[ADAM-823] referenceIndex's in SAM/ADAM seq records, Contigs

fixes bigdatagenomics#823, fixes bigdatagenomics#822

adam-apis/src/test/scala/org/bdgenomics/adam/apis/java/JavaADAMContextSuite.scala

@@ -27,14 +27,14 @@ import org.bdgenomics.formats.avro.AlignmentRecord
 class JavaADAMContextSuite extends ADAMFunSuite {
 
   sparkTest("can read a small .SAM file") {
-    val path = ClassLoader.getSystemClassLoader.getResource("small.sam").getFile
+    val path = resourcePath("small.sam")
     val ctx = new JavaADAMContext(sc)
     val reads: JavaAlignmentRecordRDD = ctx.adamRecordLoad(path)
     assert(reads.jrdd.count() === 20)
   }
 
   sparkTest("can read a small .SAM file inside of java") {
-    val path = ClassLoader.getSystemClassLoader.getResource("small.sam").getFile
+    val path = resourcePath("small.sam")
     val reads: RDD[AlignmentRecord] = sc.loadAlignments(path)
 
     val newReads: JavaAlignmentRecordRDD = JavaADAMConduit.conduit(reads)

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala

@@ -110,8 +110,9 @@ class Transform(protected val args: TransformArgs) extends BDGSparkCommand[Trans
         .fold(new ConsensusGeneratorFromReads().asInstanceOf[ConsensusGenerator])(
           new ConsensusGeneratorFromKnowns(_, sc).asInstanceOf[ConsensusGenerator])
 
-      adamRecords = adamRecords.adamRealignIndels(consensusGenerator,
-        false,
+      adamRecords = adamRecords.adamRealignIndels(
+        consensusGenerator,
+        isSorted = false,
         args.maxIndelSize,
         args.maxConsensusNumber,
         args.lodThreshold,

adam-cli/src/test/scala/org/bdgenomics/adam/cli/ADAM2FastqSuite.scala

@@ -27,7 +27,7 @@ import org.bdgenomics.formats.avro.AlignmentRecord
 class Adam2FastqSuite extends ADAMFunSuite {
 
   sparkTest("convert SAM to paired FASTQ") {
-    val readsFilepath = ClassLoader.getSystemClassLoader.getResource("bqsr1.sam").getFile
+    val readsFilepath = resourcePath("bqsr1.sam")
 
     // The following fastq files were generated by Picard's SamToFastq
 
@@ -45,8 +45,8 @@ class Adam2FastqSuite extends ADAMFunSuite {
 
     // VALIDATION_STRINGENCY=SILENT is necessary since they are unpaired reads and this matches the ADAM default
 
-    val fastq1Path = ClassLoader.getSystemClassLoader.getResource("bqsr1-r1.fq").getFile
-    val fastq2Path = ClassLoader.getSystemClassLoader.getResource("bqsr1-r2.fq").getFile
+    val fastq1Path = resourcePath("bqsr1-r1.fq")
+    val fastq2Path = resourcePath("bqsr1-r2.fq")
 
     val outputDir = Files.createTempDir()
     val outputFastqR1File = outputDir.getAbsolutePath + "/bqsr1-r1.fq"

adam-cli/src/test/scala/org/bdgenomics/adam/cli/FlagStatSuite.scala

@@ -30,7 +30,7 @@ class FlagStatSuite extends ADAMFunSuite {
 
   sparkTest("Standard FlagStat test") {
 
-    val inputpath = ClassLoader.getSystemClassLoader.getResource("features/NA12878.sam").getFile
+    val inputpath = resourcePath("features/NA12878.sam")
     val argLine = "%s".format(inputpath).split("\\s+")
 
     val args: FlagStatArgs = Args4j.apply[FlagStatArgs](argLine)

