Merge branch 'feature-cutadapt-adapterreporting' into 'develop'

Fix reporting of found Adapters with counts by Cutadapt in Json. the adapters used by Cutadapt were not reported in the json. This fix will solve this. fixes #319 fixes #325 See merge request !369

Merge branch 'feature-cutadapt-adapterreporting' into 'develop'
e980fd75 · Peter van 't Hof · 9e3d9653 · d01a6749 · e980fd75 · e980fd75
Commit e980fd75 authored 8 years ago by Peter van 't Hof
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
@@ -24,6 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }

 import scala.collection.mutable
 import scala.io.Source
+import scala.util.matching.Regex

 /**
 * Extension for cutadapt
@@ -163,6 +164,51 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
    (if (outputAsStsout) "" else required("--output", fastqOutput) +
      " > " + required(statsOutput))

+  def extractClippedAdapters(statsOutput: File): Map[String, Any] = {
+    val histoCountRow: Regex = """([\d]+)\t([\d]+)\t.*""".r
+    val adapterR = """Sequence: ([C|T|A|G]+);.*Trimmed: ([\d]+) times\.""".r
+
+    val statsFile = Source.fromFile(statsOutput)
+    val adapterRawStats: Array[String] = statsFile.mkString
+      .split("=== Adapter [\\d]+ ===")
+      .filter(_.contains("Sequence")
+      )
+    statsFile.close()
+
+    adapterRawStats.map(adapter => {
+      var adapterName = ""
+      var adapterCount = 0
+      // identify the adapter name and count
+      for (line <- adapter.split("\n")) {
+        line match {
+          case adapterR(adapter, count) => {
+            adapterName = adapter
+            adapterCount = count.toInt
+          }
+          case _ =>
+        }
+      }
+
+      // parse the block that gives the histogram of clipped bases and from which end
+      val counts = adapter.split("Overview of removed sequences ")
+        .filter(x => x.contains("length"))
+        .map(clipSideRawStats => {
+          val clipSideLabel = if (clipSideRawStats.contains("5'")) { "5p" } else { "3p" }
+
+          val histogramValues = clipSideRawStats.split("\n").flatMap({
+            case histoCountRow(length, count) => Some(length.toInt -> count.toInt)
+            case _                            => None
+          })
+          clipSideLabel -> histogramValues.toMap
+        })
+
+      adapterName -> Map(
+        "count" -> adapterCount,
+        "histogram" -> counts.toMap
+      )
+    }).toMap // converting the Array[String] containing map-items to Map with 'toMap'
+  }
+
  /** Output summary stats */
  def summaryStats: Map[String, Any] = {
    /**
@@ -177,7 +223,6 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
    val tooLongR = """.* that were too long: *([,\d]+) .*""".r

    val tooManyN = """.* with too many N: *([,\d]+) .*""".r
-    val adapterR = """Sequence ([C|T|A|G]*);.*Trimmed: ([,\d]+) times.""".r

    val basePairsProcessed = """Total basepairs processed: *([,\d]+) bp""".r
    val basePairsWritten = """Total written \(filtered\): *([,\d]+) bp .*""".r
@@ -192,24 +237,28 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
      "bpoutput" -> 0,
      "toomanyn" -> 0
    )
-    val adapterStats: mutable.Map[String, Long] = mutable.Map()
+
+    // extract the adapters with its histogram
+    val adapterStats = if (statsOutput.exists) {
+      extractClippedAdapters(statsOutput)
+    } else Map.empty

