Adam学习25之读取sam生成的alignmentRecord含recordGroupDictionary

Adam学习25之读取sam生成的alignmentRecord含recordGroupDictionary

1.代码：

package org.bdgenomics.adam.test

import java.nio.file.Files

import org.apache.spark.{SparkConf, SparkContext}
import org.bdgenomics.adam.rdd.ADAMContext._

/**
  * Created by xubo on 2016/5/28.
  */
object loadSamTest2 {
  def resourcePath(path: String) = ClassLoader.getSystemClassLoader.getResource(path).getFile

  def tmpFile(path: String) = Files.createTempDirectory("").toAbsolutePath.toString + "/" + path

  def main(args: Array[String]) {
    val conf = new SparkConf().setMaster("local[4]").setAppName(this.getClass().getSimpleName().filter(!_.equals('$')))
    val sc = new SparkContext(conf)
    val samFile = "NA12878_snp_A2G_chr20_225058.sam"
    val samLoad = sc.loadAlignments(resourcePath(samFile))
    println("model")
    samLoad.foreach(println)
    println(samLoad.count())
    samLoad.rdd.foreach(println)
    println("samLoad.recordGroups.toString:"+samLoad.recordGroups.toString)
    println(" samLoad.sequences.records:"+ samLoad.sequences.records.size)
    samLoad.sequences.records.foreach(println)
    println(samLoad.sequences.toString)
    println("end")
    sc.stop
  }
}

2.结果：

SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/D:/1win7/java/otherJar/spark-assembly-1.5.2-hadoop2.6.0.jar!/org/slf4j/impl/StaticLoggerBinder.class]
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: 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 18:24:46 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2016-05-28 18:24:49 WARN  MetricsSystem:71 - Using default name DAGScheduler for source because spark.app.id is not set.
2016-05-28 18:24:51 WARN  :139 - Your hostname, xubo-PC resolves to a loopback/non-reachable address: fe80:0:0:0:482:722f:5976:ce1f%32, but we couldn't find any external IP address!
model
{"readInFragment": 0, "contig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "start": 224958, "oldPosition": null, "end": 225059, "mapq": 60, "readName": "20GAVAAXX100126:1:28:3151:64774", "sequence": "CATCAGAAAACTAAGAATCAAGGATAGAATTTCTAGAAAGTTCCTTCCCCTAAAGCTTTCACACTTGCCTCAGTGTATATATGTGGCTATACCACTGACGG", "qual": "<BDCBDFFFEEEFFEDEFDFFEEEEFDEEFFFEEFEFFFCFFEEDFEEEEEFFFEEFFFDDDDEFFDEEFDFCFCEEEEEEFCFEEEEEEEDBEBEC78@?", "cigar": "101M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": true, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "12G86A1", "origQual": "GHHHGHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGFGGF<FFF", "attributes": "UQ:i:68\tOQ:Z:GHHHGHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGFGGF<FFF\tMQ:i:60\tSM:i:37\tNM:i:2\tAM:i:37\tRG:Z:20GAV.1\tPG:Z:BWA", "recordGroupName": "20GAV.1", "recordGroupSample": "NA12878", "mateAlignmentStart": 224658, "mateAlignmentEnd": null, "mateContig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "inferredInsertSize": -400}
