 85 0.8777014 9.555587 9
+CATAA 60 0.8756596 6.7527947 6
+ACCCT 90 0.8711856 13.436585 1
+GAACA 65 0.8667311 6.169792 7
+ACTGC 85 0.8653109 5.092265 95-96
+GGTAT 70 0.86265016 17.106354 6
+AGTTG 70 0.86265016 5.702118 7
+GAGAC 75 0.85656327 5.2844243 1
+GTGTC 85 0.8530954 13.93155 1
+GTTGC 85 0.8530954 9.2877 1
+ATAGA 55 0.84417385 7.1018047 8
+GAAAT 55 0.84417385 7.1018047 5
+CATTC 75 0.83565605 5.155441 6
+TCACA 70 0.83200157 5.499531 3
+TGCGG 90 0.8252928 8.485845 3
+GCATT 70 0.8202563 5.421894 4
+GAACC 75 0.8144686 5.0247283 6
+CTCGA 80 0.81441027 9.420691 6
+GAATC 65 0.8125023 5.7837667 6
+TACAG 65 0.81250226 11.567533 7
+TGGTA 65 0.80103225 11.404236 5
+AAGAC 60 0.80005944 6.169791 8
+CAAGG 70 0.7994591 5.2844243 2
+ATGTA 55 0.7913565 6.6574664 4
+AATGT 55 0.7913565 6.6574664 3
+CGGCA 85 0.7906042 8.607354 2
+GAGAG 65 0.7807225 5.557543 8
+ACCAT 65 0.7725729 5.499531 8
+TTCTA 60 0.7695128 5.934226 9
+TAGAA 50 0.7674308 7.1018047 9
+GCATC 75 0.7635097 9.4206915 1
+GTTCC 80 0.76345515 8.831267 6
+AGCTT 65 0.76166654 5.421894 1
+TTAGC 65 0.76166654 5.421894 9
+CTGTA 65 0.76166654 5.421894 2
+ACTTG 65 0.7616664 5.4218936 2
+GTGCT 75 0.7527313 9.287701 3
+ATCAT 55 0.7524662 6.3302927 3
+GTTTG 65 0.7509141 5.345353 9
+GTGTT 65 0.7509141 10.690706 1
+GTCAA 60 0.75000215 11.5675335 6
+AATGC 60 0.75000215 6.252721 95-96
+CAAGT 60 0.7500021 5.7837663 9
+GCAAT 60 0.7500021 5.7837663 4
+GCAAG 65 0.74235487 5.2844243 1
+AGTGT 60 0.7394144 5.7021174 1
+TTAGG 60 0.7394144 5.702118 7
+AGCGG 75 0.73364604 9.052214 1
+ATCCT 65 0.72423524 5.155441 4
+ACTCT 65 0.72423524 5.155441 9
+AGTGA 55 0.7230346 6.082693 6
+AATAA 40 0.71680677 8.291662 6
+AACCT 60 0.71314424 5.4995303 1
+ATTCT 55 0.70538664 5.9342256 7
+AGTCT 60 0.7030768 5.421894 3
+GTGCA 65 0.69590795 9.907589 6
+AAAGT 45 0.69068766 7.101804 8
+AACTG 55 0.6875019 5.7837663 1
+CGAAG 60 0.68525064 5.2844243 4
+GATTG 55 0.67779654 5.702118 6
+GTGAT 55 0.67779654 11.404236 4
+TGTTA 50 0.67440337 12.481857 5
+TTGTA 50 0.6744033 6.240928 9
+TATTG 50 0.6744033 6.240928 7
+CTCTA 60 0.6685249 5.1554413 7
+TACCT 60 0.66852486 10.310882 8
+ATGGA 50 0.65730417 6.082693 8
+ATACA 45 0.6567447 6.7527957 6
+ATCAA 45 0.65674466 6.7527947 9
+TGTAA 45 0.6474735 6.6574664 7
+GCGGT 70 0.6418945 8.485846 4
+GGCCG 80 0.63731974 7.372196 2
+GGTTT 55 0.63538885 10.690706 9
+TTGTG 55 0.63538885 5.345353 1
+TATAT 40 0.62991583 7.2865515 8
+CCTGT 65 0.62030727 8.831266 3
+GTGAG 55 0.6192789 5.2098246 1
+TAGGG 55 0.61927885 5.209824 8
+GAGTT 50 0.6161787 5.7021174 6
+ATGTG 50 0.6161787 5.702118 2
+GAATA 40 0.61394465 7.1018047 6
+CTGCG 70 0.6103493 8.068818 2