    if (statsOutput.exists) {
      val statsFile = Source.fromFile(statsOutput)
      for (line <- statsFile.getLines()) {
        line match {
-          case processedReads(m)        => stats("processed") = m.replaceAll(",", "").toLong
-          case withAdapters(m)          => stats("withadapters") = m.replaceAll(",", "").toLong
-          case readsPassingFilters(m)   => stats("passingfilters") = m.replaceAll(",", "").toLong
-          case tooShortR(m)             => stats("tooshort") = m.replaceAll(",", "").toLong
-          case tooLongR(m)              => stats("toolong") = m.replaceAll(",", "").toLong
-          case tooManyN(m)              => stats("toomanyn") = m.replaceAll(",", "").toLong
-          case basePairsProcessed(m)    => stats("bpinput") = m.replaceAll(",", "").toLong
-          case basePairsWritten(m)      => stats("bpoutput") = m.replaceAll(",", "").toLong
-          case adapterR(adapter, count) => adapterStats += (adapter -> count.toLong)
-          case _                        =>
+          case processedReads(m)      => stats("processed") = m.replaceAll(",", "").toLong
+          case withAdapters(m)        => stats("withadapters") = m.replaceAll(",", "").toLong
+          case readsPassingFilters(m) => stats("passingfilters") = m.replaceAll(",", "").toLong
+          case tooShortR(m)           => stats("tooshort") = m.replaceAll(",", "").toLong
+          case tooLongR(m)            => stats("toolong") = m.replaceAll(",", "").toLong
+          case tooManyN(m)            => stats("toomanyn") = m.replaceAll(",", "").toLong
+          case basePairsProcessed(m)  => stats("bpinput") = m.replaceAll(",", "").toLong
+          case basePairsWritten(m)    => stats("bpoutput") = m.replaceAll(",", "").toLong
+          case _                      =>
        }
      }
+      statsFile.close()
    }

    val cleanReads = stats("processed") - stats("withadapters")
@@ -223,8 +272,8 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
      "num_reads_discarded_too_long" -> stats("toolong"),
      "num_reads_discarded_many_n" -> stats("toomanyn"),
      "num_bases_input" -> stats("bpinput"),
-      "num_based_output" -> stats("bpoutput"),
-      adaptersStatsName -> adapterStats.toMap
+      "num_bases_output" -> stats("bpoutput"),
+      adaptersStatsName -> adapterStats
    )
  }


--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
@@ -16,6 +16,7 @@
 package nl.lumc.sasc.biopet.pipelines.flexiprep

 import nl.lumc.sasc.biopet.utils.config.Configurable
+import scala.collection.JavaConversions._

 /**
 * Cutadapt wrapper specific for Flexiprep.
@@ -41,23 +42,26 @@ class Cutadapt(root: Configurable, fastqc: Fastqc) extends nl.lumc.sasc.biopet.e
    val adapterCounts: Map[String, Any] = initStats.get(adaptersStatsName) match {
      // "adapters" key found in statistics
      case Some(m: Map[_, _]) => m.flatMap {
-        case (seq: String, count) =>
-          seqToNameMap.get(seq) match {
+        case (adapterSequence: String, adapterStats: Map[_, _]) =>
+          seqToNameMap.get(adapterSequence) match {
            // adapter sequence is found by FastQC
-            case Some(n) => Some(n -> Map("sequence" -> seq, "count" -> count))
+            case Some(adapterSeqName) => {
+              Some(adapterSeqName ->
+                Map("sequence" -> adapterSequence, "stats" -> adapterStats.toMap)
+              )
+            }
            // adapter sequence is clipped but not found by FastQC ~ should not happen since all clipped adapter
            // sequences come from FastQC
            case _ =>
-              throw new IllegalStateException(s"Adapter '$seq' is clipped but not found by FastQC in '$fastqInput'.")
+              throw new IllegalStateException(s"Adapter '$adapterSequence' is clipped but not found by FastQC in '$fastqInput'.")
          }
        // FastQC found no adapters
        case otherwise =>
-          ;
          logger.debug(s"No adapters found for summarizing in '$fastqInput'.")
          None
      }
      // "adapters" key not found ~ something went wrong in our part
-      case _ => throw new RuntimeException(s"Required key 'adapters' not found in stats entry '$fastqInput'.")
+      case _ => throw new RuntimeException(s"Required key '${adaptersStatsName}' not found in stats entry '${fastqInput}'.")
    }
    initStats.updated(adaptersStatsName, adapterCounts)
  }

