diff --git a/docs/config.md b/docs/config.md
index c10419859bed6d3f510c80afe0b27fea913d774f..de3342b195b1dc7acb338729792d9dabc59c5228 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -72,16 +72,16 @@ Global setting examples are:
#### Example settings config
~~~
{
- "reference": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/ucsc.hg19_nohap.fasta",
- "dbsnp": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/dbsnp_137.hg19_nohap.vcf",
+ "reference": "/references/hg19_nohap/ucsc.hg19_nohap.fasta",
+ "dbsnp": "/references/hg19_nohap/dbsnp_137.hg19_nohap.vcf",
"joint_variantcalling": false,
"haplotypecaller": { "scattercount": 100 },
"multisample": { "haplotypecaller": { "scattercount": 1000 } },
"picard": { "validationstringency": "LENIENT" },
"library_variantcalling_temp": true,
- "target_bed_temp": "/data/LGTC/projects/vandoorn-melanoma/analysis/target.bed",
+ "target_bed_temp": "analysis/target.bed",
"min_dp": 5,
- "bedtools": {"exe":"/share/isilon/system/local/BEDtools/bedtools-2.17.0/bin/bedtools"},
+ "bedtools": {"exe":"/BEDtools/bedtools-2.17.0/bin/bedtools"},
"bam_to_fastq": true,
"baserecalibrator": { "memory_limit": 8, "vmem":"16G" },
"samtofastq": {"memory_limit": 8, "vmem": "16G"},
@@ -95,4 +95,4 @@ Global setting examples are:
### JSON validation
To check if the JSON file created is correct we can use multiple options the simplest way is using [this](http://jsonformatter.curiousconcept.com/)
-website. It is also possible to use Python or Scala for validating but this requires some more knowledge.
\ No newline at end of file
+website. It is also possible to use Python or Scala for validating but this requires some more knowledge.
diff --git a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
index f71dfefb75ea9cd38ed2415161d1e794ec9ae755..5088e44c2eca6f54b23104c7695c3a03d5f762c8 100644
--- a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+++ b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
@@ -33,7 +33,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def makeLibrary(id: String) = new Library(id)
- class Library(libraryId: String) extends AbstractLibrary(libraryId) {
+ class Library(libId: String) extends AbstractLibrary(libId) {
protected def addJobs(): Unit = {}
}
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
index 147398ac798c077da0722b2078f7ea21c666b7d1..3d1b5585028f69c01934f0ddfc0d54c6a9c25169 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
@@ -13,13 +13,13 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
override def subPath = "gatk" :: super.subPath
- jarFile = config("gatk_jar", required = true)
+ jarFile = config("gatk_jar")
override val defaultVmem = "7G"
if (config.contains("intervals")) intervals = config("intervals").asFileList
if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
- reference_sequence = config("reference", required = true)
+ reference_sequence = config("reference")
if (config.contains("gatk_key")) gatk_key = config("gatk_key")
if (config.contains("pedigree")) pedigree = config("pedigree").asFileList
}
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
index 0c88447906c21a55a1e398a3c8c4786f18bebbf1..be4566211351a3d077877d1a99cf8be6ba0f58cd 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
@@ -35,17 +35,17 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
var jointGenotyping: Boolean = config("joint_genotyping", default = false)
var singleSampleCalling = config("single_sample_calling", default = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
var useAllelesOption: Boolean = config("use_alleles_option", default = false)
val externalGvcfs = config("external_gvcfs_files", default = Nil).asFileList
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def makeLibrary(id: String) = new Library(id)
- class Library(libraryId: String) extends AbstractLibrary(libraryId) {
+ class Library(libId: String) extends AbstractLibrary(libId) {
val mapping = new Mapping(qscript)
mapping.sampleId = sampleId
- mapping.libraryId = libraryId
+ mapping.libId = libId
mapping.outputDir = libDir + "/variantcalling/"
/** Library variantcalling */
@@ -66,8 +66,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
if (!bamFile.exists) throw new IllegalStateException("Bam in config does not exist, file: " + bamFile)
if (config("bam_to_fastq", default = false).asBoolean) {
- val samToFastq = SamToFastq(qscript, bamFile, libDir + sampleId + "-" + libraryId + ".R1.fastq",
- libDir + sampleId + "-" + libraryId + ".R2.fastq")
+ val samToFastq = SamToFastq(qscript, bamFile, libDir + sampleId + "-" + libId + ".R1.fastq",
+ libDir + sampleId + "-" + libId + ".R2.fastq")
samToFastq.isIntermediate = true
qscript.add(samToFastq)
mapping.input_R1 = samToFastq.fastqR1
@@ -82,17 +82,17 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
val header = inputSam.getFileHeader.getReadGroups
for (readGroup <- inputSam.getFileHeader.getReadGroups) {
if (readGroup.getSample != sampleId) logger.warn("Sample ID readgroup in bam file is not the same")
- if (readGroup.getLibrary != libraryId) logger.warn("Library ID readgroup in bam file is not the same")
- if (readGroup.getSample != sampleId || readGroup.getLibrary != libraryId) readGroupOke = false
+ if (readGroup.getLibrary != libId) logger.warn("Library ID readgroup in bam file is not the same")
+ if (readGroup.getSample != sampleId || readGroup.getLibrary != libId) readGroupOke = false
}
inputSam.close
if (!readGroupOke) {
if (config("correct_readgroups", default = false)) {
logger.info("Correcting readgroups, file:" + bamFile)
- val aorrg = AddOrReplaceReadGroups(qscript, bamFile, new File(libDir + sampleId + "-" + libraryId + ".bam"))
- aorrg.RGID = sampleId + "-" + libraryId
- aorrg.RGLB = libraryId
+ val aorrg = AddOrReplaceReadGroups(qscript, bamFile, new File(libDir + sampleId + "-" + libId + ".bam"))
+ aorrg.RGID = sampleId + "-" + libId
+ aorrg.RGLB = libId
aorrg.RGSM = sampleId
aorrg.isIntermediate = true
qscript.add(aorrg)
@@ -105,7 +105,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
Some(bamFile)
}
} else {
- logger.error("Sample: " + sampleId + ": No R1 found for run: " + libraryId)
+ logger.error("Sample: " + sampleId + ": No R1 found for run: " + libId)
None
}
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index 8bac4aaf68c33a245da877d460bc26abb9ebe564..47715e26adb11f0ed73520d2769ca55120a58d93 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -30,7 +30,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
var rawVcfInput: File = _
@Argument(doc = "Reference", shortName = "R", required = false)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Argument(doc = "OutputName", required = false)
var outputName: String = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index b6aba52ca8f6119f3bdbaea9fe0797f61ff6d0f5..2e391520b498205c3230653d4fdbca904ef2217e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -78,7 +78,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
/**
* Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
*/
- protected def checkExecutable {
+ protected[core] def checkExecutable {
if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
try if (executable != null) {
if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
@@ -91,8 +91,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
val file = new File(executable)
executable = file.getCanonicalPath
} else {
- logger.error("executable: '" + executable + "' not found, please check config")
- throw new QException("executable: '" + executable + "' not found, please check config")
+ BiopetQScript.addError("executable: '" + executable + "' not found, please check config")
}
BiopetCommandLineFunctionTrait.executableCache += oldExecutable -> executable
BiopetCommandLineFunctionTrait.executableCache += executable -> executable
@@ -113,9 +112,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
}
}
- val md5 = BiopetCommandLineFunctionTrait.executableMd5Cache(executable)
- if (md5 == null) addJobReportBinding("md5sum_exe", md5)
- else addJobReportBinding("md5sum_exe", "None")
+ val md5 = BiopetCommandLineFunctionTrait.executableMd5Cache.get(executable)
