ShivaTrait.scala 6.39 KB
Newer Older
Peter van 't Hof's avatar
Peter van 't Hof committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
package nl.lumc.sasc.biopet.pipelines.shiva

import java.io.File

import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{MultiSampleQScript, PipelineCommand}
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.picard.{AddOrReplaceReadGroups, SamToFastq, MarkDuplicates}
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import scala.collection.JavaConversions._

/**
 * Created by pjvan_thof on 2/26/15.
 */
trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
  qscript =>

  def init: Unit = {

  }

  def biopetScript: Unit = {
    addSamplesJobs()

    addSummaryJobs
  }

  def makeSample(id: String) = new Sample(id)
  class Sample(sampleId: String) extends AbstractSample(sampleId) {
    def makeLibrary(id: String) = new Library(id)

    class Library(libId: String) extends AbstractLibrary(libId) {

      def preProcess(input: File): Option[File] = None

      def makeMapping = {
        val mapping = new Mapping(qscript)
        mapping.sampleId = Some(sampleId)
        mapping.libId = Some(libId)
        mapping.outputDir = libDir
        (Some(mapping), Some(mapping.finalBamFile), preProcess(mapping.finalBamFile))
      }

      lazy val (mapping, bamFile, preProcessBam): (Option[Mapping], Option[File], Option[File]) =
        (config.contains("R1"), config.contains("bam")) match {
          case (true, _) => makeMapping // Default starting from fastq files
          case (false, true) => // Starting from bam file
            config("bam_to_fastq", default = false).asBoolean match {
              case true => makeMapping // bam file will be converted to fastq
              case false => {
                val file = new File(libDir, sampleId + "-" + libId + ".final.bam")
                (None, Some(file), preProcess(file))
              }
            }
          case _ => (None, None, None)
        }

      def addJobs(): Unit = {
        (config.contains("R1"), config.contains("bam")) match {
          case (true, _) => mapping.foreach(mapping => {
            mapping.input_R1 = config("R1")
            mapping.input_R2 = config("R2")
          })
          case (false, true) =>  config("bam_to_fastq", default = false).asBoolean match {
            case true => {
              val samToFastq = SamToFastq(qscript, config("bam"),
                new File(libDir, sampleId + "-" + libId + ".R1.fastq"),
                new File(libDir, sampleId + "-" + libId + ".R2.fastq"))
              samToFastq.isIntermediate = true
              qscript.add(samToFastq)
              mapping.foreach(mapping => {
                mapping.input_R1 = samToFastq.fastqR1
                mapping.input_R2 = Some(samToFastq.fastqR2)
              })
            }
            case false => {
              val inputSam = SamReaderFactory.makeDefault.open(config("bam"))
              val readGroups = inputSam.getFileHeader.getReadGroups

              val readGroupOke = readGroups.forall( readGroup => {
                if (readGroup.getSample != sampleId) logger.warn("Sample ID readgroup in bam file is not the same")
                if (readGroup.getLibrary != libId) logger.warn("Library ID readgroup in bam file is not the same")
                readGroup.getSample == sampleId && readGroup.getLibrary == libId
              })
              inputSam.close

              if (!readGroupOke) {
                if (config("correct_readgroups", default = false).asBoolean) {
                  logger.info("Correcting readgroups, file:" + config("bam"))
                  val aorrg = AddOrReplaceReadGroups(qscript, config("bam"), bamFile.get)
                  aorrg.RGID = sampleId + "-" + libId
                  aorrg.RGLB = libId
                  aorrg.RGSM = sampleId
                  aorrg.isIntermediate = true
                  qscript.add(aorrg)
                } else throw new IllegalStateException("Sample readgroup and/or library of input bamfile is not correct, file: " + bamFile +
                  "\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this")
              } else {
                val oldBamFile: File = config("bam")
                val oldIndex: File = new File(oldBamFile.getAbsolutePath.stripSuffix(".bam") + ".bai")
                val newIndex: File = new File(libDir, oldBamFile.getName.stripSuffix(".bam") + ".bai")
                val baiLn = Ln(qscript, oldIndex, newIndex)
                add(baiLn)

                val bamLn = Ln(qscript, oldBamFile, bamFile.get)
                bamLn.deps :+= baiLn.out
                add(bamLn)
              }

            }
          }
          case _ => logger.warn("Sample: " + sampleId + "  Library: " + libId + ", no reads found")
        }

        mapping.foreach(mapping => {
          mapping.init
          mapping.biopetScript
          addAll(mapping.functions) // Add functions of mapping to curent function pool
          addSummaryQScript(mapping)
        })

        //TODO: library variantcalling
      }
    }

    def doublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
      if (input == Nil) None
      else if (input.tail == Nil) {
        val bamFile = new File(sampleDir, input.head.getName)
        val oldIndex: File = new File(input.head.getAbsolutePath.stripSuffix(".bam") + ".bai")
        val newIndex: File = new File(sampleDir, input.head.getName.stripSuffix(".bam") + ".bai")
        val baiLn = Ln(qscript, oldIndex, newIndex)
        add(baiLn)

        val bamLn = Ln(qscript, input.head, bamFile)
        bamLn.deps :+= baiLn.out
        add(bamLn)
        Some(bamFile)
      } else {
        val md = new MarkDuplicates(qscript)
        md.input = input
        md.output = new File(sampleDir, sampleId + ".dedup.bam")
        md.outputMetrics = new File(sampleDir, sampleId + ".dedup.bam")
        md.isIntermediate = isIntermediate
        add(md)
        addSummarizable(md, "mark_duplicates", Some(sampleId))
        Some(md.output)
      }
    }

    lazy val preProcessBam: Option[File] = doublePreProcess(libraries.map(_._2.preProcessBam).filter(_.isDefined).map(_.get).toList)

    def addJobs(): Unit = {
      addPerLibJobs()

      //TODO: Singlesample variantcalling
    }
  }

  def addMultiSampleJobs(): Unit = {
    //TODO: Mutisample variantcalling
  }

  def summaryFile = new File(outputDir, "Shiva.summary.json")

  def summarySettings = Map()

  def summaryFiles = Map()
}