--- a/flexiprep/src/test/resources/ct-test.R1.clip.stats
+++ b/flexiprep/src/test/resources/ct-test.R1.clip.stats
+This is cutadapt 1.9.1 with Python 2.7.6
+Command line parameters: -b CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTG -b CAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG --error-rate 0.2 --times 2 -m 15 ct_r1.fq.gz.seqtk.fq --output ct_r1.fq.gz.cutadapt.fq
+Trimming 4 adapters with at most 20.0% errors in single-end mode ...
+Finished in 0.19 s (189 us/read; 0.32 M reads/minute).
+
+=== Summary ===
+
+Total reads processed:                   1,000
+Reads with adapters:                       440 (44.0%)
+Reads that were too short:                  15 (1.5%)
+Reads written (passing filters):           985 (98.5%)
+
+Total basepairs processed:       100,000 bp
+Total written (filtered):         89,423 bp (89.4%)
+
+=== Adapter 1 ===
+
+Sequence: CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC; Type: variable 5'/3'; Length: 63; Trimmed: 94 times.
+18 times, it overlapped the 5' end of a read
+76 times, it overlapped the 3' end or was within the read
+
+No. of allowed errors:
+0-4 bp: 0; 5-9 bp: 1; 10-14 bp: 2; 15-19 bp: 3; 20-24 bp: 4; 25-29 bp: 5; 30-34 bp: 6; 35-39 bp: 7; 40-44 bp: 8; 45-49 bp: 9; 50-54 bp: 10; 55-59 bp: 11; 60-63 bp: 12
+
+Overview of removed sequences (5')
+length	count	expect	max.err	error counts
+3	8	15.6	0	8
+4	3	3.9	0	2 1
+5	2	1.0	1	0 2
+6	4	0.2	1	1 3
+9	1	0.0	1	0 0 1
+
+
+Overview of removed sequences (3' or within)
+length	count	expect	max.err	error counts
+3	13	15.6	0	13
+4	19	3.9	0	3 16
+5	21	1.0	1	0 21
+6	18	0.2	1	1 17
+7	2	0.1	1	0 2
+9	1	0.0	1	0 0 1
+11	1	0.0	2	0 0 1
+12	1	0.0	2	0 0 1
+
+=== Adapter 2 ===
+
+Sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTG; Type: variable 5'/3'; Length: 63; Trimmed: 340 times.
+117 times, it overlapped the 5' end of a read
+223 times, it overlapped the 3' end or was within the read
+
+No. of allowed errors:
+0-4 bp: 0; 5-9 bp: 1; 10-14 bp: 2; 15-19 bp: 3; 20-24 bp: 4; 25-29 bp: 5; 30-34 bp: 6; 35-39 bp: 7; 40-44 bp: 8; 45-49 bp: 9; 50-54 bp: 10; 55-59 bp: 11; 60-63 bp: 12
+
+Overview of removed sequences (5')
+length	count	expect	max.err	error counts
+3	14	15.6	0	14
+4	29	3.9	0	6 23
+5	32	1.0	1	3 29
+6	36	0.2	1	0 36
+8	1	0.0	1	0 1
+9	1	0.0	1	0 0 1
+10	1	0.0	2	0 0 1
+11	2	0.0	2	0 0 2
+37	1	0.0	7	0 0 0 0 0 1
+
+
+Overview of removed sequences (3' or within)
+length	count	expect	max.err	error counts
+3	18	15.6	0	18
+4	9	3.9	0	5 4
+5	15	1.0	1	8 7
+6	10	0.2	1	8 2
+7	7	0.1	1	5 2
+8	10	0.0	1	9 1
+9	6	0.0	1	5 1
+10	8	0.0	2	5 0 3
+11	4	0.0	2	4
+12	4	0.0	2	4
+13	9	0.0	2	9
+14	4	0.0	2	3 0 1
+15	7	0.0	3	7
+16	2	0.0	3	2
+17	4	0.0	3	2 1 0 1
+18	2	0.0	3	2
+19	2	0.0	3	2
+20	2	0.0	4	0 1 1
+21	7	0.0	4	6 1
+22	7	0.0	4	7
+23	2	0.0	4	2
+24	3	0.0	4	3
+25	5	0.0	5	5
+26	5	0.0	5	5
+27	8	0.0	5	8
+28	6	0.0	5	5 1
+29	2	0.0	5	2
+30	5	0.0	6	5
+31	3	0.0	6	3
+32	8	0.0	6	8
+33	1	0.0	6	1
+34	5	0.0	6	0 5
+35	2	0.0	7	0 0 0 0 0 0 2
+36	3	0.0	7	0 0 0 0 0 0 3
+37	4	0.0	7	0 0 0 0 0 0 0 2 2
+38	2	0.0	7	0 0 0 0 0 0 0 0 0 2
+39	4	0.0	7	0 0 0 0 1 0 0 0 0 3
+40	3	0.0	8	0 0 0 0 0 0 0 3
+41	1	0.0	8	0 0 0 0 0 0 0 1
+42	4	0.0	8	0 0 0 0 0 0 0 0 4
+43	5	0.0	8	0 0 0 0 0 0 0 0 0 5
+44	3	0.0	8	0 0 0 0 0 0 0 0 0 0 3
+46	1	0.0	9	0 0 0 0 0 0 0 0 0 0 1