+ addJobReportBinding("md5sum_exe", md5.getOrElse("None"))
}
/**
@@ -145,6 +143,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
/** Executes the version command */
private def getVersionInternal: String = {
if (versionCommand == null || versionRegex == null) return "N/A"
+ val exe = new File(versionCommand.trim.split(" ")(0))
+ if (!exe.exists()) return "N/A"
val stdout = new StringBuffer()
val stderr = new StringBuffer()
def outputLog = "Version command: \n" + versionCommand +
@@ -206,4 +206,4 @@ object BiopetCommandLineFunctionTrait {
private val versionCache: Map[String, String] = Map()
private val executableMd5Cache: Map[String, String] = Map()
private val executableCache: Map[String, String] = Map()
-}
\ No newline at end of file
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 11f40ddf484eaacac7be762d0dae11771494e1a3..3ca783580b5f45475d79271b8f14d33b3248f3d4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -23,6 +23,7 @@ import org.broadinstitute.gatk.queue.QSettings
import org.broadinstitute.gatk.queue.function.QFunction
import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
+import scala.collection.mutable.ListBuffer
/**
* Base for biopet pipeline
@@ -33,8 +34,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
val configfiles: List[File] = Nil
var outputDir: String = {
- val temp = Config.getValueFromMap(Config.global.map, ConfigValueIndex(this.configName, configPath, "output_dir"))
- if (temp.isEmpty) throw new IllegalArgumentException("No output_dir defined in config")
+ val temp = Config.getValueFromMap(globalConfig.map, ConfigValueIndex(this.configName, configPath, "output_dir"))
+ if (temp.isEmpty) ""
else {
val t = temp.get.value.toString
if (!t.endsWith("/")) t + "/" else t
@@ -62,8 +63,9 @@ trait BiopetQScript extends Configurable with GatkLogging {
* Script from queue itself, final to force some checks for each pipeline and write report
*/
final def script() {
- outputDir = config("output_dir", required = true)
- if (!outputDir.endsWith("/")) outputDir += "/"
+ outputDir = config("output_dir")
+ if (outputDir.isEmpty) outputDir = new File(".").getAbsolutePath()
+ else if (!outputDir.endsWith("/")) outputDir += "/"
init
biopetScript
@@ -72,11 +74,17 @@ trait BiopetQScript extends Configurable with GatkLogging {
case _ =>
}
for (function <- functions) function match {
- case f: BiopetCommandLineFunctionTrait => f.afterGraph
- case _ =>
+ case f: BiopetCommandLineFunctionTrait => {
+ f.checkExecutable
+ f.afterGraph
+ }
+ case _ =>
}
- Config.global.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
+ if (new File(outputDir).canWrite) globalConfig.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
+ else BiopetQScript.addError("Output dir: '" + outputDir + "' is not writeable")
+
+ BiopetQScript.checkErrors
}
/** Get implemented from org.broadinstitute.gatk.queue.QScript */
@@ -92,3 +100,28 @@ trait BiopetQScript extends Configurable with GatkLogging {
add(function)
}
}
+
+object BiopetQScript extends Logging {
+ private val errors: ListBuffer[Exception] = ListBuffer()
+
+ def addError(error: String, debug: String = null): Unit = {
+ val msg = error + (if (debug != null && logger.isDebugEnabled) "; " + debug else "")
+ errors.append(new Exception(msg))
+ }
+
+ protected def checkErrors: Unit = {
+ if (!errors.isEmpty) {
+ logger.error("*************************")
+ logger.error("Biopet found some errors:")
+ if (logger.isDebugEnabled) {
+ for (e <- errors) {
+ logger.error(e.getMessage)
+ logger.debug(e.getStackTrace.mkString("Stack trace:\n", "\n", "\n"))
+ }
+ } else {
+ errors.map(_.getMessage).sorted.distinct.foreach(logger.error(_))
+ }
+ throw new IllegalStateException("Biopet found errors")
+ }
+ }
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index 0217615d1bedf61bdac37f878f7f1fcdf698b0ec..4184f29afacc7f6afcf6dc9d0eb45f9eddfc1993 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -28,7 +28,7 @@ trait MultiSampleQScript extends BiopetQScript {
@Argument(doc = "Only Sample", shortName = "sample", required = false)
private val onlySamples: List[String] = Nil
- require(Config.global.map.contains("samples"), "No Samples found in config")
+ require(globalConfig.map.contains("samples"), "No Samples found in config")
/**
* Sample class with basic functions build in
@@ -40,26 +40,26 @@ trait MultiSampleQScript extends BiopetQScript {
/**
* Library class with basic functions build in
- * @param libraryId
+ * @param libId
*/
- abstract class AbstractLibrary(val libraryId: String) {
+ abstract class AbstractLibrary(val libId: String) {
/** Overrules config of qscript with default sample and default library */
- val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libraryId)
+ val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libId)
/** Adds the library jobs */
final def addAndTrackJobs(): Unit = {
currentSample = Some(sampleId)
- currentLib = Some(libraryId)
+ currentLib = Some(libId)
addJobs()
currentLib = None
currentSample = None
}
/** Creates a library file with given suffix */
- def createFile(suffix: String): File = new File(libDir, sampleId + "-" + libraryId + suffix)
+ def createFile(suffix: String): File = new File(libDir, sampleId + "-" + libId + suffix)
/** Returns library directory */
- def libDir = sampleDir + "lib_" + libraryId + File.separator
+ def libDir = sampleDir + "lib_" + libId + File.separator
/** Function that add library jobs */
protected def addJobs()
@@ -80,7 +80,7 @@ trait MultiSampleQScript extends BiopetQScript {
/** returns a set with library names */
protected def libIds: Set[String] = {
- ConfigUtils.getMapFromPath(Config.global.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
+ ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
}
/** Adds sample jobs */
@@ -95,7 +95,7 @@ trait MultiSampleQScript extends BiopetQScript {
/** function add all libraries in one call */
protected final def addPerLibJobs(): Unit = {
- for ((libraryId, library) <- libraries) {
+ for ((libId, library) <- libraries) {
library.addAndTrackJobs()
}
}
@@ -125,7 +125,7 @@ trait MultiSampleQScript extends BiopetQScript {
val samples: Map[String, Sample] = sampleIds.map(id => id -> makeSample(id)).toMap
/** Returns a list of all sampleIDs */
- protected def sampleIds: Set[String] = ConfigUtils.any2map(Config.global.map("samples")).keySet
+ protected def sampleIds: Set[String] = ConfigUtils.any2map(globalConfig.map("samples")).keySet
/** Runs addAndTrackJobs method for each sample */
final def addSamplesJobs() {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
index 4ea65cb5a7fc7ceb1226853d47687a0865c818d0..e25e8ef508188adbd5f767b20ca1f688c4eed922 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
@@ -133,11 +133,11 @@ class Config(var map: Map[String, Any]) extends Logging {
*/
protected[config] def apply(module: String, path: List[String], key: String, default: Any = null, freeVar: Boolean = true): ConfigValue = {
val requestedIndex = ConfigValueIndex(module, path, key, freeVar)
- if (contains(requestedIndex)) return foundCache(requestedIndex)
+ if (contains(requestedIndex)) foundCache(requestedIndex)
else if (default != null) {
defaultCache += (requestedIndex -> ConfigValue(requestedIndex, null, default, freeVar))
- return defaultCache(requestedIndex)
- } else throw new IllegalStateException("Value in config could not be found but it seems required, index: " + requestedIndex)
+ defaultCache(requestedIndex)
+ } else ConfigValue(requestedIndex, null, null, freeVar)
}
def writeReport(id: String, directory: String): Unit = {
@@ -174,7 +174,7 @@ class Config(var map: Map[String, Any]) extends Logging {
val fullEffective = ConfigUtils.mergeMaps(effectiveFound, effectiveDefaultFound)
val fullEffectiveWithNotFound = ConfigUtils.mergeMaps(fullEffective, notFound)
- writeMapToJsonFile(Config.global.map, "input")
+ writeMapToJsonFile(this.map, "input")
writeMapToJsonFile(found, "found")
writeMapToJsonFile(effectiveFound, "effective.found")
writeMapToJsonFile(effectiveDefaultFound, "effective.defaults")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