+CGGTG 65 0.59604484 8.485845 2
+TAAGG 45 0.5915738 6.082693 9
+AAGTG 45 0.5915737 6.0826926 1
+TATTT 40 0.5905039 6.8306537 8
+GGCAT 55 0.5888452 14.861383 3
+GTATC 50 0.5858973 5.421894 4
+ATAAC 40 0.5837731 13.505591 7
+TTACT 45 0.57713455 5.934226 9
+GTATA 40 0.575532 13.314933 7
+GAGTG 50 0.5629808 5.209824 1
+GTACA 45 0.5625016 5.7837667 6
+ATAGC 45 0.5625016 5.7837667 9
+TCTAC 50 0.5571041 5.1554413 8
+GCGAG 55 0.53800714 9.052216 1
+ACGGG 55 0.5380071 9.052214 1
+GATAA 35 0.5372016 7.1018047 6
+AATAG 35 0.5372016 7.101805 7
+CAACT 45 0.53485817 5.4995303 6
+CATAC 45 0.53485817 5.4995303 5
+GATTC 45 0.52730757 5.421894 6
+AGGTA 40 0.5258433 12.165386 5
+CGGTC 60 0.52315664 8.068819 5
+ACGAG 45 0.51393795 5.2844243 7
+TATTC 40 0.5130085 5.9342256 7
+CTAAA 35 0.51080143 6.7527957 9
+TACAA 35 0.51080143 5.402236 35-39
+CCTTA 45 0.5013937 5.1554413 6
+CAGTA 40 0.50000143 5.7837667 4
+GTGTA 40 0.49294293 5.702118 4
+TAACT 35 0.47884214 6.330293 8
+CTTAA 35 0.47884214 6.330293 7
+CTATA 35 0.47884214 6.330293 4
+TTAAC 35 0.47884214 6.330293 8
+TATCA 35 0.4788421 6.3302927 5
+TCAAC 40 0.47542948 5.499531 7
+ACTCA 40 0.47542942 5.49953 8
+TTAGT 35 0.47208238 10.120425 95-96
+TGTAT 35 0.47208238 6.2409286 3
+ATTGT 35 0.47208235 6.240928 8
+GTTAC 40 0.46871787 5.421894 6
+TGTAC 40 0.46871787 10.843788 7
+AGAGT 35 0.46011293 6.082693 5
+AGTAG 35 0.46011293 6.082693 5
+CTCCG 55 0.45599285 7.672287 6
+GGTAG 40 0.45038468 5.2098246 2
+TTTAC 35 0.44888243 5.9342256 8
+CTACT 40 0.44568333 5.1554418 4
+AACTA 30 0.4378298 6.7527947 9
+TATAG 30 0.43164897 6.6574664 5
+ATATA 25 0.4199739 7.7728767 9
+CTCAA 35 0.41600078 5.499531 9
+TATAC 30 0.4104361 6.3302927 5
+ACTAT 30 0.4104361 6.3302927 6
+TACTA 30 0.4104361 6.3302927 5
+TCGAT 35 0.41012815 10.843788 7
+ACGTT 35 0.41012815 5.421894 4
+CGAAA 30 0.40002972 6.169792 9
+GTAAG 30 0.3943825 6.082693 8
+ATAGG 30 0.3943825 6.082693 3
+TCCTA 35 0.38997287 5.1554413 5
+TTACC 35 0.38997287 5.1554413 7
+ACCGA 35 0.3800853 5.0247273 7
+GCATA 30 0.37500107 5.7837667 1
+TCGAA 30 0.37500107 5.7837667 4
+GCTAA 30 0.37500107 5.7837667 8
+TAGGT 30 0.3697072 5.7021174 7
+GTTAG 30 0.3697072 5.702118 6
+CAATA 25 0.36485815 6.7527947 5
+ATACC 30 0.35657212 5.499531 6
+GACGA 30 0.3426253 5.284424 6
+AAGCG 30 0.3426253 10.568848 7
+GTTTA 25 0.33720168 6.2409286 7
+GTATT 25 0.33720168 12.481857 6
+AGATA 20 0.30697232 7.1018047 5
+CGTCA 30 0.30540386 9.420691 5
+CCTAA 25 0.29714343 5.499531 7
+TACCA 25 0.2971434 5.49953 9
+TGCTA 25 0.29294866 5.421894 7
+TACGT 25 0.29294863 5.4218936 9
+AGACG 25 0.2855211 5.284425 9
+CCTAT 25 0.2785521 5.1554418 3