+49	1	0.0	9	0 0 0 0 0 1
+
+=== Adapter 3 ===
+
+Sequence: CAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC; Type: variable 5'/3'; Length: 63; Trimmed: 0 times.
+
+=== Adapter 4 ===
+
+Sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG; Type: variable 5'/3'; Length: 63; Trimmed: 82 times.
+15 times, it overlapped the 5' end of a read
+67 times, it overlapped the 3' end or was within the read
+
+No. of allowed errors:
+0-4 bp: 0; 5-9 bp: 1; 10-14 bp: 2; 15-19 bp: 3; 20-24 bp: 4; 25-29 bp: 5; 30-34 bp: 6; 35-39 bp: 7; 40-44 bp: 8; 45-49 bp: 9; 50-54 bp: 10; 55-59 bp: 11; 60-63 bp: 12
+
+Overview of removed sequences (5')
+length	count	expect	max.err	error counts
+26	1	0.0	5	0 1
+61	2	0.0	12	0 0 0 2
+64	11	0.0	12	0 0 0 11
+72	1	0.0	12	0 0 0 0 0 0 0 0 0 0 0 1
+
+
+Overview of removed sequences (3' or within)
+length	count	expect	max.err	error counts
+45	3	0.0	9	0 0 0 3
+46	2	0.0	9	0 0 0 2
+47	3	0.0	9	0 0 0 3
+48	3	0.0	9	0 0 0 3
+49	2	0.0	9	0 0 0 2
+50	3	0.0	10	0 0 0 3
+51	2	0.0	10	0 0 0 2
+52	6	0.0	10	0 0 0 6
+53	1	0.0	10	0 0 0 1
+54	5	0.0	10	0 0 0 4 0 1
+56	2	0.0	11	0 0 0 2
+57	2	0.0	11	0 0 0 2
+58	2	0.0	11	0 0 0 2
+59	3	0.0	11	0 0 0 2 0 0 0 0 0 1
+61	1	0.0	12	0 0 0 0 0 1
+62	3	0.0	12	0 0 0 2 1
+63	1	0.0	12	0 0 0 0 1
+66	3	0.0	12	0 0 0 3
+67	3	0.0	12	0 0 0 3
+70	1	0.0	12	0 0 0 1
+72	1	0.0	12	0 0 0 1
+80	1	0.0	12	0 0 0 1
+99	14	0.0	12	0 0 0 14
+
--- a/flexiprep/src/test/resources/fqc_contaminants_v0112.txt
+++ b/flexiprep/src/test/resources/fqc_contaminants_v0112.txt
+# 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.babraham.ac.uk/bugzilla/
+# or by directly emailing simon.andrews@babraham.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
+TruSeq Adapter, Index 13						GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAACTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 14						GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCGTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 15						GATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAGTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 16						GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCCTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 18						GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 19						GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 20						GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCTTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 21						GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGGTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 22						GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACGTTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 23						GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCACTCTTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 25						GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 27						GATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTTTCTCGTATGCCGTCTTCTGCTTG
+
+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
--- a/flexiprep/src/test/resources/v0101.fq_fastqc/fastqc_data.txt
+++ b/flexiprep/src/test/resources/v0101.fq_fastqc/fastqc_data.txt
-====
-    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.
-====
-
-##FastQC	0.10.1
+##FastQC	0.11.2
