基因数据处理32之Avocado运行记录(人造数据集)

主要是需要数据正确，如果中间缺少记录，avocado一般不会成功
1.代码：
Avocado修改：

/**
  * Licensed to Big Data Genomics (BDG) under one
  * or more contributor license agreements.  See the NOTICE file
  * distributed with this work for additional information
  * regarding copyright ownership.  The BDG licenses this file
  * to you 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 org.bdgenomics.avocado.cli

import java.nio.file.Files
import org.apache.commons.configuration.HierarchicalConfiguration
import org.apache.commons.configuration.plist.PropertyListConfiguration
import org.apache.hadoop.mapreduce.Job
import org.apache.spark.rdd.RDD
import org.apache.spark.{SparkContext, Logging}
import org.kohsuke.args4j.{Option => option, Argument}
import org.bdgenomics.adam.models.{VariantContext, ReferenceRegion}
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.avocado.Timers._
import org.bdgenomics.avocado.discovery.Explore
import org.bdgenomics.avocado.genotyping.CallGenotypes
import org.bdgenomics.avocado.input.Input
import org.bdgenomics.avocado.models.Observation
import org.bdgenomics.avocado.preprocessing.Preprocessor
import org.bdgenomics.avocado.postprocessing.Postprocessor
import org.bdgenomics.avocado.stats.AvocadoConfigAndStats
import org.bdgenomics.formats.avro.{
Variant,
AlignmentRecord,
NucleotideContigFragment,
Genotype
}
import org.bdgenomics.utils.cli.{
BDGSparkCommand,
BDGCommandCompanion,
ParquetArgs,
Args4j,
Args4jBase
}
import org.bdgenomics.utils.instrumentation._

object Avocado extends BDGCommandCompanion {

  val commandName = "Avocado"
  val commandDescription = "Call variants using avocado and the ADAM preprocessing pipeline."

  def apply(args: Array[String]) = {
    new Avocado(Args4j[AvocadoArgs](args))
  }
}

class AvocadoArgs extends Args4jBase with ParquetArgs {
  @Argument(metaVar = "READS", required = true, usage = "ADAM read-oriented data", index = 0)
  var readInput: String = _

  @Argument(metaVar = "REFERENCE", required = true, usage = "ADAM or FASTA reference genome data", index = 1)
  var referenceInput: String = _

  @Argument(metaVar = "VARIANTS", required = true, usage = "ADAM variant output", index = 2)
  var variantOutput: String = _

  @Argument(metaVar = "CONFIG", required = true, usage = "avocado configuration file", index = 3)
  var configFile: String = _

  @option(name = "-debug", usage = "If set, prints a higher level of debug output.")
  var debug = false

  @option(required = false, name = "-fragment_length", usage = "Sets maximum fragment length. Default value is 10,000. Values greater than 1e9 should be avoided.")
  var fragmentLength: Long = 10000L
}

class Avocado(protected val args: AvocadoArgs) extends BDGSparkCommand[AvocadoArgs] with Logging {

  // companion object to this class - needed for BDGCommand framework
  val companion = Avocado
  /** *********add by xubo 20160528 *******************/
  println("companion:" + companion)
  println("companion.commandName:" + companion.commandName)
  println("companion.commandDescription:" + companion.commandDescription)
  //  println("companion.commandName:"+companion.)
  println("AvocadoArgs:")
  println("args:" + args)
  println("args.configFile:" + args.configFile)
  println("args.debug:" + args.debug)
  println("args.fragmentLength:" + args.fragmentLength)
  println("args.readInput:" + args.readInput)
  println("args.referenceInput:" + args.referenceInput)
  println("args.variantOutput:" + args.variantOutput)
  println("test end\n")
  /** *********add by xubo 20160528 *******************/
  // get config off classpath and load into a temp file...
  val stream = Thread.currentThread.getContextClassLoader.getResourceAsStream(args.configFile)
  val tempPath = Files.createTempDirectory("config")
  val tempFilePath = tempPath.resolve("temp.properties")
  Files.copy(stream, tempFilePath)

  /** *********add by xubo 20160528 *******************/
  println("stream:" + stream)
  println("tempFilePath:" + tempFilePath)
  /** *********add by xubo 20160528 *******************/