adam-cli/src/test/scala/org/bdgenomics/adam/cli/TransformSuite.scala

@@ -0,0 +1,60 @@
+/**
+ * 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.adam.cli
+
+import java.nio.file.Files
+
+import org.bdgenomics.adam.util.ADAMFunSuite
+
+class TransformSuite extends ADAMFunSuite {
+  sparkTest("unordered sam to unordered sam") {
+    val inputPath = resourcePath("unordered.sam")
+    val actualPath = tmpFile("unordered.sam")
+    val expectedPath = inputPath
+    Transform(Array("-single", inputPath, actualPath)).run(sc)
+    checkFiles(expectedPath, actualPath)
+  }
+
+  sparkTest("unordered sam to ordered sam") {
+    val inputPath = resourcePath("unordered.sam")
+    val actualPath = tmpFile("ordered.sam")
+    val expectedPath = resourcePath("ordered.sam")
+    Transform(Array("-single", "-sort_reads", inputPath, actualPath)).run(sc)
+    checkFiles(expectedPath, actualPath)
+  }
+
+  sparkTest("unordered sam, to adam, to sam") {
+    val inputPath = resourcePath("unordered.sam")
+    val intermediateAdamPath = tmpFile("unordered.adam")
+    val actualPath = tmpFile("unordered.sam")
+    val expectedPath = inputPath
+    Transform(Array(inputPath, intermediateAdamPath)).run(sc)
+    Transform(Array("-single", intermediateAdamPath, actualPath)).run(sc)
+    checkFiles(expectedPath, actualPath)
+  }
+
+  sparkTest("unordered sam, to adam, to ordered sam") {
+    val inputPath = resourcePath("unordered.sam")
+    val intermediateAdamPath = tmpFile("unordered.adam")
+    val actualPath = tmpFile("ordered.sam")
+    val expectedPath = resourcePath("ordered.sam")
+    Transform(Array(inputPath, intermediateAdamPath)).run(sc)
+    Transform(Array("-single", "-sort_reads", intermediateAdamPath, actualPath)).run(sc)
+    checkFiles(expectedPath, actualPath)
+  }
+}

adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala

@@ -85,8 +85,8 @@ object ReferencePosition extends Serializable {
 
 class ReferencePosition(override val referenceName: String,
                         val pos: Long,
-                        override val orientation: Strand = Strand.Independent) extends ReferenceRegion(referenceName, pos, pos + 1, orientation) {
-}
+                        override val orientation: Strand = Strand.Independent)
+    extends ReferenceRegion(referenceName, pos, pos + 1, orientation)
 
 class ReferencePositionSerializer extends Serializer[ReferencePosition] {
   private val enumValues = Strand.values()

adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala

@@ -122,7 +122,12 @@ object ReferenceRegion {
  *            which is <i>not</i> in the region -- i.e. [start, end) define a 0-based
  *            half-open interval.
  */
-case class ReferenceRegion(referenceName: String, start: Long, end: Long, orientation: Strand = Strand.Independent) extends Comparable[ReferenceRegion] with Interval {
+case class ReferenceRegion(referenceName: String,
+                           start: Long,
+                           end: Long,
+                           orientation: Strand = Strand.Independent)
+    extends Comparable[ReferenceRegion]
+    with Interval {
 
   assert(start >= 0 && end >= start, "Failed when trying to create region %s %d %d on %s strand.".format(referenceName, start, end, orientation))
 
@@ -180,7 +185,7 @@ case class ReferenceRegion(referenceName: String, start: Long, end: Long, orient
    * @return True if regions are adjacent.
    */
   def isAdjacent(region: ReferenceRegion): Boolean =
-    distance(region).map(_ == 1).getOrElse(false)
+    distance(region).exists(_ == 1)
 
   /**
    * Returns the distance between this reference region and another region in the reference space.

adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala

@@ -80,6 +80,8 @@ class SequenceDictionary(val records: Vector[SequenceRecord]) extends Serializab
   private val byName: Map[String, SequenceRecord] = records.view.map(r => r.name -> r).toMap
   assert(byName.size == records.length, "SequenceRecords with duplicate names aren't permitted")
 
+  private val hasSequenceOrdering = records.forall(_.referenceIndex.isDefined)
+
   def isCompatibleWith(that: SequenceDictionary): Boolean = {
     for (record <- that.records) {
       val myRecord = byName.get(record.name)
@@ -109,7 +111,11 @@ class SequenceDictionary(val records: Vector[SequenceRecord]) extends Serializab
    * @return Returns a SAM formatted sequence dictionary.
    */
   def toSAMSequenceDictionary: SAMSequenceDictionary = {
-    import SequenceRecord._
+    implicit val ordering: Ordering[SequenceRecord] =
+      if (hasSequenceOrdering)
+        SequenceOrderingByRefIdx
+      else
+        SequenceOrderingByName
     new SAMSequenceDictionary(records.sorted.map(_ toSAMSequenceRecord).toList)
   }
 