 >>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	
+#Measure	Value
+Filename	ct_r1.fq.gz
+File type	Conventional base calls
+Encoding	Sanger / Illumina 1.9
+Total Sequences	1000
+Sequences flagged as poor quality	0
+Sequence length	100
+%GC	53
 >>END_MODULE
 >>Per base sequence quality	fail
 #Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
@@ -36,26 +20,111 @@ Sequence length	100
 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
+10-11	37.709	39.0	37.0	39.0	35.0	39.0
+12-13	37.6135	39.0	37.0	39.0	35.0	39.0
+14-15	38.793	40.0	38.0	41.0	34.5	41.0
+16-17	39.033500000000004	40.5	38.0	41.0	35.0	41.0
+18-19	38.942	40.0	38.0	41.0	35.0	41.0
+20-21	38.888	40.0	38.0	41.0	35.0	41.0
+22-23	38.807	40.0	38.0	41.0	35.0	41.0
+24-25	38.702	40.0	38.0	41.0	34.0	41.0
+26-27	38.65	40.0	38.0	41.0	34.5	41.0
+28-29	38.4885	40.0	38.0	41.0	34.5	41.0
+30-31	38.307	40.0	38.0	41.0	34.0	41.0
+32-33	38.433499999999995	40.0	38.0	41.0	34.0	41.0
+34-35	38.3425	40.0	38.0	41.0	33.5	41.0
+36-37	38.1185	40.0	37.5	41.0	33.5	41.0
+38-39	38.088499999999996	40.0	37.0	41.0	33.5	41.0
+40-41	37.555	40.0	36.0	41.0	32.5	41.0
+42-43	37.504999999999995	40.0	36.0	41.0	33.0	41.0
+44-45	37.167	39.0	35.5	41.0	32.0	41.0
+46-47	36.980999999999995	39.0	35.0	41.0	31.0	41.0
+48-49	36.8635	39.0	35.0	40.5	31.0	41.0
+50-51	36.4125	38.5	35.0	40.0	30.5	41.0
+52-53	35.528000000000006	37.5	34.5	40.0	28.5	41.0
+54-55	34.925	37.0	33.5	40.0	27.5	41.0
+56-57	34.8735	37.0	34.0	40.0	27.5	41.0
+58-59	34.7225	36.0	33.5	40.0	28.0	41.0
+60-61	34.67400000000001	36.0	34.0	39.0	28.5	40.5
+62-63	33.841499999999996	35.0	33.0	38.5	26.5	40.0
+64-65	33.549	35.0	33.0	38.0	26.0	40.0
+66-67	32.971999999999994	35.0	33.0	37.0	26.0	40.0
+68-69	32.1635	35.0	32.0	37.0	22.5	39.0
+70-71	30.002000000000002	34.0	30.5	36.0	2.0	39.0
+72-73	29.0695	34.0	29.0	35.5	2.0	38.5
+74-75	28.641	34.0	29.0	35.0	2.0	38.0
+76-77	27.8495	33.0	27.5	35.0	2.0	36.0
+78-79	26.5345	33.0	24.0	35.0	2.0	36.5
+80-81	26.140500000000003	33.0	23.0	35.0	2.0	36.0
+82-83	25.784	33.0	21.5	35.0	2.0	35.0
+84-85	25.6115	33.0	20.0	35.0	2.0	35.0
+86-87	25.1755	33.0	17.0	35.0	2.0	35.0
+88-89	24.600499999999997	31.5	13.5	34.0	2.0	35.0
+90-91	24.088	31.5	6.5	34.0	2.0	35.0
+92-93	24.16	32.0	8.5	34.0	2.0	35.0
+94-95	23.02	30.0	2.0	34.0	2.0	35.0
+96-97	23.183	30.5	2.0	34.0	2.0	35.0
+98-99	22.75	30.5	2.0	34.0	2.0	35.0
 100	21.984	30.0	2.0	34.0	2.0	35.0
 >>END_MODULE
+>>Per tile sequence quality	pass
+#Tile	Base	Mean
+1101	1	0.0
+1101	2	0.0
+1101	3	0.0
+1101	4	0.0
+1101	5	0.0
+1101	6	0.0
+1101	7	0.0
+1101	8	0.0
+1101	9	0.0
+1101	10-11	0.0
+1101	12-13	0.0
+1101	14-15	0.0
+1101	16-17	0.0
+1101	18-19	0.0
+1101	20-21	0.0
+1101	22-23	0.0
+1101	24-25	0.0
+1101	26-27	0.0
+1101	28-29	0.0
+1101	30-31	0.0
+1101	32-33	0.0
+1101	34-35	0.0
+1101	36-37	0.0
+1101	38-39	0.0
+1101	40-41	0.0
+1101	42-43	0.0
+1101	44-45	0.0
+1101	46-47	0.0
+1101	48-49	0.0
+1101	50-51	0.0
+1101	52-53	0.0
+1101	54-55	0.0
+1101	56-57	0.0
+1101	58-59	0.0
+1101	60-61	0.0
+1101	62-63	0.0
+1101	64-65	0.0
+1101	66-67	0.0
+1101	68-69	0.0
+1101	70-71	0.0
+1101	72-73	0.0
+1101	74-75	0.0
+1101	76-77	0.0
+1101	78-79	0.0
+1101	80-81	0.0
+1101	82-83	0.0
+1101	84-85	0.0
+1101	86-87	0.0
+1101	88-89	0.0
+1101	90-91	0.0
+1101	92-93	0.0
+1101	94-95	0.0
+1101	96-97	0.0