  // load config
  val config: HierarchicalConfiguration = new PropertyListConfiguration(tempFilePath.toFile)
  val preprocessorNames = getStringArrayFromConfig("preprocessorNames")
  val preprocessorAlgorithms = getStringArrayFromConfig("preprocessorAlgorithms")
  assert(preprocessorNames.length == preprocessorAlgorithms.length,
    "Must have a 1-to-1 mapping between preprocessor names and algorithms.")
  val preprocessingStagesZippedWithNames = preprocessorNames.zip(preprocessorAlgorithms)

  val explorerName = config.getString("explorerName")
  val explorerAlgorithm = config.getString("explorerAlgorithm")

  val genotyperName = config.getString("genotyperName")
  val genotyperAlgorithm = config.getString("genotyperAlgorithm")

  val postprocessorNames = getStringArrayFromConfig("postprocessorNames")
  val postprocessorAlgorithms = getStringArrayFromConfig("postprocessorAlgorithms")
  assert(postprocessorNames.length == postprocessorAlgorithms.length,
    "Must have a 1-to-1 mapping between postprocessor names and algoritms.")
  val postprocessorsZipped = postprocessorNames.zip(postprocessorAlgorithms)

  val debug = args.debug
  /** *********add by xubo 20160528 *******************/
  println("config:" + config)
  println("preprocessorNames:" + preprocessorNames)
  preprocessorNames.foreach(println)
  println("preprocessorAlgorithms:" + preprocessorAlgorithms)
  preprocessorAlgorithms.foreach(println)
  println("preprocessingStagesZippedWithNames:" + preprocessingStagesZippedWithNames)
  preprocessorNames.foreach(println)
  println("explorerName:" + explorerName)
  println("explorerAlgorithm:" + explorerAlgorithm)
  println("genotyperName:" + genotyperName)
  println("genotyperAlgorithm:" + genotyperAlgorithm)
  println("postprocessorNames:" + postprocessorNames)
  postprocessorNames.foreach(println)
  println("postprocessorAlgorithms:" + postprocessorAlgorithms)
  postprocessorAlgorithms.foreach(println)
  println("postprocessorsZipped:" + postprocessorsZipped)
  postprocessorsZipped.foreach(println)
  println("stream:" + stream)
  println("stream:" + stream)
  println("stream:" + stream)
  println("stream:" + stream)

  /** *********add by xubo 20160528 *******************/
  private def getStringArrayFromConfig(name: String): Array[String] = {
    config.getStringArray(name).map(_.toString)
  }

  /**
    * Applies several pre-processing steps to the read pipeline. Currently, these are the default
    * steps in the ADAM processing pipeline.
    *
    * @param reads RDD of reads to process.
    * @return RDD containing reads that have been sorted and deduped.
    */
  def preProcessReads(reads: RDD[AlignmentRecord]): RDD[AlignmentRecord] = PreprocessReads.time {
    var processedReads = reads //.cache

    if (debug) {
      log.info("avocado: Preprocessing " + processedReads.count + " reads.")
    }

    // loop over preprocessing stages and apply
    preprocessingStagesZippedWithNames.foreach(p => {
      val (stageName, stageAlgorithm) = p

      log.info("avocado: Running " + stageName)

      // run this preprocessing stage
      processedReads = Preprocessor(processedReads, stageName, stageAlgorithm, config)
    })

    // return processed reads
    processedReads
  }

  /**
    * Applies variant calling algorithms to reads and pileups. Reduces down and returns called variants.
    *
    * @param reads
    * @param stats
    * @return Joined output of variant calling algorithms.
    */
  def callVariants(reads: RDD[AlignmentRecord], stats: AvocadoConfigAndStats): RDD[VariantContext] = CallVariants.time {
    val discoveries: RDD[Observation] = Explore(explorerAlgorithm,
      explorerName,
      reads,
      stats,
      config)
    CallGenotypes(genotyperAlgorithm,
      genotyperName,
      discoveries,
      stats,
      config)
  }

  /**
    * Applies variant post-processing methods to called variants. Post-processing can
    * include methods which modify the information in variant calls, or alternatively,
    * methods that filter out spurious variant calls.
    *
    * @param variants RDD of variants to process.
    * @return Post-processed variants.
    */
  def postProcessVariants(variants: RDD[VariantContext], stats: AvocadoConfigAndStats): RDD[VariantContext] = PostprocessVariants.time {
    var rdd = variants

