Commit d7260ac8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Reorganize tools

Fix for #29
parent 5edfb6af
......@@ -18,9 +18,9 @@ object BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.basty.Basty,
nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp),
"tool" -> List(
nl.lumc.sasc.biopet.core.apps.WipeReads,
nl.lumc.sasc.biopet.core.apps.BiopetFlagstat,
nl.lumc.sasc.biopet.core.apps.CheckAllelesVcfInBam)
nl.lumc.sasc.biopet.tools.WipeReads,
nl.lumc.sasc.biopet.tools.BiopetFlagstat,
nl.lumc.sasc.biopet.tools.CheckAllelesVcfInBam)
)
/**
......
......@@ -4,7 +4,7 @@ import nl.lumc.sasc.biopet.scripts.CoverageStats
import org.broadinstitute.gatk.queue.QScript
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import java.io.File
import nl.lumc.sasc.biopet.core.apps.{ BedToInterval, BiopetFlagstat }
import nl.lumc.sasc.biopet.tools.{ BedToInterval, BiopetFlagstat }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
import nl.lumc.sasc.biopet.extensions.picard.{ CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics, CollectAlignmentSummaryMetrics }
......
......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand}
import java.io.File
import nl.lumc.sasc.biopet.core.apps.{ MpileupToVcf, VcfFilter }
import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.{AnalyzeCovariates,BaseRecalibrator,GenotypeGVCFs,HaplotypeCaller,IndelRealigner,PrintReads,RealignerTargetCreator, SelectVariants, CombineVariants, UnifiedGenotyper}
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
......
......@@ -4,7 +4,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import java.io.File
import java.util.Date
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.apps.FastqSplitter
import nl.lumc.sasc.biopet.tools.FastqSplitter
import nl.lumc.sasc.biopet.extensions.aligners.{ Bwa, Star , Bowtie, Stampy}
import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, SortSam, MergeSamFiles, AddOrReplaceReadGroups}
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
......
package nl.lumc.sasc.biopet.core.apps
package nl.lumc.sasc.biopet.tools
import htsjdk.samtools.SAMFileReader
import htsjdk.samtools.SAMSequenceRecord
......
package nl.lumc.sasc.biopet.core.apps
package nl.lumc.sasc.biopet.tools
import htsjdk.samtools.SAMFileReader
import htsjdk.samtools.SAMRecord
......
package nl.lumc.sasc.biopet.core.apps
package nl.lumc.sasc.biopet.tools
import htsjdk.samtools.SAMFileReader
import htsjdk.samtools.SAMRecord
......
package nl.lumc.sasc.biopet.core.apps
package nl.lumc.sasc.biopet.tools
import java.io.{ BufferedInputStream, File, FileInputStream, PrintWriter }
import java.util.zip.GZIPInputStream
......
package nl.lumc.sasc.biopet.core.apps
package nl.lumc.sasc.biopet.tools
import java.io.File
import java.io.PrintWriter
......
package nl.lumc.sasc.biopet.core.apps
package nl.lumc.sasc.biopet.tools
import htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
......
......@@ -2,7 +2,7 @@
* Copyright (c) 2014 Leiden University Medical Center - Sequencing Analysis Support Core <sasc@lumc.nl>
* @author Wibowo Arindrarto <w.arindrarto@lumc.nl>
*/
package nl.lumc.sasc.biopet.core.apps
package nl.lumc.sasc.biopet.tools
import java.io.{ File, IOException }
......
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