+1101	98-99	0.0
+1101	100	0.0
+>>END_MODULE
 >>Per sequence quality scores	pass
 #Quality	Count
 11	1.0
@@ -99,57 +168,53 @@ Sequence length	100
 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
+10-11	25.15	24.0	27.55	23.3
+12-13	26.200000000000003	22.3	24.65	26.85
+14-15	24.75	21.95	26.3	27.0
+16-17	25.4	21.7	26.55	26.35
+18-19	27.650000000000002	21.6	25.85	24.9
+20-21	24.8	21.8	24.3	29.099999999999998
+22-23	25.900000000000002	23.05	24.15	26.900000000000002
+24-25	24.85	21.4	25.900000000000002	27.85
+26-27	24.7	20.849999999999998	25.0	29.45
+28-29	24.4	23.3	24.95	27.35
+30-31	27.35	20.95	25.15	26.55
+32-33	24.9	22.05	23.400000000000002	29.65
+34-35	25.6	22.15	25.900000000000002	26.35
+36-37	24.95	21.2	23.400000000000002	30.45
+38-39	24.8	23.35	23.7	28.15
+40-41	27.0	23.35	23.599999999999998	26.05
+42-43	25.15	22.35	23.799999999999997	28.7
+44-45	26.200000000000003	20.7	24.3	28.799999999999997
+46-47	26.3	24.0	23.150000000000002	26.55
+48-49	25.5	23.3	24.05	27.150000000000002
+50-51	27.55	22.75	23.7	26.0
+52-53	24.45	23.400000000000002	23.1	29.049999999999997
+54-55	27.450000000000003	21.85	23.0	27.700000000000003
+56-57	25.85	22.15	23.5	28.499999999999996
+58-59	24.05	22.75	25.6	27.6
+60-61	25.25	20.95	23.45	30.349999999999998
+62-63	27.3	21.9	23.7	27.1
+64-65	26.178535606820464	24.57372116349047	22.617853560682047	26.629889669007024
+66-67	25.7	23.75	22.05	28.499999999999996
+68-69	25.405679513184587	23.52941176470588	24.036511156186613	27.028397565922923
+70-71	25.159574468085104	23.085106382978722	23.138297872340424	28.617021276595743
+72-73	26.031065881092662	26.513122656668454	20.51419389394751	26.941617568291377
+74-75	25.197680548234054	26.56826568265683	21.929362150764366	26.304691618344755
+76-77	25.911812738160044	23.51660315732172	24.550898203592812	26.02068590092542
+78-79	26.16345062429058	22.985244040862657	21.793416572077184	29.05788876276958
+80-81	26.98324022346369	25.474860335195533	21.005586592178773	26.536312849162012
+82-83	26.46370023419204	24.355971896955502	22.131147540983605	27.049180327868854
+84-85	26.124567474048444	23.18339100346021	22.145328719723185	28.546712802768166
+86-87	25.976331360946748	25.443786982248522	22.36686390532544	26.21301775147929
+88-89	25.503742084052966	23.54634427173287	23.316062176165804	27.63385146804836
+90-91	23.832052040212893	21.525724423418097	25.901833234772326	28.74039030159669
+92-93	24.525139664804467	22.849162011173185	23.743016759776538	28.88268156424581
+94-95	25.161987041036717	24.028077753779698	22.4622030237581	28.347732181425485
+96-97	25.37393162393162	24.412393162393162	23.664529914529915	26.549145299145298
+98-99	25.67703109327984	23.620862587763288	22.71815446339017	27.9839518555667
 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
@@ -265,24 +330,51 @@ Sequence length	100
 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
+10-11	0.0
+12-13	0.0
+14-15	0.0
+16-17	0.0
+18-19	0.0
+20-21	0.0
+22-23	0.0
+24-25	0.0
+26-27	0.0
+28-29	0.0
+30-31	0.0
+32-33	0.0
+34-35	0.0
+36-37	0.0
+38-39	0.0
+40-41	0.0
+42-43	0.0
+44-45	0.0
+46-47	0.0
+48-49	0.0
+50-51	0.0
+52-53	0.0
+54-55	0.0
+56-57	0.0
+58-59	0.0
+60-61	0.0
+62-63	0.0
+64-65	0.3
+66-67	0.0
+68-69	1.4000000000000001
+70-71	6.0
+72-73	6.65
+74-75	5.1499999999999995