index 54e6dfd170a8cb2e68f5c63dd8ca2675513cee7d..51997ccb8a12fb5c3a234e5e7d95c001dd704b4f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
@@ -21,6 +21,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
trait Configurable extends ImplicitConversions {
/** Should be object of parant object */
val root: Configurable
+ val globalConfig: Config = if (root != null) root.globalConfig else Config.global
/** subfix to the path */
def subPath: List[String] = Nil
@@ -79,7 +80,6 @@ trait Configurable extends ImplicitConversions {
* @param key Name of value
* @param default Default value if not found
* @param submodule Adds to the path
- * @param required Default false, if true and value is not found this function will raise an exception
* @param freeVar Default true, if set false value must exist in module
* @param sample Default null, when set path is prefixed with "samples" -> "sampleID"
* @param library Default null, when set path is prefixed with "libraries" -> "libraryID"
@@ -88,7 +88,6 @@ trait Configurable extends ImplicitConversions {
def apply(key: String,
default: Any = null,
submodule: String = null,
- required: Boolean = false,
freeVar: Boolean = true,
sample: String = null,
library: String = null): ConfigValue = {
@@ -100,14 +99,8 @@ trait Configurable extends ImplicitConversions {
val value = Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar))
if (value.isDefined) value.get.value else default
}
- if (!contains(key, submodule, freeVar, sample = s, library = l) && d == null) {
- if (required) {
- Logging.logger.error("Value in config could not be found but it is required, key: " + key + " module: " + m + " path: " + p)
- throw new IllegalStateException("Value in config could not be found but it is required, key: " + key + " module: " + m + " path: " + p)
- } else return null
- }
- if (d == null) return Config.global(m, p, key, freeVar = freeVar)
- else return Config.global(m, p, key, d, freeVar)
+ if (d == null) globalConfig(m, p, key, freeVar = freeVar)
+ else globalConfig(m, p, key, d, freeVar)
}
/**
@@ -129,7 +122,7 @@ trait Configurable extends ImplicitConversions {
val m = if (submodule != null) submodule else configName
val p = path(s, l, submodule)
- Config.global.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
+ globalConfig.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
}
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
index 6e1a86cd7f3aaa3d56d10263de84f4bca41a0c32..3aaab82b6bad27c00a94f572eaf024c61913ceb6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
@@ -83,19 +83,15 @@ object BiopetQCommandLine extends GatkLogging {
Runtime.getRuntime.addShutdownHook(shutdownHook)
+ CommandLineProgram.start(qCommandLine, argv)
try {
- CommandLineProgram.start(qCommandLine, argv)
- try {
- Runtime.getRuntime.removeShutdownHook(shutdownHook)
- qCommandLine.shutdown()
- } catch {
- case e: Exception => /* ignore, example 'java.lang.IllegalStateException: Shutdown in progress' */
- }
- if (CommandLineProgram.result != 0)
- System.exit(CommandLineProgram.result)
+ Runtime.getRuntime.removeShutdownHook(shutdownHook)
+ qCommandLine.shutdown()
} catch {
- case e: Exception => CommandLineProgram.exitSystemWithError(e)
+ case e: Exception => /* ignore, example 'java.lang.IllegalStateException: Shutdown in progress' */
}
+ if (CommandLineProgram.result != 0)
+ System.exit(CommandLineProgram.result)
}
}
@@ -116,21 +112,28 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
private var qScriptClasses: File = _
private var shuttingDown = false
+ /**
+ * we modified this in Biopet to skip compiling and show full stacktrace again
+ */
private lazy val qScriptPluginManager = {
qScriptClasses = IOUtils.tempDir("Q-Classes-", "", settings.qSettings.tempDirectory)
- //qScriptManager.loadScripts(scripts, qScriptClasses)
- //var temp: Seq[URL] = Seq()
for (t <- scripts) {
val is = getClass.getResourceAsStream(t.getAbsolutePath)
val os = new FileOutputStream(qScriptClasses.getAbsolutePath + "/" + t.getName)
org.apache.commons.io.IOUtils.copy(is, os)
os.close()
- //temp :+= this.getClass.getResource(t.toString)
- //logger.info(this.getClass.getResource(t.toString))
val s = if (t.getName.endsWith("/")) t.getName.substring(0, t.getName.length - 1) else t.getName
pipelineName = s.substring(0, s.lastIndexOf(".")) + "." + System.currentTimeMillis
}
- new PluginManager[QScript](qPluginType, List(qScriptClasses.toURI.toURL))
+
+ // override createByType to pass the correct exceptions
+ new PluginManager[QScript](qPluginType, List(qScriptClasses.toURI.toURL)) {
+ override def createByType(plugintype: Class[_ <: QScript]) = {
+ val noArgsConstructor = plugintype.getDeclaredConstructor()
+ noArgsConstructor.setAccessible(true)
+ noArgsConstructor.newInstance()
+ }
+ }
}
private lazy val qCommandPlugin = {
@@ -188,12 +191,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
//if (settings.run)
script.pullInputs()
script.qSettings = settings.qSettings
- try {
- script.script()
- } catch {
- case e: Exception =>
- throw new UserException.CannotExecuteQScript(script.getClass.getSimpleName + ".script() threw the following exception: " + e, e)
- }
+ script.script()
if (remoteFileConverter != null) {
if (remoteFileConverter.convertToRemoteEnabled)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
index e192a845be6db96d2a754d2d2ff6a5e393d136ca..9ac74448e880d7be01063a3f12bdd613141b34a4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
@@ -29,7 +29,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "R")
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
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..7bda8792544eea2d863ab06192b51b55ae900077 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
@@ -25,16 +25,16 @@ 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 = _
+ var fastqfile: File = null
@Output(doc = "Output", shortName = "out")
- var output: File = _
+ var output: File = null
executable = config("exe", default = "fastqc")
var java_exe: String = config("exe", default = "java", submodule = "java", freeVar = false)
@@ -50,17 +50,31 @@ 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)
+
+ val fastqcDir = new File(executable).getParent
+
+ contaminants = contaminants match {
+ // user-defined contaminants file take precedence
+ case userDefinedValue @ Some(_) => userDefinedValue
+ // otherwise, use default contaminants file (depending on FastQC version)
+ case None =>
+ val defaultContams = getVersion match {
+ case "v0.11.2" => new File(fastqcDir + "/Configuration/contaminant_list.txt")
+ case _ => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
+ }
+ config("contaminants", default = defaultContams)
+ }
+
+ adapters = adapters match {
+ // user-defined contaminants file take precedence
+ case userDefinedValue @ Some(_) => userDefinedValue
+ // otherwise, check if adapters are already present (depending on FastQC version)
+ case None =>
+ val defaultAdapters = getVersion match {
+ case "v0.11.2" => Option(new File(fastqcDir + "/Configuration/adapter_list.txt"))
+ case _ => None
+ }
+ defaultAdapters.collect { case adp => config("adapters", default = adp) }
}
}
@@ -74,6 +88,6 @@ 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/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
index 4f6236179755659b3b42d74cef6c722713fbf4c9..1d7b45ec9617091a457f073e4110ff5e01932e24 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
@@ -50,6 +50,8 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
@Argument(doc = "Output directory", required = true)
var w: String = _
+ var noBfgs: Boolean = config("no_bfgs", default = false)
+
@Input(required = false)
var t: File = _
@@ -101,5 +103,6 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
optional("-f", f) +
optional("-t", t) +
optional("-z", z) +
+ conditional(noBfgs, "--no-bgfs") +
required("-T", threads)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
index a7bfeab78447e62eee1634c73ca09c880679327e..1db8f6d67c8d892e6188aa750efb40b814fbbf1e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
@@ -29,13 +29,13 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "ref")
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Input(doc = "The genome prefix.")