    // loop over post processing steps
    postprocessorsZipped.foreach(p => {
      val (ppStageName, ppAlgorithm) = p

      rdd = Postprocessor(rdd, ppStageName, ppAlgorithm, stats, config)
    })

    rdd
  }

  /**
    * Main method. Implements body of variant caller. SparkContext and Hadoop Job are provided
    * by the ADAMSparkCommand shell.
    *
    * @param sc  SparkContext for RDDs.
    * @param job Hadoop Job container for file I/O.
    */

  def run(sc: SparkContext) {

    log.info("Starting avocado...")

    // load in reference from ADAM file
    val reference: RDD[NucleotideContigFragment] = LoadContigs.time {
      sc.loadSequence(args.referenceInput, fragmentLength = args.fragmentLength)
    }

    log.info("Loading reads in from " + args.readInput)
    // load in reads from ADAM file
    val reads: RDD[AlignmentRecord] = LoadReads.time {
      Input(sc, args.readInput, reference, config)
    }

    /** *********add by xubo 20160528 *******************/
    println("readInput:")
    reads.foreach(println)
    /** *********add by xubo 20160528 *******************/
    // create stats/config item
    val stats = new AvocadoConfigAndStats(sc, args.debug, reads, reference)

    /** *********add by xubo 20160528 *******************/
    println("stats:" + stats)
    println("stats.contigLengths:" + stats.contigLengths)
    //    println("stats.coverage:" + stats.coverage)
    println("stats.debug:" + stats.debug)
    println("stats.referenceObservations:" + stats.referenceObservations)
    //    println("stats.referenceSeq:" + stats.referenceSeq)
    //    stats.referenceSeq.foreach(println)
    println("stats.samplesInDataset:" + stats.samplesInDataset)
    stats.samplesInDataset.foreach(println)
    println("stats.sequenceDict:" + stats.sequenceDict)
    //    println("stats.contigLengths:"+stats)
    /** *********add by xubo 20160528 *******************/


    // apply read translation steps
    log.info("Processing reads.")
    var cleanedReads = preProcessReads(reads)

    /** *********add by xubo 20160528 *******************/
    println("cleanedReads:" + cleanedReads)
    println("cleanedReads.count:" + cleanedReads.count())
    cleanedReads.foreach(println)
    val cleanedReads2 = cleanedReads.map { each =>
      each.setRecordGroupSample("hello")
      each
    }
    //    cleanedReads.adamGetReadGroupDictionary()
    //    cleanedReads.getSequenc
    //    cleanedReads.foreach(each => println(each.getSequence + " " + each.referenceLength))
    println("cleanedReads2:")
    cleanedReads2.foreach(println)

    /** *********add by xubo 20160528 *******************/

    // call variants on filtered reads and pileups
    log.info("Calling variants.")
//    val calledVariants = callVariants(cleanedReads, stats)
    val calledVariants = callVariants(cleanedReads2, stats)

    /** *********add by xubo 20160528 *******************/
    println("calledVariants:" + calledVariants)
    println("calledVariants.count:" + calledVariants.count())
    //        calledVariants.take(10).foreach(each=>println(each.databases+" "+each.position+" "+each.variant+" "=each.genotypes))
    //    calledVariants.take(10).foreach(println)

    /** *********add by xubo 20160528 *******************/


    // post process variants
    log.info("Post-processing variants.")
    val processedGenotypes: RDD[Genotype] = postProcessVariants(calledVariants, stats).flatMap(variantContext => variantContext.genotypes)

    /** *********add by xubo 20160528 *******************/
    println("processedGenotypes:" + calledVariants)
    println("processedGenotypes.count:" + processedGenotypes.count())
    processedGenotypes.foreach(println)

    /** *********add by xubo 20160528 *******************/

    // save variants to output file
    log.info("Writing calls to disk.")
    SaveVariants.time {
      processedGenotypes.adamParquetSave(args.variantOutput,
        args.blockSize,
        args.pageSize,
        args.compressionCodec,
        args.disableDictionaryEncoding)

      /** ***********add ***************/
      processedGenotypes.foreach { each => println("processedGenotypes:" + each) }
      //      processedGenotypes.
    }
  }
}