+TAAGC 20 0.25000072 5.7837667 9
+CTAAG 20 0.25000072 5.7837667 8
+CGATT 20 0.23435894 5.421894 9
+GGGTA 20 0.22519234 5.2098246 2
+ACGCA 20 0.21719159 5.0247273 5
+GCGAA 15 0.17131266 5.284425 3
+CGAAC 15 0.16289368 5.0247273 5
+>>END_MODULE
diff --git a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
new file mode 100644
index 0000000000000000000000000000000000000000..0951bea84834b611c323c8e0b1b77ae55f0461b1
--- /dev/null
+++ b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
@@ -0,0 +1,80 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+class FastqcV0101Test extends TestNGSuite with Matchers {
+
+ /** Returns the absolute path to test resource directory as a File object */
+ private val resourceDir: File = new File(Paths.get(getClass.getResource("/").toURI).toString)
+
+ /** Given a resource file name, returns the the absolute path to it as a File object */
+ private def resourceFile(p: String): File = new File(resourceDir, p)
+
+ /** Mock output file of a FastQC v0.10.1 run */
+ // the file doesn't actually exist, we just need it so the outputDir value can be computed correctly
+ private val outputv0101: File = resourceFile("v0101.fq_fastqc.zip")
+
+ @Test def testOutputDir() = {
+ val fqc = new Fastqc(null)
+ fqc.output = outputv0101
+ fqc.outputDir shouldBe new File(resourceDir, "v0101.fq_fastqc")
+ }
+
+ @Test def testQcModules() = {
+ val fqc = new Fastqc(null)
+ fqc.output = outputv0101
+ // 11 QC modules
+ fqc.qcModules.size shouldBe 11
+ // first module
+ fqc.qcModules.keySet should contain("Basic Statistics")
+ // mid (6th module)
+ fqc.qcModules.keySet should contain("Per sequence GC content")
+ // last module
+ fqc.qcModules.keySet should contain("Kmer Content")
+ }
+
+ @Test def testSingleQcModule() = {
+ val fqc = new Fastqc(null)
+ fqc.output = outputv0101
+ fqc.qcModules("Basic Statistics").name should ===("Basic Statistics")
+ fqc.qcModules("Basic Statistics").status should ===("pass")
+ fqc.qcModules("Basic Statistics").lines.size shouldBe 8
+ }
+
+ @Test def testEncoding() = {
+ val fqc = new Fastqc(null)
+ fqc.output = outputv0101
+ fqc.encoding shouldBe "Sanger / Illumina 1.9"
+ }
+
+ @Test def testFoundAdapter() = {
+ val fqc = new Fastqc(null)
+ fqc.output = outputv0101
+ fqc.contaminants = Option(resourceFile("fqc_contaminants_v0101.txt"))
+ val adapters = fqc.foundAdapters
+ adapters.size shouldBe 1
+ adapters.head.name should ===("TruSeq Adapter, Index 1")
+ // from fqc_contaminants_v0101.txt
+ adapters.head.seq should ===("GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG")
+ }
+}
\ No newline at end of file