- var genome: File = config("genome", required = true)
+ var genome: File = config("genome")
@Input(doc = "The hash prefix")
- var hash: File = config("hash", required = true)
+ var hash: File = config("hash")
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
index e0b8bd68bda46a6b3dc6915a54482b093cfd43d6..98ee6de521d499710e186bb2c196d9d471c6aa5d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
@@ -29,7 +29,7 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
var R2: File = _
@Input(doc = "Bowtie index", shortName = "bti")
- var bowtie_index: File = config("bowtie_index", required = true)
+ var bowtie_index: File = config("bowtie_index")
@Argument(doc = "Output Directory")
var outputDir: String = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
index bfd0a5846e6531b47f285453a2d848b1b7f1bafe..3298702fcfd5cd98e1eaf0bae8f6b059d353d2c9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
@@ -13,7 +13,7 @@ class BwaAln(val root: Configurable) extends Bwa {
var fastq: File = _
@Input(doc = "The reference file for the bam files.", required = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", required = false)
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
index fc790b183b5bae2922a1b5f89ec66fcf4f5b85b2..74cdad0cea290e5a8cdcc2b360fa3fa32444791c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
@@ -29,7 +29,7 @@ class BwaMem(val root: Configurable) extends Bwa {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "R")
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
index b857eea014ac52acb9608debb94db9cd75cef929..255811561e732b229b1417c95d866fad4694c0c9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
@@ -26,7 +26,7 @@ class BwaSampe(val root: Configurable) extends Bwa {
var saiR2: File = _
@Input(doc = "The reference file for the bam files.", required = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", required = false)
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
index 51f9a0f30eaf73a897fefaa2b6cf69d4e3386b62..8bbf918474e21d2e2837ce01d5bc4490e13bd087 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
@@ -16,7 +16,7 @@ class BwaSamse(val root: Configurable) extends Bwa {
var sai: File = _
@Input(doc = "The reference file for the bam files.", required = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", required = false)
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
new file mode 100644
index 0000000000000000000000000000000000000000..d017864f6988828100f6bbda421fbf734a9a5878
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
@@ -0,0 +1,14 @@
+/**
+ * Created by wyleung on 5-1-15.
+ */
+
+package nl.lumc.sasc.biopet.extensions.igvtools
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+
+abstract class IGVTools extends BiopetCommandLineFunction {
+ executable = config("exe", default = "igvtools", submodule = "igvtools", freeVar = false)
+ override def versionCommand = executable + " version"
+ override val versionRegex = """IGV Version: ([\d\.]) .*""".r
+ override val versionExitcode = List(0)
+}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
new file mode 100644
index 0000000000000000000000000000000000000000..8037616834ecd4de02e9949883b75d20b45c7347
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
@@ -0,0 +1,105 @@
+
+package nl.lumc.sasc.biopet.extensions.igvtools
+
+import java.nio.file.InvalidPathException
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+import java.io.{ FileNotFoundException, File }
+
+/**
+ * IGVTools `count` wrapper
+ *
+ * @constructor create a new IGVTools instance from a `.bam` file
+ *
+ */
+
+class IGVToolsCount(val root: Configurable) extends IGVTools {
+ @Input(doc = "Bam File")
+ var input: File = _
+
+ @Input(doc = "<genome>.chrom.sizes File")
+ var genomeChromSizes: File = _
+
+ @Output
+ var tdf: Option[File] = _
+
+ @Output
+ var wig: Option[File] = _
+
+ var maxZoom: Option[Int] = config("maxZoom")
+ var windowSize: Option[Int] = config("windowSize")
+ var extFactor: Option[Int] = config("extFactor")
+
+ var preExtFactor: Option[Int] = config("preExtFactor")
+ var postExtFactor: Option[Int] = config("postExtFactor")
+
+ var windowFunctions: Option[String] = config("windowFunctions")
+ var strands: Option[String] = config("strands")
+ var bases: Boolean = config("bases", default = false)
+
+ var query: Option[String] = config("query")
+ var minMapQuality: Option[Int] = config("minMapQuality")
+ var includeDuplicates: Boolean = config("includeDuplicates", default = false)
+
+ var pairs: Boolean = config("pairs", default = false)
+
+ override def afterGraph {
+ super.afterGraph
+ if (!input.exists()) throw new FileNotFoundException("Input bam is required for IGVToolsCount")
+
+ if (!wig.isEmpty && !wig.get.getAbsolutePath.endsWith(".wig")) throw new IllegalArgumentException("Wiggle file should have a .wig file-extension")
+ if (!tdf.isEmpty && !tdf.get.getAbsolutePath.endsWith(".tdf")) throw new IllegalArgumentException("TDF file should have a .tdf file-extension")
+ }
+
+ def cmdLine = {
+ required(executable) +
+ required("count") +
+ optional("--maxZoom", maxZoom) +
+ optional("--windowSize", windowSize) +
+ optional("--extFactor", extFactor) +
+ optional("--preExtFactor", preExtFactor) +
+ optional("--postExtFactor", postExtFactor) +
+ optional("--windowFunctions", windowFunctions) +
+ optional("--strands", strands) +
+ conditional(bases, "--bases") +
+ optional("--query", query) +
+ optional("--minMapQuality", minMapQuality) +
+ conditional(includeDuplicates, "--includeDuplicates") +
+ conditional(pairs, "--pairs") +
+ required(input) +
+ required(outputArg) +
+ required(genomeChromSizes)
+ }
+
+ /**
+ * This part should never fail, these values are set within this wrapper
+ *
+ */
+ private def outputArg: String = {
+ (tdf, wig) match {
+ case (None, None) => throw new IllegalArgumentException("Either TDF or WIG should be supplied");
+ case (Some(a), None) => a.getAbsolutePath;
+ case (None, Some(b)) => b.getAbsolutePath;
+ case (Some(a), Some(b)) => a.getAbsolutePath + "," + b.getAbsolutePath;
+ }
+ }
+}
+
+object IGVToolsCount {
+ /**
+ * Create an object by specifying the `input` (.bam),
+ * and the `genomename` (hg18,hg19,mm10)
+ *
+ * @param input Bamfile to count reads from
+ * @return a new IGVToolsCount instance
+ * @throws FileNotFoundException bam File is not found
+ * @throws IllegalArgumentException tdf or wig not supplied
+ */
+ def apply(root: Configurable, input: File, genomeChromSizes: File): IGVToolsCount = {
+ val counting = new IGVToolsCount(root)
+ counting.input = input
+ counting.genomeChromSizes = genomeChromSizes
+ return counting
+ }
+}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
index 7ffcb50d8fec02138c07e4fc95d7608e8bfba72e..9cab9bfc90298f243f6cfdc8e051e7d451a4cf90 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