AvocadoSuite没有上传，在个人idea的package org.bdgenomics.avocado.cli中
数据为：

val samFile = "artificial.realigned.sam"
 val faFile = "artificial.fa"

2.运行记录;

D:\1win7\java\jdk\bin\java -Didea.launcher.port=7532 "-Didea.launcher.bin.path=D:\1win7\idea\IntelliJ IDEA Community Edition 15.0.4\bin" -Dfile.encoding=UTF-8 -classpath 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IDEA Community Edition 15.0.4\lib\idea_rt.jar" com.intellij.rt.execution.application.AppMain org.bdgenomics.avocado.cli.AvocadoSuite
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/D:/1win7/java/apache-maven-3.3.9-bin/Repository/org/slf4j/slf4j-log4j12/1.7.12/slf4j-log4j12-1.7.12.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/D:/1win7/java/apache-maven-3.3.9-bin/Repository/org/bdgenomics/adam/adam-cli_2.10/0.18.2/adam-cli_2.10-0.18.2.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
2016-05-28 18:42:08 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
/D:/all/idea/avocado-master/avocado-cli/target/scala-2.10.3/test-classes/artificial.realigned.sam
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 0, "oldPosition": 10, "end": 70, "mapq": 100, "readName": "read2", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "34M10D26M", "oldCigar": "44M10D16M", "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": null, "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tOP:i:11\tNM:i:10\tRG:Z:read_group_id\tOC:Z:44M10D16M", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 110, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 111}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 5, "oldPosition": null, "end": 75, "mapq": 90, "readName": "read1", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "29M10D31M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "29^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G11", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:20\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 105, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 101}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 10, "oldPosition": 20, "end": 80, "mapq": 100, "readName": "read4", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "24M10D36M", "oldCigar": "34M10D26M", "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": null, "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tOP:i:21\tNM:i:10\tRG:Z:read_group_id\tOC:Z:34M10D26M", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 120, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 111}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 15, "oldPosition": null, "end": 85, "mapq": 90, "readName": "read3", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "19M10D41M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "19^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G21", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:20\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 115, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 101}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 25, "oldPosition": null, "end": 95, "mapq": 90, "readName": "read5", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "9M10D51M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "9^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G31", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:20\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 125, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 101}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 105, "oldPosition": null, "end": 165, "mapq": 90, "readName": "read1", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 5, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -101}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 110, "oldPosition": null, "end": 170, "mapq": 90, "readName": "read2", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:100\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 0, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -111}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 115, "oldPosition": null, "end": 175, "mapq": 90, "readName": "read3", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 15, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -101}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 120, "oldPosition": null, "end": 180, "mapq": 90, "readName": "read4", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:100\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 10, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -111}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 125, "oldPosition": null, "end": 185, "mapq": 90, "readName": "read5", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 25, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -101}
faLoad:
/D:/all/idea/avocado-master/avocado-cli/target/scala-2.10.3/test-classes/artificial.fa
{"contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": null}, "description": "fasta", "fragmentSequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "fragmentNumber": 0, "fragmentStartPosition": 0, "fragmentLength": 1120, "numberOfFragmentsInContig": 1}
C:\Users\xubo\AppData\Local\Temp\83178325081869260/var
/D:/all/idea/avocado-master/avocado-cli/target/scala-2.10.3/test-classes/basic.properties
(%s,123)
D:\all\idea\avocado-master\avocado-cli\src\test\resources\output\var20160528184213248
companion:org.bdgenomics.avocado.cli.Avocado$@3e4e92e3
companion.commandName:Avocado
companion.commandDescription:Call variants using avocado and the ADAM preprocessing pipeline.
AvocadoArgs:
args:org.bdgenomics.avocado.cli.AvocadoArgs@188d950a
args.configFile:basic.properties
args.debug:false
args.fragmentLength:10000
args.readInput:/D:/all/idea/avocado-master/avocado-cli/target/scala-2.10.3/test-classes/artificial.realigned.sam
args.referenceInput:/D:/all/idea/avocado-master/avocado-cli/target/scala-2.10.3/test-classes/artificial.fa
args.variantOutput:D:\all\idea\avocado-master\avocado-cli\src\test\resources\output\var20160528184213248
test end