@@ -118,26 +124,41 @@ class SequenceDictionary(val records: Vector[SequenceRecord]) extends Serializab
   }
 }
 
-object SequenceOrdering extends Ordering[SequenceRecord] {
+object SequenceOrderingByName extends Ordering[SequenceRecord] {
   def compare(a: SequenceRecord,
               b: SequenceRecord): Int = {
     a.name.compareTo(b.name)
   }
 }
 
+object SequenceOrderingByRefIdx extends Ordering[SequenceRecord] {
+  def compare(a: SequenceRecord,
+              b: SequenceRecord): Int = {
+    (for {
+      aRefIdx <- a.referenceIndex
+      bRefIdx <- b.referenceIndex
+    } yield {
+      aRefIdx.compareTo(bRefIdx)
+    }).getOrElse(
+      throw new Exception(s"Missing reference index when comparing SequenceRecords: $a, $b")
+    )
+  }
+}
+
 /**
  * Utility class within the SequenceDictionary; represents unique reference name-to-id correspondence
  *
  */
-class SequenceRecord(
-    val name: String,
-    val length: Long,
-    val url: Option[String] = None,
-    val md5: Option[String] = None,
-    val refseq: Option[String] = None,
-    val genbank: Option[String] = None,
-    val assembly: Option[String] = None,
-    val species: Option[String] = None) extends Serializable {
+case class SequenceRecord(
+    name: String,
+    length: Long,
+    url: Option[String],
+    md5: Option[String],
+    refseq: Option[String],
+    genbank: Option[String],
+    assembly: Option[String],
+    species: Option[String],
+    referenceIndex: Option[Int]) extends Serializable {
 
   assert(name != null && !name.isEmpty, "SequenceRecord.name is null or empty")
   assert(length > 0, "SequenceRecord.length <= 0")
@@ -170,6 +191,8 @@ class SequenceRecord(
     // set genbank accession number if available
     genbank.foreach(rec.setAttribute("GENBANK", _))
 
+    referenceIndex.foreach(rec.setSequenceIndex)
+
     // return record
     rec
   }
@@ -191,7 +214,7 @@ object SequenceRecord {
   val REFSEQ_TAG = "REFSEQ"
   val GENBANK_TAG = "GENBANK"
 
-  implicit def ordering = SequenceOrdering
+  //implicit def ordering = SequenceOrderingByName
 
   def apply(name: String,
             length: Long,
@@ -200,7 +223,8 @@ object SequenceRecord {
             refseq: String = null,
             genbank: String = null,
             assembly: String = null,
-            species: String = null): SequenceRecord = {
+            species: String = null,
+            referenceIndex: Option[Int] = None): SequenceRecord = {
     new SequenceRecord(
       name,
       length,
@@ -209,7 +233,9 @@ object SequenceRecord {
       Option(refseq).map(_.toString),
       Option(genbank).map(_.toString),
       Option(assembly).map(_.toString),
-      Option(species).map(_.toString))
+      Option(species).map(_.toString),
+      referenceIndex
+    )
   }
 
   /*
@@ -227,7 +253,9 @@ object SequenceRecord {
       refseq = record.getAttribute(REFSEQ_TAG),
       genbank = record.getAttribute(GENBANK_TAG),
       assembly = record.getAssembly,
-      species = record.getAttribute(SAMSequenceRecord.SPECIES_TAG))
+      species = record.getAttribute(SAMSequenceRecord.SPECIES_TAG),
+      referenceIndex = if (record.getSequenceIndex == -1) None else Some(record.getSequenceIndex)
+    )
 
   }
   def toSAMSequenceRecord(record: SequenceRecord): SAMSequenceRecord = {
@@ -244,7 +272,9 @@ object SequenceRecord {
       md5 = contig.getContigMD5,
       url = contig.getReferenceURL,
       assembly = contig.getAssembly,
-      species = contig.getSpecies)
+      species = contig.getSpecies,
+      referenceIndex = Option(contig.getReferenceIndex).map(Integer2int)
+    )
   }
 
   def toADAMContig(record: SequenceRecord): Contig = {
@@ -255,6 +285,7 @@ object SequenceRecord {
     record.url.foreach(builder.setReferenceURL)
     record.assembly.foreach(builder.setAssembly)
     record.species.foreach(builder.setSpecies)
+    record.referenceIndex.foreach(builder.setReferenceIndex(_))
     builder.build
   }
 