+76-77	8.15
+78-79	11.899999999999999
+80-81	10.5
+82-83	14.6
+84-85	13.3
+86-87	15.5
+88-89	13.15
+90-91	15.45
+92-93	10.5
+94-95	7.3999999999999995
+96-97	6.4
+98-99	0.3
 100	0.0
 >>END_MODULE
 >>Sequence Length Distribution	pass
@@ -290,565 +382,85 @@ Sequence length	100
 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
+#Total Deduplicated Percentage	97.2
+#Duplication Level	Percentage of deduplicated	Percentage of total
+1	99.38271604938271	96.6
+2	0.411522633744856	0.8
+3	0.0	0.0
+4	0.0	0.0
+5	0.0	0.0
+6	0.0	0.0
+7	0.0	0.0
+8	0.0	0.0
+9	0.0	0.0
+>10	0.205761316872428	2.6
+>50	0.0	0.0
+>100	0.0	0.0
+>500	0.0	0.0
+>1k	0.0	0.0
+>5k	0.0	0.0
+>10k+	0.0	0.0
 >>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)
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCCAAGATCTCGTAT	14	1.4000000000000001	TruSeq Adapter, Index 18 (97% over 37bp)
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCCAAGATCTCGTATG	12	1.2	TruSeq Adapter, Index 18 (97% over 37bp)
 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)
+CGGAAGAGCACACGTCTGAACTCCAGTCACTTCCAAGATCTCGTATGCCG	2	0.2	TruSeq Adapter, Index 18 (97% over 34bp)
+>>END_MODULE
+>>Adapter Content	fail
+#Position	Illumina Universal Adapter	Illumina Small RNA Adapter	Nextera Transposase Sequence
+1	1.4	0.0	0.0
+2	1.4	0.0	0.0
+3	1.4	0.0	0.0
+4	1.4	0.0	0.0
+5	1.4	0.0	0.0
+6	1.4	0.0	0.0
+7	1.4	0.0	0.0
+8	1.4	0.0	0.0
+9	1.4	0.0	0.0
+10-11	1.4	0.0	0.0
+12-13	1.4	0.0	0.0
+14-15	1.4	0.0	0.0
+16-17	1.4	0.0	0.0
+18-19	1.4	0.0	0.0
+20-21	1.5	0.0	0.0
+22-23	1.5	0.0	0.0
+24-25	1.5	0.0	0.0
+26-27	1.5	0.0	0.0
+28-29	1.6	0.0	0.0
+30-31	1.7	0.0	0.0
+32-33	1.9	0.0	0.0
+34-35	2.4	0.0	0.0
+36-37	2.45	0.0	0.0
+38-39	2.95	0.0	0.0
+40-41	3.25	0.0	0.0
+42-43	3.75	0.0	0.0
+44-45	4.2	0.0	0.0
+46-47	4.9	0.0	0.0
+48-49	5.699999999999999	0.0	0.0
+50-51	6.300000000000001	0.0	0.0
+52-53	6.949999999999999	0.0	0.0
+54-55	7.65	0.0	0.0
+56-57	8.399999999999999	0.0	0.0
+58-59	9.350000000000001	0.0	0.0
+60-61	9.899999999999999	0.0	0.0
+62-63	10.600000000000001	0.0	0.0
+64-65	11.3	0.0	0.0
+66-67	12.0	0.0	0.0
+68-69	13.05	0.0	0.0
+70-71	13.6	0.0	0.0
+72-73	14.5	0.0	0.0
+74-75	15.55	0.0	0.0
+76-77	16.15	0.0	0.0
+78-79	17.2	0.0	0.0
+80-81	17.700000000000003	0.0	0.0
+82-83	18.15	0.0	0.0
+84-85	18.75	0.0	0.0
+86-87	19.799999999999997	0.0	0.0
+88	20.6	0.0	0.0
 >>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
+>>Kmer Content	pass
 >>END_MODULE
--- a/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CutadaptTest.scala
+++ b/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CutadaptTest.scala
+/**
+ * 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 org.testng.annotations.Test
+
+class CutadaptTest extends FastqcV0101Test {
+  /** Mock output file of a Cutadapt 1.9 run */
+  private[flexiprep] val cutadaptOut: File = resourceFile("ct-test.R1.clip.stats")
+
+  def testFastQCinstance: Fastqc = {
+    val fqc = new Fastqc(null)
+    fqc.output = outputv0101
+    fqc.contaminants = Option(resourceFile("fqc_contaminants_v0112.txt"))
+    //    fqc.beforeGraph()
+    fqc
+  }
+
+  def testCutadaptInst: Cutadapt = {
+    val caExe = new Cutadapt(null, testFastQCinstance)
+    caExe.statsOutput = cutadaptOut
+    caExe
+  }
+
+  @Test def testAdapterFound() = {