stream:java.io.BufferedInputStream@7733d01d
tempFilePath:C:\Users\xubo\AppData\Local\Temp\config4218631409097485876\temp.properties
config:org.apache.commons.configuration.plist.PropertyListConfiguration@305e0ade
preprocessorNames:[Ljava.lang.String;@6e1b8da0
preprocessorAlgorithms:[Ljava.lang.String;@58424e18
preprocessingStagesZippedWithNames:[Lscala.Tuple2;@6fc8f5d9
explorerName:readExplorer
explorerAlgorithm:ReadExplorer
genotyperName:biallelicGenotyper
genotyperAlgorithm:BiallelicGenotyper
postprocessorNames:[Ljava.lang.String;@65fcd178
nonRef
postprocessorAlgorithms:[Ljava.lang.String;@7230adcb
filterReferenceCalls
postprocessorsZipped:[Lscala.Tuple2;@deacdcc
(nonRef,filterReferenceCalls)
stream:java.io.BufferedInputStream@7733d01d
stream:java.io.BufferedInputStream@7733d01d
stream:java.io.BufferedInputStream@7733d01d
stream:java.io.BufferedInputStream@7733d01d
Loading reads in from /D:/all/idea/avocado-master/avocado-cli/target/scala-2.10.3/test-classes/artificial.realigned.sam
readInput:
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 0, "oldPosition": 10, "end": 70, "mapq": 100, "readName": "read2", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "34M10D26M", "oldCigar": "44M10D16M", "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": null, "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tOP:i:11\tNM:i:10\tRG:Z:read_group_id\tOC:Z:44M10D16M", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 110, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 111}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 5, "oldPosition": null, "end": 75, "mapq": 90, "readName": "read1", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "29M10D31M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "29^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G11", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:20\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 105, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 101}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 10, "oldPosition": 20, "end": 80, "mapq": 100, "readName": "read4", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "24M10D36M", "oldCigar": "34M10D26M", "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": null, "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tOP:i:21\tNM:i:10\tRG:Z:read_group_id\tOC:Z:34M10D26M", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 120, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 111}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 15, "oldPosition": null, "end": 85, "mapq": 90, "readName": "read3", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "19M10D41M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "19^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G21", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:20\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 115, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 101}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 25, "oldPosition": null, "end": 95, "mapq": 90, "readName": "read5", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "9M10D51M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "9^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G31", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:20\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 125, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 101}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 105, "oldPosition": null, "end": 165, "mapq": 90, "readName": "read1", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 5, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -101}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 110, "oldPosition": null, "end": 170, "mapq": 90, "readName": "read2", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:100\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 0, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -111}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 115, "oldPosition": null, "end": 175, "mapq": 90, "readName": "read3", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 15, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -101}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 120, "oldPosition": null, "end": 180, "mapq": 90, "readName": "read4", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:100\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 10, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -111}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 125, "oldPosition": null, "end": 185, "mapq": 90, "readName": "read5", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 25, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -101}
stats:org.bdgenomics.avocado.stats.AvocadoConfigAndStats@32b9c6f7
stats.contigLengths:Map(artificial -> 1120)
stats.debug:false
stats.referenceObservations:MapPartitionsRDD[26] at flatMap at SliceReference.scala:28
stats.samplesInDataset:[Ljava.lang.String;@551a9433
sequencing_center
stats.sequenceDict:SequenceDictionary{
artificial->1120}
cleanedReads:MapPartitionsRDD[21] at map at ADAMContext.scala:289
cleanedReads.count:10
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 0, "oldPosition": 10, "end": 70, "mapq": 100, "readName": "read2", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "34M10D26M", "oldCigar": "44M10D16M", "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": null, "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tOP:i:11\tNM:i:10\tRG:Z:read_group_id\tOC:Z:44M10D16M", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 110, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 111}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 5, "oldPosition": null, "end": 75, "mapq": 90, "readName": "read1", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "29M10D31M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "29^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G11", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:20\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 105, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 101}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 10, "oldPosition": 20, "end": 80, "mapq": 100, "readName": "read4", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "24M10D36M", "oldCigar": "34M10D26M", "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": null, "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tOP:i:21\tNM:i:10\tRG:Z:read_group_id\tOC:Z:34M10D26M", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 120, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 111}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 15, "oldPosition": null, "end": 85, "mapq": 90, "readName": "read3", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "19M10D41M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "19^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G21", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:20\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 115, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 