{"readInFragment": 1, "contig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "start": 224960, "oldPosition": null, "end": 225061, "mapq": 60, "readName": "20GAVAAXX100126:6:44:10235:172597", "sequence": "TCAGAAAACTAAGAATCAAGGATAGAATTTCTAGAAAGTTCCTTCCCCTAAAGCTTTCACACTTGCCTCAGTGTATATATGTGGCTATACCACTGACGGGC", "qual": "4@A?C7?<DB@E<@:;BEE?A=>C<D<?@DABDBD?E@A8;@95ABE;<>E;D;5<7@>A9A:DD=?BDEBEDD?EBD@F?EEDEED8ACCC?@?B4A:5?", "cigar": "101M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": true, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "10G86A3", "origQual": "0<::>2:3=?<?:;57?A?;>9==:A<=<@@@>@@9>?:6:<74?@B7;<B9A;6<7@<@:@=AB=@?AAAABA;B?A<B>BBABBA9?@AB;;?B=@51@", "attributes": "UQ:i:63\tOQ:Z:0<::>2:3=?<?:;57?A?;>9==:A<=<@@@>@@9>?:6:<74?@B7;<B9A;6<7@<@:@=AB=@?AAAABA;B?A<B>BBABBA9?@AB;;?B=@51@\tMQ:i:60\tSM:i:37\tNM:i:2\tAM:i:23\tRG:Z:20GAV.6\tPG:Z:BWA", "recordGroupName": "20GAV.6", "recordGroupSample": "NA12878", "mateAlignmentStart": 224657, "mateAlignmentEnd": null, "mateContig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "inferredInsertSize": -403}
{"readInFragment": 1, "contig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "start": 224961, "oldPosition": null, "end": 225062, "mapq": 60, "readName": "20FUKAAXX100202:7:1:3289:160642", "sequence": "CAGAAAACTGAGAATCAAGGATAGAATTTCTAGAAAGTTCCTTCCCCTAAAGCTTTCACACTTGCCTCAGTGTATATATGTGGCTATACCACTGACAGGCC", "qual": "?BCCBCECFDFEFFEEFEEEFEEEFFEEEDFEEFFFEEEDDFEDEEEFEFFEDFEEDEBEBFADCEEEEEC?CCDCCCDEEBDDEC<DBCEBDB@ACAA2=", "cigar": "101M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": true, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "101", "origQual": "HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHIHIHGIGHIHIHD@EGGIEFIHGEIIGF4GGGGGDGCGGDG8G", "attributes": "UQ:i:0\tOQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHIHIHGIGHIHIHD@EGGIEFIHGEIIGF4GGGGGDGCGGDG8G\tMQ:i:60\tSM:i:37\tNM:i:0\tAM:i:37\tRG:Z:20FUK.7\tPG:Z:BWA", "recordGroupName": "20FUK.7", "recordGroupSample": "NA12878", "mateAlignmentStart": 225249, "mateAlignmentEnd": null, "mateContig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "inferredInsertSize": 388}
{"readInFragment": 1, "contig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "start": 224961, "oldPosition": null, "end": 225062, "mapq": 60, "readName": "20GAVAAXX100126:6:41:8052:51486", "sequence": "CAGAAAACTAAGAATCAAGGATAGAATTTCTAGAAAGTTCCTTCCCCTAAAGCTTTCACACTTGCCTCAGTGTATATATGTGGCTATACCACTGACGGGCC", "qual": "ACBCDDDDCDEECEDCDGDDECECCDBDDEBFEDEGCEEDEEBEEEEEEDFCECDEBCDCCFCEDEEEFEEDFGEGEGFCDEEEFGFCEEDEDDB;BCCB?", "cigar": "101M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": true, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "9G86A4", "origQual": "BAA@AA?B?ABA@B?AAB@BB@A@@B@B@BABBABBAAABBA@BBBBBBBBBBABBCABABBBBBBBCBCBCCCBCBCCBABBBCCCBBBABABBBBBBBB", "attributes": "UQ:i:68\tOQ:Z:BAA@AA?B?ABA@B?AAB@BB@A@@B@B@BABBABBAAABBA@BBBBBBBBBBABBCABABBBBBBBCBCBCCCBCBCCBABBBCCCBBBABABBBBBBBB\tMQ:i:60\tSM:i:37\tNM:i:2\tAM:i:37\tRG:Z:20GAV.6\tPG:Z:BWA", "recordGroupName": "20GAV.6", "recordGroupSample": "NA12878", "mateAlignmentStart": 224494, "mateAlignmentEnd": null, "mateContig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "inferredInsertSize": -567}