@@ -35,7 +35,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
var outputSummary: File = _
@Argument(doc = "Reference file", required = false)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Argument(doc = "Window size", required = false)
var windowSize: Option[Int] = config("windowsize")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
index 271c06085ddd086a5f015c88d84e29a008272c89..7d46c4b8fb910398f61e9fb3b873f682efaf023f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
@@ -26,7 +26,7 @@ class MultisamplePipelineTemplate(val root: Configurable) extends QScript with M
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def makeLibrary(id: String) = new Library(id)
- class Library(libraryId: String) extends AbstractLibrary(libraryId) {
+ class Library(libId: String) extends AbstractLibrary(libId) {
protected def addJobs(): Unit = {
// Library jobs
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
index 24ddb994e641914e0de9fab3d21e56c9d05d7f02..76f8887cced08a6c2ef0e16ca469f1700a7ee208 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
@@ -26,6 +26,7 @@ import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import scala.collection.JavaConversions._
+import scala.io.Source
class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName
@@ -58,6 +59,7 @@ class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
object VcfFilter extends ToolCommand {
case class Args(inputVcf: File = null,
outputVcf: File = null,
+ invertedOutputVcf: Option[File] = None,
minQualscore: Option[Double] = None,
minSampleDepth: Int = -1,
minTotalDepth: Int = -1,
@@ -69,7 +71,8 @@ object VcfFilter extends ToolCommand {
diffGenotype: List[(String, String)] = Nil,
filterHetVarToHomVar: List[(String, String)] = Nil,
filterRefCalls: Boolean = false,
- filterNoCalls: Boolean = false) extends AbstractArgs
+ filterNoCalls: Boolean = false,
+ iDset: Set[String] = Set()) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('I', "inputVcf") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
@@ -78,6 +81,9 @@ object VcfFilter extends ToolCommand {
opt[File]('o', "outputVcf") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
c.copy(outputVcf = x)
} text ("Output vcf file")
+ opt[File]("invertedOutputVcf") maxOccurs (1) valueName ("<file>") action { (x, c) =>
+ c.copy(invertedOutputVcf = Some(x))
+ } text ("inverted output vcf file")
opt[Int]("minSampleDepth") unbounded () valueName ("<int>") action { (x, c) =>
c.copy(minSampleDepth = x)
} text ("Min value for DP in genotype fields")
@@ -116,6 +122,12 @@ object VcfFilter extends ToolCommand {
opt[Double]("minQualscore") unbounded () action { (x, c) =>
c.copy(minQualscore = Some(x))
} text ("Min qual score")
+ opt[String]("id") unbounded () action { (x, c) =>
+ c.copy(iDset = c.iDset + x)
+ } text ("Id that may pass the filter")
+ opt[File]("id-file") unbounded () action { (x, c) =>
+ c.copy(iDset = c.iDset ++ Source.fromFile(x).getLines())
+ } text ("File that contain list of IDs to get from vcf file")
}
var commandArgs: Args = _
@@ -124,6 +136,7 @@ object VcfFilter extends ToolCommand {
* @param args the command line arguments
*/
def main(args: Array[String]): Unit = {
+ logger.info("Start")
val argsParser = new OptParser
commandArgs = argsParser.parse(args, Args()) getOrElse sys.exit(1)
@@ -132,6 +145,11 @@ object VcfFilter extends ToolCommand {
val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder().setOutputFile(commandArgs.outputVcf).build)
writer.writeHeader(header)
+ val invertedWriter = commandArgs.invertedOutputVcf.collect { case x => new VariantContextWriterBuilder().setOutputFile(x).build }
+ invertedWriter.foreach(_.writeHeader(header))
+
+ var counterTotal = 0
+ var counterLeft = 0
for (record <- reader) {
if (minQualscore(record) &&
filterRefCalls(record) &&
@@ -143,12 +161,20 @@ object VcfFilter extends ToolCommand {
mustHaveVariant(record) &&
notSameGenotype(record) &&
filterHetVarToHomVar(record) &&
- denovoInSample(record)) {
+ denovoInSample(record) &&
+ inIdSet(record)) {
writer.add(record)
- }
+ counterLeft += 1
+ } else
+ invertedWriter.foreach(_.add(record))
+ counterTotal += 1
+ if (counterTotal % 100000 == 0) logger.info(counterTotal + " variants processed, " + counterLeft + " left")
}
+ logger.info(counterTotal + " variants processed, " + counterLeft + " left")
reader.close
writer.close
+ invertedWriter.foreach(_.close())
+ logger.info("Done")
}
def minQualscore(record: VariantContext): Boolean = {
@@ -241,4 +267,9 @@ object VcfFilter extends ToolCommand {
}
return true
}
+
+ def inIdSet(record: VariantContext): Boolean = {
+ if (commandArgs.iDset.isEmpty) true
+ else record.getID.split(",").exists(commandArgs.iDset.contains(_))
+ }
}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
index 9f1cddb7913cf7846daa72c7b9e695988b3a14c6..2c9165036824f135f9552b69fa3b4085be25fc93 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
@@ -16,6 +16,7 @@
package nl.lumc.sasc.biopet.utils
import java.io.File
+import nl.lumc.sasc.biopet.core.BiopetQScript
import nl.lumc.sasc.biopet.core.Logging
import nl.lumc.sasc.biopet.core.config.ConfigValue
import argonaut._, Argonaut._
@@ -330,14 +331,27 @@ object ConfigUtils extends Logging {
trait ImplicitConversions {
import scala.language.implicitConversions
+ private def requiredValue(value: ConfigValue): Boolean = {
+ val exist = valueExists(value)
+ if (!exist)
+ BiopetQScript.addError("Value does not exist but is required, key: " + value.requestIndex.key +
+ " module: " + value.requestIndex.module,
+ (if (value.requestIndex.path != Nil) " path: " + value.requestIndex.path.mkString("->") else null))
+ exist
+ }
+
+ private def valueExists(value: ConfigValue): Boolean = {
+ value != null && value.value != null && value.value != None
+ }
+
/**
* Convert ConfigValue to File
* @param value Input ConfigValue
* @return
*/
implicit def configValue2file(value: ConfigValue): File = {
- if (value != null && value.value != null && value.value != None) new File(any2string(value.value))
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) new File(any2string(value.value))
+ else new File("")
}
/**
@@ -346,7 +360,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionFile(value: ConfigValue): Option[File] = {
- if (value != null && value.value != null && value.value != None) Some(new File(any2string(value.value)))
+ if (valueExists(value)) Some(new File(any2string(value.value)))
else None
}
@@ -356,8 +370,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2string(value: ConfigValue): String = {
- if (value != null && value.value != null && value.value != None) any2string(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2string(value.value)
+ else ""
}
