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Commit 706ca942 authored by Peter van 't Hof's avatar Peter van 't Hof
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Fix compile errors

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public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+ 2
− 11
View file @ 706ca942
......@@ -15,21 +15,12 @@
*/
package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
import java.io.File
import htsjdk.samtools.{ SAMSequenceRecord, SamReaderFactory }
import htsjdk.samtools.reference.IndexedFastaSequenceFile
import htsjdk.variant.variantcontext.VariantContext
import htsjdk.variant.vcf.VCFFileReader
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ Reference, ToolCommand, ToolCommandFuntion }
import nl.lumc.sasc.biopet.utils.VcfUtils._
import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
import scala.collection.mutable.ListBuffer
import scala.collection.parallel.ParMap
class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with Reference {
javaMainClass = getClass.getName
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
+ 2
− 5
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......@@ -15,15 +15,12 @@
*/
package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
import java.io.File
import htsjdk.samtools.{ SAMSequenceRecord, SamReaderFactory }
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.io.Source
/**
* @deprecated Use picard.util.BedToIntervalList instead
*/
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
+ 2
− 5
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......@@ -15,15 +15,12 @@
*/
package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.{ mutable, SortedMap }
import scala.io.Source
class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
+ 3
− 7
View file @ 706ca942
......@@ -15,18 +15,14 @@
*/
package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
import java.io.File
import htsjdk.samtools.{ SAMRecord, SamReaderFactory }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
import scala.collection.mutable
class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
javaMainClass = getClass.getName
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
+ 1
− 2
View file @ 706ca942
......@@ -17,9 +17,8 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+ 2
− 5
View file @ 706ca942
......@@ -17,14 +17,11 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader, FastqRecord }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.annotation.tailrec
import scala.collection.JavaConverters._
import scala.io.Source
import scala.util.matching.Regex
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+ 1
− 9
View file @ 706ca942
......@@ -17,18 +17,10 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import htsjdk.samtools.reference.FastaSequenceFile
import htsjdk.variant.variantcontext.{ Allele, VariantContext, VariantContextBuilder }
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.vcf.{ VCFFileReader, VCFHeader }
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
import scala.collection.{ mutable, SortedMap }
import scala.collection.mutable.{ Map, Set }
class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
+ 2
− 3
View file @ 706ca942
......@@ -15,14 +15,13 @@
*/
package nl.lumc.sasc.biopet.tools
import java.io.{ BufferedWriter, File, FileWriter, OutputStreamWriter }
import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.mutable.{ Set => MutSet }
import scala.io.{ BufferedSource, Source }
/**
* Biopet wrapper for the [[MergeTables]] command line tool.
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+ 3
− 7
View file @ 706ca942
......@@ -15,20 +15,16 @@
*/
package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
import java.io.File
import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ Reference, ToolCommand, ToolCommandFuntion }
import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
import scala.collection.mutable
import scala.collection.mutable.ArrayBuffer
import scala.io.Source
import scala.math.{ floor, round }
class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Reference {
javaMainClass = getClass.getName
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
+ 2
− 3
View file @ 706ca942
......@@ -17,9 +17,8 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader, FastqRecord }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
......@@ -51,7 +50,7 @@ class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
optional("-s", prefixSeq)
}
object PrefixFastq extends ToolCommand {
object PrefixFastq {
/**
* Create a PrefixFastq class object with a sufix ".prefix.fastq" in the output folder
*
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
+ 2
− 6
View file @ 706ca942
......@@ -15,16 +15,12 @@
*/
package nl.lumc.sasc.biopet.tools
import java.io.{ File, FileReader, PrintWriter }
import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
import org.biojava3.sequencing.io.fastq.{ Fastq, SangerFastqReader, StreamListener }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.{ mutable, SortedMap }
import scala.collection.mutable.Map
class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
+ 2
− 9
View file @ 706ca942
......@@ -15,19 +15,12 @@
*/
package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
import org.biojava3.core.sequence.DNASequence
import org.biojava3.core.sequence.io.FastaReaderHelper
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
import scala.collection.{ mutable, SortedMap }
import scala.collection.mutable.{ Map, Set }
import scala.util.matching.Regex
class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
+ 2
− 6
View file @ 706ca942
......@@ -15,16 +15,12 @@
*/
package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.{ mutable, SortedMap }
import scala.collection.mutable.Map
import scala.io.Source
class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
+ 6
− 0
View file @ 706ca942
......@@ -2,6 +2,12 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Seqstat function class for usage in Biopet pipelines
*
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
+ 2
− 2
View file @ 706ca942
......@@ -2,9 +2,9 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by pjvanthof on 22/08/15.
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+ 2
− 7
View file @ 706ca942
......@@ -17,14 +17,9 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantContextWriterBuilder}
import htsjdk.variant.variantcontext.{GenotypeType, VariantContext}
import htsjdk.variant.vcf.VCFFileReader
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import scala.collection.JavaConversions._
import scala.io.Source
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+ 5
− 14
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......@@ -15,23 +15,14 @@
*/
package nl.lumc.sasc.biopet.tools
import java.io.{File, FileOutputStream, PrintWriter}
import htsjdk.samtools.reference.FastaSequenceFile
import htsjdk.samtools.util.Interval
import htsjdk.variant.variantcontext.{Allele, Genotype, VariantContext}
import htsjdk.variant.vcf.VCFFileReader
import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.core.summary.{Summarizable, SummaryQScript}
import java.io.File
import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
import scala.collection.mutable
import scala.io.Source
import scala.sys.process.{Process, ProcessLogger}
import scala.util.Random
/**
* This tool will generate statistics from a vcf file
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
+ 2
− 8
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......@@ -16,16 +16,10 @@
package nl.lumc.sasc.biopet.tools
import java.io.File
import java.util
import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantContextWriterBuilder}
import htsjdk.variant.variantcontext.{VariantContext, VariantContextBuilder}
import htsjdk.variant.vcf._
import nl.lumc.sasc.biopet.utils.VcfUtils.scalaListToJavaObjectArrayList
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import scala.collection.JavaConversions._
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Biopet extension for tool VcfWithVcf
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
+ 2
− 8
View file @ 706ca942
......@@ -17,15 +17,9 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import htsjdk.tribble.TribbleException
import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantContextWriterBuilder}
import htsjdk.variant.variantcontext.{VariantContext, VariantContextBuilder}
import htsjdk.variant.vcf._
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import scala.collection.JavaConversions._
import scala.collection.mutable.{Map => MMap}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* This tool parses a VEP annotated VCF into a standard VCF file.
......
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
+ 2
− 10
View file @ 706ca942
......@@ -17,17 +17,9 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import com.google.common.hash.{BloomFilter, Funnel}
import htsjdk.samtools.util.{Interval, IntervalTreeMap}
import htsjdk.samtools.{QueryInterval, SAMFileWriter, SAMFileWriterFactory, SAMRecord, SamReader, SamReaderFactory, ValidationStringency}
import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import org.apache.commons.io.FilenameUtils.getExtension
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import scala.collection.JavaConverters._
import scala.io.Source
import scala.math.{max, min}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
// TODO: finish implementation for usage in pipelines
/**
......
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