{"readInFragment": 0, "contig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "start": 224964, "oldPosition": null, "end": 225065, "mapq": 60, "readName": "20FUKAAXX100202:6:28:12642:185083", "sequence": "AAAACTGAGAATCAAGGATAGAATTTCTAGAAAGTTCCTTCCCCTAAAGCTTTCACACTTGCCTCAGTGTATATATGTGGCTATACCACTGACAGGCCGCC", "qual": "ACDFCFEFEFGFEFFEEFEEEFFEEEEFEEFFFECEDDFEDEDEFEFFEDFEE1ECECF<EEEFDEEBE>EEEDCEED?9EFEFBDEFDGEGDC@ECD<??", "cigar": "101M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": true, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "101", "origQual": "HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHH;HHHHHDHHHHHHHEHCHHHGGHHIC@HHHHFHHHHHHHHEEHFHHDD", "attributes": "UQ:i:0\tOQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHHHHHHHHHHHH;HHHHHDHHHHHHHEHCHHHGGHHIC@HHHHFHHHHHHHHEEHFHHDD\tMQ:i:60\tSM:i:37\tNM:i:0\tAM:i:37\tRG:Z:20FUK.6\tPG:Z:BWA", "recordGroupName": "20FUK.6", "recordGroupSample": "NA12878", "mateAlignmentStart": 225268, "mateAlignmentEnd": null, "mateContig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "inferredInsertSize": 404}
{"readInFragment": 1, "contig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "start": 224966, "oldPosition": null, "end": 225067, "mapq": 60, "readName": "20FUKAAXX100202:6:48:15418:77607", "sequence": "AACTAAGAATCAAGGATAGAATTTCTAGAAAGTTCCTTCCCCTAAAGCTTTCACACTTGCCTCAGTGTATATATGTGGCTATACCACTGACGGGCCGCCAG", "qual": ";A@BEEBEDGCDEDCDEEDFDCFECBFCEEECFEEEDDEEEECEEEDEEFEECECEBEDEEFEFCECEEEEEEEBDCEEEBEAEEEEDDE=DDDD:ACBC?", "cigar": "101M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": true, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "4G86A9", "origQual": "GGGGHGGIGHEFGGGEHIIHIGHGGEHIHHIHHGHHIFHHHHGHHGHHIHIHGHIHGHHHHHHHHHHHHHHHHHHHHHHHFHFHHHHHHHHHHHHHHHHHH", "attributes": "UQ:i:71\tOQ:Z:GGGGHGGIGHEFGGGEHIIHIGHGGEHIHHIHHGHHIFHHHHGHHGHHIHIHGHIHGHHHHHHHHHHHHHHHHHHHHHHHFHFHHHHHHHHHHHHHHHHHH\tMQ:i:60\tSM:i:37\tNM:i:2\tAM:i:37\tRG:Z:20FUK.6\tPG:Z:BWA", "recordGroupName": "20FUK.6", "recordGroupSample": "NA12878", "mateAlignmentStart": 224762, "mateAlignmentEnd": null, "mateContig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "inferredInsertSize": -304}
{"readInFragment": 0, "contig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "start": 224967, "oldPosition": null, "end": 225068, "mapq": 60, "readName": "20GAVAAXX100126:3:61:9225:75287", "sequence": "ACTGAGAATCAAGGATAGAATTTCTAGAAAGTTCCTTCCCCTAAAGCTTTCACACTTGCCTCAGTGTATATATGTGGCTATACCACTGACAGGCCGCCAGT", "qual": "A@DDFEFGEEFFEEFAEEFDEFFEFEEFFFEDFDDFFDDDDFEFFEDFFFDFCECFFDEDFDFEDDDEEEEEEEDDEEFEEECEFCFEFCFEEED=DCDB9", "cigar": "101M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": true, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "101", "origQual": "HHHHHHHHHHHHHHHFHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH:", "attributes": "UQ:i:0\tOQ:Z:HHHHHHHHHHHHHHHFHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHIHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH:\tMQ:i:60\tSM:i:37\tNM:i:0\tAM:i:37\tRG:Z:20GAV.3\tPG:Z:BWA", "recordGroupName": "20GAV.3", "recordGroupSample": "NA12878", "mateAlignmentStart": 225198, "mateAlignmentEnd": null, "mateContig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "inferredInsertSize": 331}