/**
@@ -366,7 +380,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionString(value: ConfigValue): Option[String] = {
- if (value != null && value.value != null && value.value != None) Some(any2string(value.value))
+ if (valueExists(value)) Some(any2string(value.value))
else None
}
@@ -376,8 +390,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2long(value: ConfigValue): Long = {
- if (value != null && value.value != null && value.value != None) any2long(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2long(value.value)
+ else 0L
}
/**
@@ -386,7 +400,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionLong(value: ConfigValue): Option[Long] = {
- if (value != null && value.value != null && value.value != None) Option(any2long(value.value))
+ if (valueExists(value)) Option(any2long(value.value))
else None
}
@@ -396,8 +410,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2int(value: ConfigValue): Int = {
- if (value != null && value.value != null && value.value != None) any2int(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2int(value.value)
+ else 0
}
/**
@@ -406,7 +420,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionInt(value: ConfigValue): Option[Int] = {
- if (value != null && value.value != null && value.value != None) Option(any2int(value.value))
+ if (valueExists(value)) Option(any2int(value.value))
else None
}
@@ -416,8 +430,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2double(value: ConfigValue): Double = {
- if (value != null && value.value != null && value.value != None) any2double(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2double(value.value)
+ else 0.0
}
/**
@@ -426,7 +440,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionDouble(value: ConfigValue): Option[Double] = {
- if (value != null && value.value != null && value.value != None) Option(any2double(value.value))
+ if (valueExists(value)) Option(any2double(value.value))
else None
}
@@ -436,8 +450,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2float(value: ConfigValue): Float = {
- if (value != null && value.value != null && value.value != None) any2float(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2float(value.value)
+ else 0f
}
/**
@@ -446,7 +460,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionFloat(value: ConfigValue): Option[Float] = {
- if (value != null && value.value != null && value.value != None) Option(any2float(value.value))
+ if (valueExists(value)) Option(any2float(value.value))
else None
}
@@ -456,8 +470,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2boolean(value: ConfigValue): Boolean = {
- if (value != null && value.value != null && value.value != None) any2boolean(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2boolean(value.value)
+ else false
}
/**
@@ -466,7 +480,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionBoolean(value: ConfigValue): Option[Boolean] = {
- if (value != null && value.value != null && value.value != None) Option(any2boolean(value.value))
+ if (valueExists(value)) Option(any2boolean(value.value))
else None
}
@@ -476,8 +490,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2list(value: ConfigValue): List[Any] = {
- if (value != null && value.value != null && value.value != None) any2list(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2list(value.value)
+ else Nil
}
/**
@@ -486,8 +500,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2stringList(value: ConfigValue): List[String] = {
- if (value != null && value.value != null && value.value != None) any2stringList(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2stringList(value.value)
+ else Nil
}
/**
@@ -496,8 +510,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2stringSet(value: ConfigValue): Set[String] = {
- if (value != null && value.value != null && value.value != None) any2stringList(value.value).toSet
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2stringList(value.value).toSet
+ else Set()
}
/**
@@ -506,8 +520,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2map(value: ConfigValue): Map[String, Any] = {
- if (value != null && value.value != null && value.value != None) any2map(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2map(value.value)
+ else Map()
}
}
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
index 92d0b9f63f60ad1a6c9489ba1d71fd3f25ab6828..b7353b2ad1d4a91cd05340edbd7a61a51e64e266 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
@@ -30,9 +30,6 @@ class ConfigTest extends TestNGSuite with Matchers with ConfigUtils.ImplicitConv
@Test def testApply: Unit = {
ConfigTest.config("m1", Nil, "k1").asString shouldBe "v2"
ConfigTest.config("m1", Nil, "notexist", default = "default").asString shouldBe "default"
- intercept[IllegalStateException] {
- ConfigTest.config("m1", Nil, "notexist")
- }
}
@Test def testMergeConfigs: Unit = {
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
index 1b493f2e14df822b75534fed3722f88917882fe1..19940fde2ecb2c923cdbed79b9fcb85bd1ab4e39 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
@@ -11,10 +11,10 @@ import org.testng.annotations.Test
*/
class ConfigurableTest extends TestNGSuite with Matchers {
@Test def testConfigurable: Unit = {
- Config.global.map = Map()
- Config.global.loadConfigFile(ConfigurableTest.file)
-
- val classC = new ClassC
+ val classC = new ClassC {
+ override def configName = "classc"
+ override val globalConfig = new Config(ConfigurableTest.map)
+ }
classC.configPath shouldBe Nil
classC.configFullPath shouldBe List("classc")
@@ -27,10 +27,6 @@ class ConfigurableTest extends TestNGSuite with Matchers {
classC.classB.get("k1").asString shouldBe "c1"
classC.classB.classA.get("k1").asString shouldBe "c1"
- classC.get("notexist") shouldBe null
- intercept[IllegalStateException] {
- classC.get("notexist", required = true)
- }
classC.get("notexist", default = "default").asString shouldBe "default"
classC.get("k1", freeVar = false).asString shouldBe "c1"
@@ -47,23 +43,24 @@ abstract class Cfg extends Configurable {
def get(key: String,
default: String = null,
submodule: String = null,
- required: Boolean = false,
freeVar: Boolean = true,
sample: String = null,
library: String = null) = {
- config(key, default, submodule, required, freeVar = freeVar, sample = sample, library = library)
+ config(key, default, submodule, freeVar = freeVar, sample = sample, library = library)
}
}
class ClassA(val root: Configurable) extends Cfg
class ClassB(val root: Configurable) extends Cfg {
- val classA = new ClassA(this)
+ lazy val classA = new ClassA(this)
+ // Why this needs to be lazy?
}
class ClassC(val root: Configurable) extends Cfg {
def this() = this(null)
- val classB = new ClassB(this)
+ lazy val classB = new ClassB(this)
+ // Why this needs to be lazy?