@@ -289,7 +320,8 @@ object SequenceRecord {
       SequenceRecord(
         rec.get(schema.getField("referenceName").pos()).toString,
         rec.get(schema.getField("referenceLength").pos()).asInstanceOf[Long],
-        url = rec.get(schema.getField("referenceUrl").pos()).toString)
+        url = rec.get(schema.getField("referenceUrl").pos()).toString
+      )
     } else if (schema.getField("contig") != null) {
       val pos = schema.getField("contig").pos()
       fromADAMContig(rec.get(pos).asInstanceOf[Contig])

adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala

@@ -232,8 +232,7 @@ class ADAMContext(val sc: SparkContext) extends Serializable with Logging {
     }
   }
 
-  def loadBam(
-    filePath: String): RDD[AlignmentRecord] = {
+  def loadBam(filePath: String): RDD[AlignmentRecord] = {
 
     val path = new Path(filePath)
 

adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMRDDFunctions.scala

@@ -100,7 +100,7 @@ abstract class ADAMSequenceDictionaryRDDAggregator[T](rdd: RDD[T]) extends Seria
    *
    * @return A sequence dictionary describing the reference contigs in this dataset.
    */
-  def adamGetSequenceDictionary(): SequenceDictionary = {
+  def adamGetSequenceDictionary(performLexSort: Boolean = false): SequenceDictionary = {
     def mergeRecords(l: List[SequenceRecord], rec: T): List[SequenceRecord] = {
       val recs = getSequenceRecordsFromElement(rec)
 
@@ -118,8 +118,16 @@ abstract class ADAMSequenceDictionaryRDDAggregator[T](rdd: RDD[T]) extends Seria
       SequenceDictionary(recs: _*)
     }
 
-    rdd.mapPartitions(iter => Iterator(foldIterator(iter)), preservesPartitioning = true)
-      .reduce(_ ++ _)
+    val sd =
+      rdd
+        .mapPartitions(iter => Iterator(foldIterator(iter)), preservesPartitioning = true)
+        .reduce(_ ++ _)
+
+    if (performLexSort) {
+      implicit val ordering = SequenceOrderingByName
+      SequenceDictionary(sd.records.map(_.copy(referenceIndex = None)).sorted: _*)
+    } else
+      sd
   }
 
 }

adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDFunctions.scala

@@ -118,7 +118,7 @@ class NucleotideContigFragmentRDDFunctions(rdd: RDD[NucleotideContigFragment]) e
    */
   def flankAdjacentFragments(flankLength: Int,
                              optSd: Option[SequenceDictionary] = None): RDD[NucleotideContigFragment] = {
-    FlankReferenceFragments(rdd, optSd.getOrElse(adamGetSequenceDictionary), flankLength)
+    FlankReferenceFragments(rdd, optSd.getOrElse(adamGetSequenceDictionary(performLexSort = false)), flankLength)
   }
 
   /**

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctions.scala

@@ -68,11 +68,11 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
                    isSorted: Boolean = false): Boolean = {
     if (args.outputPath.endsWith(".sam")) {
       log.info("Saving data in SAM format")
-      rdd.adamSAMSave(args.outputPath, asSingleFile = args.asSingleFile)
+      rdd.adamSAMSave(args.outputPath, asSingleFile = args.asSingleFile, isSorted = isSorted)
       true
     } else if (args.outputPath.endsWith(".bam")) {
       log.info("Saving data in BAM format")
-      rdd.adamSAMSave(args.outputPath, asSam = false, asSingleFile = args.asSingleFile)
+      rdd.adamSAMSave(args.outputPath, asSam = false, asSingleFile = args.asSingleFile, isSorted = isSorted)
       true
     } else
       false
@@ -234,7 +234,7 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
    */
   def adamConvertToSAM(isSorted: Boolean = false): (RDD[SAMRecordWritable], SAMFileHeader) = ConvertToSAM.time {
     // collect global summary data
-    val sd = rdd.adamGetSequenceDictionary()
+    val sd = rdd.adamGetSequenceDictionary(isSorted)
     val rgd = rdd.adamGetReadGroupDictionary()
 