{"readInFragment": 0, "contig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "start": 224969, "oldPosition": null, "end": 225070, "mapq": 60, "readName": "20FUKAAXX100202:6:1:12225:19943", "sequence": "TAAGAATCAAGGATAGAATTTCTAGAAAGTTCCTTCCCCTAAAGCTTTCACACTTGCCTCAGTGTATATATGTGGCTATACCACTGACGGGCCGCCAGTCA", "qual": "#ACDEDEB@GEEDBFDBDGDECDECEEDCFDEEFEEEEEEEEFEEFFFEDEDEFEDEEFEFCECEEEEEEECEEEEEEEBEEEEFEE=EEEF=EFEFCDBA", "cigar": "101M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": true, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "1G86A12", "origQual": "#FGHHGGDEHHHIFIIGIHFIGIIGIHGHHFHHHIHHHHHHHHHHHHHHGHIHHHHHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHH", "attributes": "UQ:i:68\tOQ:Z:#FGHHGGDEHHHIFIIGIHFIGIIGIHGHHFHHHIHHHHHHHHHHHHHHGHIHHHHHHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHH\tMQ:i:60\tSM:i:37\tNM:i:2\tAM:i:37\tRG:Z:20FUK.6\tPG:Z:BWA", "recordGroupName": "20FUK.6", "recordGroupSample": "NA12878", "mateAlignmentStart": 224722, "mateAlignmentEnd": null, "mateContig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "inferredInsertSize": -347}
{"readInFragment": 0, "contig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "start": 224972, "oldPosition": null, "end": 225073, "mapq": 60, "readName": "20GAVAAXX100126:6:3:14903:184943", "sequence": "GAATCAAGGATAGAATTTCTAGAAAGTTCCTTCCCCTAAAGCTTTCACACTTGCCTCAGTGTATATATGTGGCTATACCACTGACAGGCCGCCAGTCATTA", "qual": "@CADDFFEEFEEEFFEFFEFEEFFFEEFEEFFDDEDFEFFEDFFFDECECFFDEDFDFEDEEEEEEEEECDEEFEEECEFAFEFCFEEEE=EEFEDCDCCB", "cigar": "101M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": true, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "101", "origQual": "HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHFHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHH", "attributes": "UQ:i:0\tOQ:Z:HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHFHHHHHHHHHHIHHHHHHHHHHHHHHHHHHHH\tMQ:i:60\tSM:i:37\tNM:i:0\tAM:i:37\tRG:Z:20GAV.6\tPG:Z:BWA", "recordGroupName": "20GAV.6", "recordGroupSample": "NA12878", "mateAlignmentStart": 225258, "mateAlignmentEnd": null, "mateContig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "inferredInsertSize": 386}
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90
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{"readInFragment": 1, "contig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "start": 225057, "oldPosition": null, "end": 225158, "mapq": 60, "readName": "20GAVAAXX100126:6:47:6085:14272", "sequence": "GGGCCGCCAGTCATTAAATTCAAGCTCCAAGAGACAAACTCTTGAAAAAAAGGCAGCCTAGGAGAAAGCAACATGATTTTTCACATATTTTAACTTGGTTT", "qual": "?BCCB;CDEEDEFFDFGGGDFFGFEFFEFFEFEEAEEF?FAFDDEEBEFDFEEEFEDDEDEDEEEEFEEEDCECBDDECEDDFDEC=ECEDDECEDCCCAA", "cigar": "101M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": false, "mateNegativeStrand": true, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "0A100", "origQual": "BBBBBBBBBBABCCCCCCCCCCCCBBCBCBBBBBCCBBCBCBBCBBCBBBBBBBBBBBBABBABAABBBBBBBBB@AA@BBABBB@:B@A@B@BB@BA;?B", "attributes": "UQ:i:30\tOQ:Z:BBBBBBBBBBABCCCCCCCCCCCCBBCBCBBBBBCCBBCBCBBCBBCBBBBBBBBBBBBABBABAABBBBBBBBB@AA@BBABBB@:B@A@B@BB@BA;?B\tMQ:i:60\tSM:i:37\tNM:i:1\tAM:i:37\tRG:Z:20GAV.6\tPG:Z:BWA", "recordGroupName": "20GAV.6", "recordGroupSample": "NA12878", "mateAlignmentStart": 225306, "mateAlignmentEnd": null, "mateContig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "inferredInsertSize": 349}