}
object ConfigurableTest {
@@ -85,6 +82,4 @@ object ConfigurableTest {
)
)
)
-
- val file = ConfigUtilsTest.writeTemp(ConfigUtils.mapToJson(map).spaces2)
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
index 26f989c5369c4e138ded82620d1d03f0c076ce7c..ddcf887d819eb0edc09bfc5b6a42954115e62192 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
@@ -4,6 +4,7 @@ import java.io.{ PrintWriter, File }
import argonaut.Argonaut._
import argonaut.Json
+import nl.lumc.sasc.biopet.core.BiopetQScript
import nl.lumc.sasc.biopet.core.config.{ ConfigValueIndex, ConfigValue }
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
@@ -170,79 +171,23 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
val index = ConfigValueIndex("test", Nil, "test")
new ImplicitConversions {
configValue2list(ConfigValue(index, index, List(""))) shouldBe List("")
- intercept[IllegalStateException] {
- configValue2list(ConfigValue(index, index, null))
- }
-
configValue2stringList(ConfigValue(index, index, List(""))) shouldBe List("")
- intercept[IllegalStateException] {
- configValue2stringList(ConfigValue(index, index, null))
- }
-
configValue2stringSet(ConfigValue(index, index, List(""))) shouldBe Set("")
- intercept[IllegalStateException] {
- configValue2stringSet(ConfigValue(index, index, null))
- }
var int: Int = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- int = ConfigValue(index, index, null)
- }
-
var long: Long = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- long = ConfigValue(index, index, null)
- }
-
var double: Double = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- double = ConfigValue(index, index, null)
- }
-
var float: Float = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- float = ConfigValue(index, index, null)
- }
-
var boolean: Boolean = ConfigValue(index, index, true)
- intercept[IllegalStateException] {
- boolean = ConfigValue(index, index, null)
- }
-
var intOption: Option[Int] = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- int = ConfigValue(index, index, null)
- }
-
var longOption: Option[Long] = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- long = ConfigValue(index, index, null)
- }
-
var doubleOption: Option[Double] = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- double = ConfigValue(index, index, null)
- }
-
var floatOption: Option[Float] = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- float = ConfigValue(index, index, null)
- }
-
var booleanOption: Option[Boolean] = ConfigValue(index, index, true)
- intercept[IllegalStateException] {
- boolean = ConfigValue(index, index, null)
- }
-
var string: String = ConfigValue(index, index, "test")
- intercept[IllegalStateException] {
- string = ConfigValue(index, index, null)
- }
-
var file: File = ConfigValue(index, index, "test")
- intercept[IllegalStateException] {
- file = ConfigValue(index, index, null)
- }
+
+ //TODO: test BiopetQScript error message
}
}
}
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index f0ff3f4eb54cc109ebe2e2b7bb7659cc99b7c76b..578f3afc79f6cac8d2621399bb577222383ee2bb 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -44,14 +44,14 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def makeLibrary(id: String) = new Library(id)
- class Library(libraryId: String) extends AbstractLibrary(libraryId) {
+ class Library(libId: String) extends AbstractLibrary(libId) {
val mapping = new Mapping(qscript)
def addJobs(): Unit = {
if (config.contains("R1")) {
mapping.input_R1 = config("R1")
if (config.contains("R2")) mapping.input_R2 = config("R2")
- mapping.libraryId = libraryId
+ mapping.libId = libId
mapping.sampleId = sampleId
mapping.outputDir = libDir
@@ -59,7 +59,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
mapping.biopetScript
addAll(mapping.functions)
- } else logger.error("Sample: " + sampleId + ": No R1 found for library: " + libraryId)
+ } else logger.error("Sample: " + sampleId + ": No R1 found for library: " + libId)
}
}
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..21cb069d658623ab5a7b8986e454db6000f927fa 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.
+ */
+ 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.
+ */
+ def encoding: String = {
+ if (dataFile.exists) // On a dry run this file does not yet exist
+ qcModules("Basic Statistics") //FIXME: not save
+ .lines
+ .dropWhile(!_.startsWith("Encoding"))
+ .head
+ .stripPrefix("Encoding\t")
+ .stripSuffix("\t")
+ else ""
+ }
- val seqs = getSeqs(adapters) ::: getSeqs(contaminants)
+ /** Case class representing a known adapter sequence */
+ protected case class AdapterSequence(name: String, seq: String)
- val block = getDataBlock("Overrepresented sequences")
- if (block == null) return Nil
+ /**
+ * Retrieves overrepresented sequences found by FastQ.
+ *
+ * @return a [[Set]] of [[AdapterSequence]] objects.
+ */
+ def foundAdapters: Set[AdapterSequence] = {
+ if (dataFile.exists) { // On a dry run this file does not yet exist
+ /** 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)))
+ } else Set()
}
- 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 + File.separator + 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/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 42ea3b6d9d9f407476d359268b5ac3c40798b745..9ab16032bd095d40728e91f92a611366b400af2f 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -30,7 +30,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
var input_R1: File = _
@Input(doc = "R2 fastq file (gzipped allowed)", shortName = "R2", required = false)
- var input_R2: Option[File] = _
+ var input_R2: Option[File] = None
/** Skip Trim fastq files */
var skipTrim: Boolean = config("skip_trim", default = false)
@@ -38,13 +38,17 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
/** Skip Clip fastq files */
var skipClip: Boolean = config("skip_clip", default = false)
+ // TODO: hide sampleId and libId from the command line so they do not interfere with our config values
+
/** Sample name */
+ @Argument(doc = "Sample ID", shortName = "sample", required = true)
var sampleId: String = _
/** Library name */
- var libraryId: String = _
+ @Argument(doc = "Library ID", shortName = "library", required = true)
+ var libId: String = _
- var paired: Boolean = (input_R2 != null)
+ var paired: Boolean = input_R2.isDefined
var R1_ext: String = _
var R2_ext: String = _
var R1_name: String = _
@@ -58,11 +62,12 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
val summary = new FlexiprepSummary(this)
def init() {
- if (input_R1 == null) throw new IllegalStateException("Missing R1 on flexiprep module")
- if (outputDir == null) throw new IllegalStateException("Missing Output directory on flexiprep module")
- if (sampleId == null) throw new IllegalStateException("Missing Sample name on flexiprep module")
- if (libraryId == null) throw new IllegalStateException("Missing Library name on flexiprep module")
- else if (!outputDir.endsWith("/")) outputDir += "/"
+ require(outputDir != null, "Missing output directory on flexiprep module")
+ require(input_R1 != null, "Missing input R1 on flexiprep module")
+ require(sampleId != null, "Missing sample ID on flexiprep module")
+ require(libId != null, "Missing library ID on flexiprep module")
+
+ paired = input_R2.isDefined
if (input_R1.endsWith(".gz")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gz"))
else if (input_R1.endsWith(".gzip")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gzip"))
@@ -82,7 +87,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
case _ =>
}
- summary.out = outputDir + sampleId + "-" + libraryId + ".qc.summary.json"
+ summary.out = outputDir + sampleId + "-" + libId + ".qc.summary.json"
}
def biopetScript() {
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 84acd18206b1f44e37e60b7c6d3b703e1b0d2d21..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
@@ -121,7 +121,7 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
md5Summary()
val summary =
("samples" := ( flexiprep.sampleId :=
- ("libraries" := ( flexiprep.libraryId := (
+ ("libraries" := ( flexiprep.libId := (
("flexiprep" := (
("clipping" := !flexiprep.skipClip) ->:
("trimming" := !flexiprep.skipTrim) ->:
@@ -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..05236e13cacae24e5b5dffb408e1aa01b1c297e4 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
@@ -25,13 +25,14 @@ 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 null => None
case s if (s.contains("Sanger / Illumina 1.9")) => None
- case s if (s.contains("Illumina <1.3")) => Option(64)
- case s if (s.contains("Illumina 1.3")) => Option(64)
- case s if (s.contains("Illumina 1.5")) => Option(64)
+ case s if (s.contains("Illumina <1.3")) => Option(64)
+ case s if (s.contains("Illumina 1.3")) => Option(64)
+ case s if (s.contains("Illumina 1.5")) => Option(64)
+ case _ => None
}
if (Q != None) V = true
}
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
diff --git a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
index 5360b4ac78824c2e26649a12e1cc3c35262a8b50..94b3bcbe619ee5b01bd29bea6aa9b9e707934a6d 100644
--- a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
+++ b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
@@ -36,7 +36,7 @@ class Kopisu(val root: Configurable) extends QScript with MultiSampleQScript {
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def makeLibrary(id: String) = new Library(id)
- class Library(libraryId: String) extends AbstractLibrary(libraryId) {
+ class Library(libId: String) extends AbstractLibrary(libId) {
def addJobs(): Unit = {
}
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 74779fc20935b6163dceb4f1c3ab57cda0c34c80..9094d38cddbe70d8c7b6787200d2afe94e19d486 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -66,8 +66,15 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
/** Readgroup ID */
protected var readgroupId: String = _
+ // TODO: hide sampleId and libId from the command line so they do not interfere with our config values
+
/** Readgroup Library */
- var libraryId: String = _
+ @Argument(doc = "Library ID", shortName = "library", required = true)
+ var libId: String = _
+
+ /**Readgroup sample */
+ @Argument(doc = "Sample ID", shortName = "sample", required = true)
+ var sampleId: String = _
/** Readgroup Platform */
protected var platform: String = config("platform", default = "illumina")
@@ -75,9 +82,6 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
/** Readgroup platform unit */
protected var platformUnit: String = config("platform_unit", default = "na")
- /**Readgroup sample */
- var sampleId: String = _
-
/** Readgroup sequencing center */
protected var readgroupSequencingCenter: Option[String] = config("readgroup_sequencing_center")
@@ -95,14 +99,14 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
def finalBamFile: File = outputDir + outputName + ".final.bam"
def init() {
- if (outputDir == null) throw new IllegalStateException("Missing Output directory on mapping module")
- else if (!outputDir.endsWith("/")) outputDir += "/"
- if (input_R1 == null) throw new IllegalStateException("Missing FastQ R1 on mapping module")
+ require(outputDir != null, "Missing output directory on mapping module")
+ require(input_R1 != null, "Missing output directory on mapping module")
+ require(sampleId != null, "Missing sample ID on mapping module")
+ require(libId != null, "Missing library ID on mapping module")
+
paired = input_R2.isDefined
- if (libraryId == null) libraryId = config("library_id")
- if (sampleId == null) sampleId = config("sample_id")
- if (readgroupId == null && sampleId != null && libraryId != null) readgroupId = sampleId + "-" + libraryId
+ if (readgroupId == null && sampleId != null && libId != null) readgroupId = sampleId + "-" + libId
else if (readgroupId == null) readgroupId = config("readgroup_id")
if (outputName == null) outputName = readgroupId
@@ -127,7 +131,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
flexiprep.input_R1 = input_R1
flexiprep.input_R2 = input_R2
flexiprep.sampleId = this.sampleId
- flexiprep.libraryId = this.libraryId
+ flexiprep.libId = this.libId
flexiprep.init
flexiprep.runInitialJobs
}
@@ -281,7 +285,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var RG: String = "ID:" + readgroupId + ","
RG += "SM:" + sampleId + ","
- RG += "LB:" + libraryId + ","
+ RG += "LB:" + libId + ","
if (readgroupDescription != null) RG += "DS" + readgroupDescription + ","
RG += "PU:" + platformUnit + ","
if (predictedInsertsize.getOrElse(0) > 0) RG += "PI:" + predictedInsertsize.get + ","
@@ -332,7 +336,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
addOrReplaceReadGroups.createIndex = true
addOrReplaceReadGroups.RGID = readgroupId
- addOrReplaceReadGroups.RGLB = libraryId
+ addOrReplaceReadGroups.RGLB = libId
addOrReplaceReadGroups.RGPL = platform
addOrReplaceReadGroups.RGPU = platformUnit
addOrReplaceReadGroups.RGSM = sampleId
@@ -346,7 +350,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
def getReadGroup(): String = {
var RG: String = "@RG\\t" + "ID:" + readgroupId + "\\t"
- RG += "LB:" + libraryId + "\\t"
+ RG += "LB:" + libId + "\\t"
RG += "PL:" + platform + "\\t"
RG += "PU:" + platformUnit + "\\t"
RG += "SM:" + sampleId + "\\t"
diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index e51be1d7164bd1234f831418e7c1eedaca2f7235..77dba4b1469eba2d75bedafc9f53be7c23acb557 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -59,16 +59,16 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def makeLibrary(id: String) = new Library(id)
- class Library(libraryId: String) extends AbstractLibrary(libraryId) {
- val inputFastq: File = config("R1", required = true)
+ class Library(libId: String) extends AbstractLibrary(libId) {
+ val inputFastq: File = config("R1")
val prefixFastq: File = createFile(".prefix.fastq")
val flexiprep = new Flexiprep(qscript)
flexiprep.sampleId = sampleId
- flexiprep.libraryId = libraryId
+ flexiprep.libId = libId
val mapping = new Mapping(qscript)
- mapping.libraryId = libraryId
+ mapping.libId = libId
mapping.sampleId = sampleId
protected def addJobs(): Unit = {
@@ -93,8 +93,8 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
qscript.addAll(mapping.functions)
if (config("library_counts", default = false).asBoolean) {
- addBedtoolsCounts(mapping.finalBamFile, sampleId + "-" + libraryId, libDir)
- addTablibCounts(pf.outputFastq, sampleId + "-" + libraryId, libDir)
+ addBedtoolsCounts(mapping.finalBamFile, sampleId + "-" + libId, libDir)
+ addTablibCounts(pf.outputFastq, sampleId + "-" + libId, libDir)
}
}
}
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
index 8e3ef0af511f28b19dda8403258b024ab8936b42..6e7257c7d94967eac350fc212e7c7b37ebf5dc58 100644
--- a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
@@ -35,7 +35,7 @@ import org.broadinstitute.gatk.queue.engine.JobRunInfo
class Yamsvp(val root: Configurable) extends QScript with BiopetQScript { //with MultiSampleQScript {
def this() = this(null)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
var finalBamFiles: List[File] = Nil
/*
class LibraryOutput extends AbstractLibraryOutput {
@@ -124,11 +124,11 @@ class Yamsvp(val root: Configurable) extends QScript with BiopetQScript { //with
// Called for each run from a sample
- def runSingleLibraryJobs(libraryId: String, sampleID: String): LibraryOutput = {
+ def runSingleLibraryJobs(libId: String, sampleID: String): LibraryOutput = {
val libraryOutput = new LibraryOutput
val alignmentDir: String = outputDir + sampleID + "/alignment/"
- val runDir: String = alignmentDir + "run_" + libraryId + "/"
+ val runDir: String = alignmentDir + "run_" + libId + "/"
if (config.contains("R1")) {
val mapping = new Mapping(this)
@@ -140,7 +140,7 @@ class Yamsvp(val root: Configurable) extends QScript with BiopetQScript { //with
mapping.input_R1 = config("R1")
mapping.input_R2 = config("R2")
mapping.paired = (mapping.input_R2 != null)
- mapping.RGLB = libraryId
+ mapping.RGLB = libId
mapping.RGSM = sampleID
mapping.RGPL = config("PL")
mapping.RGPU = config("PU")
@@ -154,7 +154,7 @@ class Yamsvp(val root: Configurable) extends QScript with BiopetQScript { //with
// start sambamba dedup
libraryOutput.mappedBamFile = mapping.outputFiles("finalBamFile")
- } else this.logger.error("Sample: " + sampleID + ": No R1 found for library: " + libraryId)
+ } else this.logger.error("Sample: " + sampleID + ": No R1 found for library: " + libId)
return libraryOutput
// logger.debug(outputFiles)
// return outputFiles