     // create conversion object

adam-core/src/test/resources/ordered.sam

@@ -0,0 +1,14 @@
+@HD	VN:1.4	SO:unsorted
+@SQ	SN:14	LN:107349540	M5:14
+@SQ	SN:GL000211.1	LN:166566	M5:GL000211.1
+@SQ	SN:GL000244.1	LN:39929	M5:GL000244.1
+@SQ	SN:chr22	LN:51304566	M5:CHR22
+@RG	ID:SRR062634	SM:HG00096	CN:WUGSC	DS:SRP001294	LB:2845856850	PI:206	PL:ILLUMINA
+SRR062634.6859057	163	14	16050606	37	100M	=	16050680	174	GGTTTACTGTGTCAGAACAGAGTGTGCCGATTGTGGTCAGGACTCCATAGCATTTCACCATTGAGTTATTTCCGCCCCCTTACGTGTCTCTCTTCAGCGG	GFFGGGGGGGGGGFGGGGGGGGGGGGGGGFGGGBGGCGGGDDEFFGEEFFGFEGEEEEEEEGFEGEEEEDEFEEEEEEE=DBCCBCCCCCACCAC,A@??	X0:i:1	X1:i:0	LB:Z:2845856850	MD:Z:0A1G0C1T1A0A0G1C0A0C0T0C0G0A1A0T0C1C1A1T0T0G0C0A1A0T0T0C0T1C0A1A0A0A0G1G0T0A0T0T1C0A0A1A1T0G0G0T0C0C2C0A0A0A0A0G0A0A0A0G0G0T1C1A0T1C1G0G0G0A0G0A1A1A0T1C0	RG:Z:SRR062634	XG:i:0	AM:i:0	NM:i:0	SM:i:37	XM:i:0	XO:i:0	XT:A:U
+SRR062634.6859057	83	14	16050680	36	100M	=	16050606	-174	CCCCCTTACGTGTCTCTCTTCAGCGGTCTATTATCTCCAAGAGGGCATAAAACACTGAGTAAACAGCTCTTTTATATGTGTTTCCTGGATGAGCCTTCTT	9<5=;;A7B<?A?A?AABB:C:CC=CACE?DDCCD@EEFEEFEFEFGFGGGEGEGGGGGGGEGFGEGGGGFGGGGGGGGGEGGGGGGGGGGGGGFGFGGG	X0:i:2	X1:i:0	XA:Z:14,+19792222,100M,0;	LB:Z:2845856850	MD:Z:0A0A0G0G0T1C1A0T1C1G0G0G0A0G0A1A1A0T1C0A0T0A0C0A1C0A1A0A0A2A0G0T0T0T1T0C1G2T0T3T0C2G0T0T0T0T0T0A0T0G1G0A1G2A1T1C0C0T0T2C0C0A0C0C0A0T0A0G0G1C1	RG:Z:SRR062634	XG:i:0	AM:i:0	NM:i:0	SM:i:0	XM:i:0	XO:i:0	XT:A:R
+SRR062634.20563591	99	GL000211.1	100	0	100M	=	500	161	GGACAACATTCACCTTTAAAAGTTTATTGATCTTTTGTGACATGCACGTGGGTTCCCAGTAGCAAGAAACTAAAGGGTCGCAGGCCGGTTTCTGCTAATT	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGFGGGGGGGFGGGGGEGGGGGGEFGFGGFGGGGFBGGGDE>EEECBCCEEC>E:A@=ADBCAB	X0:i:2	X1:i:0	XA:Z:14,-19792774,100M,0;	LB:Z:2845856850	MD:Z:0T0C0T0A0C0G0A1A0A0A1A0T3T0C0C1A0A0C1G0C1C1A0T0C0A0A0A0A0G0A1A0G0G0T0T0C0A0A0C0T0C0T0G1G0A0G1T0G1A0T0G0C0A0C1C0A1T0T0C0A0A0A0G0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0	RG:Z:SRR062634	XG:i:0	AM:i:0	NM:i:0	SM:i:0	XM:i:0	XO:i:0	XT:A:R
+SRR062634.20563591	147	GL000211.1	500	0	100M	=	100	-161	GCAAGAAACTAAAGGGTCGCAGGCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAAATATTTTCTTATTAACTTCCTGGAGGGAGGCTTATCA	=DDFECDCFEDFEFFFEEFD:EF?FBFFFFBACEF?EGGGEDGGBGEGFGGGGGGFGGGGGGGGGFGGGGFFGGGGGGGFGGGGGGGGGGGGGGGGGGGG	X0:i:2	X1:i:0	XA:Z:14,+19792713,100M,0;	LB:Z:2845856850	MD:Z:0A0T0G0C0A0C1C0A1T0T0C0A0A0A0G0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0A0T0A0G0C0T0T3T0G0T2A0G0A1A1T0T0C2T2C0C0A0C0C0C1A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0	RG:Z:SRR062634	XG:i:0	AM:i:0	NM:i:0	SM:i:0	XM:i:0	XO:i:0	XT:A:R
