Commit da908cbb authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Changed to SamReaderFactory

parent ef085f81
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.MultiSampleQScript
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import htsjdk.samtools.SAMFileReader
import htsjdk.samtools.SamReaderFactory
import scala.collection.JavaConversions._
import java.io.File
import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, CombineGVCFs }
......@@ -185,7 +185,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
libraryOutput.mappedBamFile = mapping.outputFiles("finalBamFile")
} else {
var readGroupOke = true
val inputSam = new SAMFileReader(bamFile)
val inputSam = SamReaderFactory.makeDefault.open(bamFile)
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")
......
package nl.lumc.sasc.biopet.tools
import htsjdk.samtools.SAMFileReader
import htsjdk.samtools.SAMSequenceRecord
import htsjdk.samtools.{ SAMSequenceRecord, SamReaderFactory }
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.ToolCommand
......@@ -68,7 +67,7 @@ object BedToInterval extends ToolCommand {
val writer = new PrintWriter(commandArgs.outputFile)
val inputSam = new SAMFileReader(commandArgs.bamFile)
val inputSam = SamReaderFactory.makeDefault.open(commandArgs.bamFile)
val refs = for (SQ <- inputSam.getFileHeader.getSequenceDictionary.getSequences.toArray) yield {
val record = SQ.asInstanceOf[SAMSequenceRecord]
writer.write("@SQ\tSN:" + record.getSequenceName + "\tLN:" + record.getSequenceLength + "\n")
......
package nl.lumc.sasc.biopet.tools
import htsjdk.samtools.SAMFileReader
import htsjdk.samtools.SAMRecord
import htsjdk.samtools.{ SAMRecord, SamReaderFactory }
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.ToolCommand
......@@ -57,7 +56,7 @@ object BiopetFlagstat extends ToolCommand {
val argsParser = new OptParser
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
val inputSam = new SAMFileReader(commandArgs.inputFile)
val inputSam = SamReaderFactory.makeDefault.open(commandArgs.inputFile)
val iterSam = if (commandArgs.region == None) inputSam.iterator else {
val regionRegex = """(.*):(.*)-(.*)""".r
commandArgs.region.get match {
......
package nl.lumc.sasc.biopet.tools
import htsjdk.samtools.SAMFileReader
import htsjdk.samtools.QueryInterval
import htsjdk.samtools.SAMRecord
import htsjdk.samtools.{ QueryInterval, SamReaderFactory, SAMRecord, SamReader }
import htsjdk.variant.variantcontext.VariantContext
import htsjdk.variant.variantcontext.VariantContextBuilder
import htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
......@@ -69,7 +67,8 @@ object CheckAllelesVcfInBam extends ToolCommand {
if (commandArgs.bamFiles.size != commandArgs.samples.size)
logger.warn("Number of samples is diffrent then number of bam files, left over will be removed")
val bamReaders: Map[String, SAMFileReader] = Map(commandArgs.samples zip commandArgs.bamFiles.map(x => new SAMFileReader(x)): _*)
val samReaderFactory = SamReaderFactory.makeDefault
val bamReaders: Map[String, SamReader] = Map(commandArgs.samples zip commandArgs.bamFiles.map(x => samReaderFactory.open(x)): _*)
val bamHeaders = bamReaders.map(x => (x._1, x._2.getFileHeader))
val reader = new VCFFileReader(commandArgs.inputFile, false)
......
/*
* Copyright 2014 pjvan_thof.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package nl.lumc.sasc.biopet.tools
import htsjdk.samtools.QueryInterval
import htsjdk.samtools.SAMFileReader
import htsjdk.samtools.ValidationStringency
import htsjdk.samtools.SAMRecord
import htsjdk.samtools.{ QueryInterval, SAMRecord, SamReaderFactory, ValidationStringency }
import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommand
import scala.io.Source
......@@ -44,8 +25,9 @@ object FindRepeatsPacBio extends ToolCommand {
val argsParser = new OptParser
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
val bamReader = new SAMFileReader(commandArgs.inputBam)
bamReader.setValidationStringency(ValidationStringency.SILENT)
val bamReader = SamReaderFactory.makeDefault
.validationStringency(ValidationStringency.SILENT)
.open(commandArgs.inputBam)
val bamHeader = bamReader.getFileHeader
val header = List("chr", "startPos", "stopPos", "Repeat_seq", "repeatLength",
......
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