+    val cutadapt = testCutadaptInst
+    val adapters = cutadapt.extractClippedAdapters(cutadaptOut)
+    adapters.keys.size shouldBe 4
+
+    adapters.get("CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC") shouldBe Some(
+      Map(
+        "count" -> 94,
+        "histogram" -> Map(
+          "5p" -> Map(5 -> 2, 6 -> 4, 9 -> 1, 3 -> 8, 4 -> 3),
+          "3p" -> Map(5 -> 21, 6 -> 18, 9 -> 1, 12 -> 1, 7 -> 2, 3 -> 13, 11 -> 1, 4 -> 19)
+        )
+      )
+    )
+
+    adapters.get("CAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC") shouldBe Some(
+      Map(
+        "count" -> 0,
+        "histogram" -> Map()
+      )
+    )
+  }
+
+  @Test def testSummary() = {
+    val cutadapt = testCutadaptInst
+    val summary = cutadapt.summaryStats
+
+    summary.keys shouldBe Set("num_bases_input", "num_reads_input", "num_reads_output",
+      "num_reads_with_adapters", "num_reads_affected", "num_reads_discarded_too_long",
+      "adapters", "num_reads_discarded_many_n", "num_reads_discarded_too_short", "num_bases_output")
+
+    summary.keys.size shouldBe 10
+    summary("adapters").asInstanceOf[Map[String, Map[String, Any]]].keys.size shouldBe 4
+
+    summary("num_bases_input") shouldBe 100000
+    summary("num_reads_input") shouldBe 1000
+    summary("num_reads_output") shouldBe 985
+    summary("num_reads_with_adapters") shouldBe 440
+    summary("num_reads_affected") shouldBe 425
+    summary("num_reads_discarded_too_long") shouldBe 0
+    summary("num_reads_discarded_many_n") shouldBe 0
+    summary("num_reads_discarded_too_short") shouldBe 15
+    summary("num_bases_output") shouldBe 89423
+  }
+}
--- a/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
+++ b/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
@@ -25,14 +25,14 @@ 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)
+  private[flexiprep] 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)
+  private[flexiprep] 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")
+  private[flexiprep] val outputv0101: File = resourceFile("v0101.fq_fastqc.zip")

  @Test def testOutputDir() = {
    val fqc = new Fastqc(null)
@@ -44,7 +44,7 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
    val fqc = new Fastqc(null)
    fqc.output = outputv0101
    // 11 QC modules
-    fqc.qcModules.size shouldBe 11
+    fqc.qcModules.size shouldBe 12
    // first module
    fqc.qcModules.keySet should contain("Basic Statistics")
    // mid (6th module)
@@ -83,4 +83,23 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
    adapters.last.seq shouldEqual "GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG"

  }
+
+  @Test def testPerBaseSequenceQuality() = {
+    val fqc = new Fastqc(null)
+    fqc.output = outputv0101
+
+    val perBaseSequenceQuality = fqc.perBaseSequenceQuality
+    perBaseSequenceQuality.size shouldBe 55
+    perBaseSequenceQuality.keys should contain("54-55")
+  }
+
+  @Test def testPerBaseSequenceContent() = {
+    val fqc = new Fastqc(null)
+    fqc.output = outputv0101
+
+    val perBaseSequenceContent: Map[String, Map[String, Double]] = fqc.perBaseSequenceContent
+    perBaseSequenceContent.size shouldBe 55
+    perBaseSequenceContent.keys should contain("1")
+  }
+
 }
\ No newline at end of file