+SRR062634.5613583	99	GL000244.1	200	0	100M	=	600	158	TGCAGGCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAATTATTTTCTTATTAACTTCCTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGA	GGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDEGEFEGDCEEEBF?DDEEGDGEEEGE=ABB?	X0:i:2	X1:i:0	XA:Z:14,-19792696,100M,2;	LB:Z:2845856850	MD:Z:0A0A0G0T0T0T1T0C0A0G0A0A0T1C0T1C0T0G0C0A0T0A0G0C0T0T3T0G0T2A0G0A1A1T0T0C0A1T2C0C0A0C0C0C1A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0A0C0A0G0G0C0A0G0A2C0C1C0A1	RG:Z:SRR062634	XG:i:0	AM:i:0	NM:i:2	SM:i:0	XM:i:2	XO:i:0	XT:A:R
+SRR062634.5613583	147	GL000244.1	600	0	100M	=	200	-158	TAACTTCCTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGATTCTAAGTACCAGCTAAAATACAGCTATCATTCATTTTCCTTGATTTGGGAGCCTAAT	@E=EAEEEEGF?EEGEGFFEDBGEGFGGGGFGFFGFGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG	X0:i:2	X1:i:0	XA:Z:14,+19792638,100M,0;	LB:Z:2845856850	MD:Z:0A0G0G1C2A0A0A1C0A0C0T0C1A0A0A1G2C0A0C0A0G0G0C0A0G0A2C0C1C0A1A0A0A0G1G0T0A0T0T0T0C0A0A0A1C0T0G0G0T1C0A0T0C1A0A0G0G0A0A1G0A3A0G0C0T0C1G1T1A1T0G0A0A0T0G0C0	RG:Z:SRR062634	XG:i:0	AM:i:0	NM:i:0	SM:i:0	XM:i:0	XO:i:0	XT:A:R
+SRR062634.11091461	99	chr22	16050471	0	100M	=	16050505	134	CAAGTAGTAGTGCCATAATTACCAAACATAAAGCCAACTGAGATGCCCAAAGGGGGCCACTCTCCTTGCTTTTCCTCCTTTTTAGAGGATTTATTTCCCA	GGGGGFFFFFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGGEGGEFEEBEEECFEEEBEFBACDBEEEEEACC?AAAA7=5::59BBBCB6/=CA	X0:i:2	X1:i:0	XA:Z:14,-19792431,100M,0;	LB:Z:2845856850	MD:Z:1T1C0A1A0A2A1T0T0T1T1C0A1A1T0G0C0T0C0A1T0C0A0A0A0G0G0A0A0A0G1T1C0A0A1T0C0T1T0A0A1A0T0G0A0A1C1A0C0A0T0A1C0A0C0A0A0A0G0A0A0G3C0T0C0A0A1A2C2C0T0G0T0C0	RG:Z:SRR062634	XG:i:0	AM:i:0	NM:i:0	SM:i:0	XM:i:0	XO:i:0	XT:A:R
+SRR062634.11091461	147	chr22	16050505	0	100M	=	16050471	-134	CAACTGAGATGCCCAAAGGGGGCCACTCTCCTTGCTTTTCCTCCTTTTTAGAGGATTTATTTCCCATTTTTCTTAAAAAGGAAGAACAAACTGTGCCCTA	=@@?CCCD?@DCDCC@CEFEEGEEEFFFFDEFEGAGGFGGGGGGGGGGGGGFGGGGGFGGDGEGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGG	X0:i:2	X1:i:0	XA:Z:14,+19792397,100M,0;	LB:Z:2845856850	MD:Z:0A0G0G0A0A0A0G1T1C0A0A1T0C0T1T0A0A1A0T0G0A0A1C1A0C0A0T0A1C0A0C0A0A0A0G0A0A0G3C0T0C0A0A1A2C2C0T0G0T0C0C0A0G2G3C0G0T0G0A0A0G1T0G0T0T0T0T0C0T1T1C1A0A0C1	RG:Z:SRR062634	XG:i:0	AM:i:0	NM:i:0	SM:i:0	XM:i:0	XO:i:0	XT:A:R