{"readInFragment": 0, "contig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "start": 225057, "oldPosition": null, "end": 225148, "mapq": 60, "readName": "20FUKAAXX100202:4:47:20584:49257", "sequence": "TACCACGGACAGGCCGCCAGTCATTAAATTCAAGCTCCAAGAGACAAACTCTTGAAAAAAAGGCAGCCTAGGAGAAAGCAACATGATTTTTCACATATTTT", "qual": "###########D=C=EEEFCFEEFEFEEFFEEFEECEEEFEFDEEEEDEFEFEBBEEEEEFEDEFDEEEFEEFEEEFEEEEEEEEEFFFGFEEEFEEFDCA", "cigar": "10S91M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": true, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "91", "origQual": "###########I@FIHIHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHIHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH", "attributes": "UQ:i:0\tOQ:Z:###########I@FIHIHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHIHHHHHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\tMQ:i:60\tSM:i:37\tNM:i:0\tAM:i:37\tRG:Z:20FUK.4\tPG:Z:BWA", "recordGroupName": "20FUK.4", "recordGroupSample": "NA12878", "mateAlignmentStart": 224760, "mateAlignmentEnd": null, "mateContig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "inferredInsertSize": -387}
{"readInFragment": 0, "contig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "start": 225057, "oldPosition": null, "end": 225149, "mapq": 60, "readName": "20FUKAAXX100202:7:65:8106:6840", "sequence": "ACCACTGACAGGCCGCCAGTCATTAAATTCAAGCTCCAAGAGACAAACTCTTGAAAAAAAGGCAGCCTAGGAGAAAGCAACATGATTTTTCACATATTTTA", "qual": "##########?>D<AADFDFEEGEFFEEFEEFEEFE>EFEFEDEEEDEEEFE>AEEEEEFEDEFEEEEFEEFDEEFEEEEEEFEEFFFFFEEEFEEFFEBA", "cigar": "9S92M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": true, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "92", "origQual": "##########@AGGDEIHHHHHHHHHHIHHHHHHHHDHHHHHIHHHIHIHHHEGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH", "attributes": "UQ:i:0\tOQ:Z:##########@AGGDEIHHHHHHHHHHIHHHHHHHHDHHHHHIHHHIHIHHHEGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\tMQ:i:60\tSM:i:37\tNM:i:0\tAM:i:37\tRG:Z:20FUK.7\tPG:Z:BWA", "recordGroupName": "20FUK.7", "recordGroupSample": "NA12878", "mateAlignmentStart": 224797, "mateAlignmentEnd": null, "mateContig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "inferredInsertSize": -351}
{"readInFragment": 1, "contig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "start": 225057, "oldPosition": null, "end": 225131, "mapq": 60, "readName": "20GAVAAXX100126:2:46:5468:93666", "sequence": "GTTTATATATGTGGCTATCCCACTGACAGGCCGCCAGTCATTAAATTCAAGCTCCAAGAGACAAACTCTTGAAAAAAAGGCAGCCTAGGAGAAAGCAACAT", "qual": "############################B3C<ACCCBFDFDEECFEEDBGDCCDDEEBEEDEEB>EBCFEEEEEDDEFEEEGFEFEFFEFEDDECAABBC?", "cigar": "27S74M", "oldCigar": null, "basesTrimmedFromStart": 0, "basesTrimmedFromEnd": 0, "readPaired": true, "properPair": true, "readMapped": true, "mateMapped": true, "failedVendorQualityChecks": false, "duplicateRead": false, "readNegativeStrand": true, "mateNegativeStrand": false, "primaryAlignment": true, "secondaryAlignment": false, "supplementaryAlignment": false, "mismatchingPositions": "74", "origQual": "############################A3A?