101}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 25, "oldPosition": null, "end": 95, "mapq": 90, "readName": "read5", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "9M10D51M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "9^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G31", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:20\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 125, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 101}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 105, "oldPosition": null, "end": 165, "mapq": 90, "readName": "read1", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 5, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -101}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 110, "oldPosition": null, "end": 170, "mapq": 90, "readName": "read2", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:100\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 0, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -111}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 115, "oldPosition": null, "end": 175, "mapq": 90, "readName": "read3", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 15, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -101}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 120, "oldPosition": null, "end": 180, "mapq": 90, "readName": "read4", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:100\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 10, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -111}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 125, "oldPosition": null, "end": 185, "mapq": 90, "readName": "read5", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "sequencing_center", "mateAlignmentStart": 25, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -101}
cleanedReads2:
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 0, "oldPosition": 10, "end": 70, "mapq": 100, "readName": "read2", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "34M10D26M", "oldCigar": "44M10D16M", "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": null, "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tOP:i:11\tNM:i:10\tRG:Z:read_group_id\tOC:Z:44M10D16M", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "hello", "mateAlignmentStart": 110, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 111}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 5, "oldPosition": null, "end": 75, "mapq": 90, "readName": "read1", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "29M10D31M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "29^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G11", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:20\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "hello", "mateAlignmentStart": 105, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 101}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 10, "oldPosition": 20, "end": 80, "mapq": 100, "readName": "read4", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "24M10D36M", "oldCigar": "34M10D26M", "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": null, "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tOP:i:21\tNM:i:10\tRG:Z:read_group_id\tOC:Z:34M10D26M", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "hello", "mateAlignmentStart": 120, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 111}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 15, "oldPosition": null, "end": 85, "mapq": 90, "readName": "read3", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "19M10D41M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "19^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G21", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:20\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "hello", "mateAlignmentStart": 115, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 101}
{"readNum": 0, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 25, "oldPosition": null, "end": 95, "mapq": 90, "readName": "read5", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "9M10D51M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "9^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G31", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:20\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "hello", "mateAlignmentStart": 125, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": 101}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 105, "oldPosition": null, "end": 165, "mapq": 90, "readName": "read1", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "hello", "mateAlignmentStart": 5, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -101}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 110, "oldPosition": null, "end": 170, "mapq": 90, "readName": "read2", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:100\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "hello", "mateAlignmentStart": 0, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -111}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 115, "oldPosition": null, "end": 175, "mapq": 90, "readName": "read3", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "hello", "mateAlignmentStart": 15, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -101}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 120, "oldPosition": null, "end": 180, "mapq": 90, "readName": "read4", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:100\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "hello", "mateAlignmentStart": 10, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -111}
{"readNum": 1, "contig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "start": 125, "oldPosition": null, "end": 185, "mapq": 90, "readName": "read5", "sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "qual": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", "cigar": "60M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "60", "origQual": null, "attributes": "XS:i:70\tAS:i:70\tMQ:i:90\tNM:i:0\tRG:Z:read_group_id", "recordGroupName": "read_group_id", "recordGroupSequencingCenter": null, "recordGroupDescription": null, "recordGroupRunDateEpoch": null, "recordGroupFlowOrder": null, "recordGroupKeySequence": null, "recordGroupLibrary": "library", "recordGroupPredictedMedianInsertSize": null, "recordGroupPlatform": "illumina", "recordGroupPlatformUnit": "platform_unit", "recordGroupSample": "hello", "mateAlignmentStart": 25, "mateAlignmentEnd": null, "mateContig": {"contigName": "artificial", "contigLength": 1120, "contigMD5": null, "referenceURL": null, "assembly": null, "species": null, "referenceIndex": 0}, "inferredInsertSize": -101}
calledVariants:InstrumentedRDD[41] at mapPartitions at BiallelicGenotyper.scala:398
calledVariants.count:1110
processedGenotypes:InstrumentedRDD[41] at mapPartitions at BiallelicGenotyper.scala:398
processedGenotypes.count:11
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SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
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*************end*************

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