<?@@BBBBBBBBBAABBBBB@BBBBCBBABBB?B@BBBBBBBCCBABBBBCBCBBCCBCBBBBCBBCBB", "attributes": "UQ:i:0\tOQ:Z:############################A3A?<?@@BBBBBBBBBAABBBBB@BBBBCBBABBB?B@BBBBBBBCCBABBBBCBCBBCCBCBBBBCBBCBB\tMQ:i:60\tSM:i:37\tNM:i:0\tAM:i:37\tRG:Z:20GAV.2\tPG:Z:BWA", "recordGroupName": "20GAV.2", "recordGroupSample": "NA12878", "mateAlignmentStart": 224756, "mateAlignmentEnd": null, "mateContig": {"contigName": "20", "contigLength": 63025520, "contigMD5": "0dec9660ec1efaaf33281c0d5ea2560f", "referenceURL": "http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta", "assembly": "GRCh37", "species": "Homo Sapiens", "referenceIndex": 0}, "inferredInsertSize": -374}
samLoad.recordGroups.toString:RecordGroupDictionary(RecordGroup(NA12878,20FUK.1,Some(BI),None,Some(1265086800000),None,None,Some(Solexa-18483),None,Some(illumina),Some(20FUKAAXX100202.1)),RecordGroup(NA12878,20FUK.2,Some(BI),None,Some(1265086800000),None,None,Some(Solexa-18484),None,Some(illumina),Some(20FUKAAXX100202.2)),RecordGroup(NA12878,20FUK.3,Some(BI),None,Some(1265086800000),None,None,Some(Solexa-18483),None,Some(illumina),Some(20FUKAAXX100202.3)),RecordGroup(NA12878,20FUK.4,Some(BI),None,Some(1265086800000),None,None,Some(Solexa-18484),None,Some(illumina),Some(20FUKAAXX100202.4)),RecordGroup(NA12878,20FUK.5,Some(BI),None,Some(1265086800000),None,None,Some(Solexa-18483),None,Some(illumina),Some(20FUKAAXX100202.5)),RecordGroup(NA12878,20FUK.6,Some(BI),None,Some(1265086800000),None,None,Some(Solexa-18484),None,Some(illumina),Some(20FUKAAXX100202.6)),RecordGroup(NA12878,20FUK.7,Some(BI),None,Some(1265086800000),None,None,Some(Solexa-18483),None,Some(illumina),Some(20FUKAAXX100202.7)),RecordGroup(NA12878,20FUK.8,Some(BI),None,Some(1265086800000),None,None,Some(Solexa-18484),None,Some(illumina),Some(20FUKAAXX100202.8)),RecordGroup(NA12878,20GAV.1,Some(BI),None,Some(1264482000000),None,None,Some(Solexa-18483),None,Some(illumina),Some(20GAVAAXX100126.1)),RecordGroup(NA12878,20GAV.2,Some(BI),None,Some(1264482000000),None,None,Some(Solexa-18484),None,Some(illumina),Some(20GAVAAXX100126.2)),RecordGroup(NA12878,20GAV.3,Some(BI),None,Some(1264482000000),None,None,Some(Solexa-18483),None,Some(illumina),Some(20GAVAAXX100126.3)),RecordGroup(NA12878,20GAV.4,Some(BI),None,Some(1264482000000),None,None,Some(Solexa-18484),None,Some(illumina),Some(20GAVAAXX100126.4)),RecordGroup(NA12878,20GAV.5,Some(BI),None,Some(1264482000000),None,None,Some(Solexa-18483),None,Some(illumina),Some(20GAVAAXX100126.5)),RecordGroup(NA12878,20GAV.6,Some(BI),None,Some(1264482000000),None,None,Some(Solexa-18484),None,Some(illumina),Some(20GAVAAXX100126.6)),RecordGroup(NA12878,20GAV.7,Some(BI),None,Some(1264482000000),None,None,Some(Solexa-18483),None,Some(illumina),Some(20GAVAAXX100126.7)),RecordGroup(NA12878,20GAV.8,Some(BI),None,Some(1264482000000),None,None,Some(Solexa-18484),None,Some(illumina),Some(20GAVAAXX100126.8)))
 samLoad.sequences.records:1
20->63025520, 0
SequenceDictionary{
20->63025520, 0}
end