added BWA SW alignment

The pipeline now accepts fasta/fastq files and aligns them using BWA SW, adds default basequalities, creates read groups and performs BQSR.

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala

@@ -5,6 +5,8 @@ import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.util.QScriptUtils
 import net.sf.samtools.SAMFileHeader.SortOrder
 import org.broadinstitute.sting.queue.extensions.picard.{SortSam, AddOrReplaceReadGroups}
+import org.broadinstitute.sting.utils.exceptions.UserException
+import org.broadinstitute.sting.commandline.Hidden
 
 /**
  * Created by IntelliJ IDEA.
@@ -16,7 +18,7 @@ import org.broadinstitute.sting.queue.extensions.picard.{SortSam, AddOrReplaceRe
 
 class RecalibrateBaseQualities extends QScript {
 
-  @Input(doc="input FASTA file, BAM file - or list of FASTA/BAM files. ", shortName="i", required=true)
+  @Input(doc="input FASTA/FASTQ/BAM file - or list of FASTA/FASTQ/BAM files. ", shortName="i", required=true)
   var input: File = _
 
   @Input(doc="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=true)
@@ -28,51 +30,67 @@ class RecalibrateBaseQualities extends QScript {
   @Input(doc="dbsnp VCF file to use ", shortName="D", required=true)
   var dbSNP: File = _
 
-  @Input(doc="Default base qualities. Overrides the file's original base qualities with given value. Must be used if the file does not have base qualities." , shortName = "dbq", required=false)
+  @Input(doc="Number of jobs to scatter/gather. Default: 0." , shortName = "sg", required=false)
-  var dbq: Int = -1
+  var threads: Int = 0
 
-  @Input(doc="Number of jobs to scatter/gather. Default is the number of contigs in the dataset" , shortName = "sg", required=false)
+  @Input(doc="Sample Name to fill in the Read Group information (only necessary if using fasta/fastq)" , shortName = "sn", required=false)
-  var threads: Int = -1
+  var sample: String = "NA"
 
-  @Input(doc="Sample Name" , shortName = "sn", required=false)
+  @Input(doc="The path to the binary of bwa to align fasta/fastq files", fullName="path_to_bwa", shortName="bwa", required=false)
-  var sample: String = ""
-
-  @Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
   var bwaPath: File = _
 
+  @Hidden
+  @Input(doc="The default base qualities to use before recalibration. Default is Q20 (should be good for every dataset)." , shortName = "dbq", required=false)
+  var dbq: Int = 20
+
 
 
 
 
   val queueLogDir: String = ".qlog/"
-  var nContigs: Int = 0
-  var ADD_BASE_QUALITIES = false
 
   def script = {
 
-    if (dbq >= 0)
+    val fileList: List[File] = QScriptUtils.createListFromFile(input)
-      ADD_BASE_QUALITIES = true
 
-    val fileList = QScriptUtils.createListFromFile(input)
+    for (file: File <- fileList) {
-    nContigs = if (threads >= 0) {threads} else {QScriptUtils.getNumberOfContigs(fileList(0))}
 
-    for (file <- fileList) {
+      var USE_BWA: Boolean = false
-      val qualBam: File = swapExt(file, ".bam", ".quals.bam")
+
-      val rgBam: File = if (ADD_BASE_QUALITIES)  {swapExt(file, ".bam", ".rg.bam")} else {file}
+      println("DEBUG: processing " + file + "\nDEBUG: name -- " + file.getName)
-      val recalFile1: File = swapExt(file, ".bam", ".recal1.csv")
+
-      val recalFile2: File = swapExt(file, ".bam", ".recal2.csv")
+      if (file.endsWith(".fasta") || file.endsWith(".fq")) {
-      val recalBam: File   = swapExt(file, ".bam", ".recal.bam")
+        if (bwaPath == null) {
+          throw new UserException("You provided a fasta/fastq file but didn't provide the path for BWA");
+        }
+        USE_BWA = true
+      }
+
+      // FASTA -> BAM steps
+      val alignedSam: File = file.getName + ".aligned.sam"
+      val sortedBam: File = swapExt(alignedSam, ".sam", ".bam")
+      val qualBam: File = swapExt(sortedBam, ".bam", ".q.bam")
+      val rgBam: File = swapExt(file, ".bam", ".rg.bam")
+
+      val bamBase = if (USE_BWA) {rgBam} else {file}
+
+      // BAM Steps
+      val recalFile1: File = swapExt(bamBase, ".bam", ".recal1.csv")
+      val recalFile2: File = swapExt(bamBase, ".bam", ".recal2.csv")
+      val recalBam: File   = swapExt(bamBase, ".bam", ".recal.bam")
       val path1: String    = recalBam + ".before"
       val path2: String    = recalBam + ".after"
 
 
-      if (ADD_BASE_QUALITIES) {
+      if (USE_BWA) {
-        add(addQuals(file, qualBam, dbq),
+        add(align(file, alignedSam),
+            sortSam(alignedSam, sortedBam),
+            addQuals(sortedBam, qualBam, dbq),
             addReadGroup(qualBam, rgBam, sample))
       }
 
-      add(cov(rgBam, recalFile1),
+      add(cov(bamBase, recalFile1),
-          recal(rgBam, recalFile1, recalBam),
+          recal(bamBase, recalFile1, recalBam),
           cov(recalBam, recalFile2),
           analyzeCovariates(recalFile1, path1),
           analyzeCovariates(recalFile2, path2))
@@ -86,7 +104,7 @@ class RecalibrateBaseQualities extends QScript {
     this.isIntermediate = true
   }
 
-  trait CommandLineGATKArgs extends CommandLineGATK {
+  trait CommandLineGATKArgs extends CommandLineGATK with ExternalCommonArgs {
     this.reference_sequence = reference
   }
 
@@ -112,7 +130,7 @@ class RecalibrateBaseQualities extends QScript {
     this.DBQ = qual
   }
 
-  case class addReadGroup (inBam: File, outBam: File, sample: String) extends AddOrReplaceReadGroups {
+  case class addReadGroup (inBam: File, outBam: File, sample: String) extends AddOrReplaceReadGroups with ExternalCommonArgs {
     @Output(doc="output bai file") var bai = swapExt(outBam, ".bam", ".bai")
     this.input = List(inBam)
     this.output = outBam
@@ -133,7 +151,7 @@ class RecalibrateBaseQualities extends QScript {
     this.recal_file = outRecalFile
     this.analysisName = queueLogDir + outRecalFile + ".covariates"
     this.jobName = queueLogDir + outRecalFile + ".covariates"
-    this.scatterCount = nContigs
+    this.scatterCount = threads
   }
 
   case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
@@ -143,7 +161,7 @@ class RecalibrateBaseQualities extends QScript {
     this.isIntermediate = false
     this.analysisName = queueLogDir + outBam + ".recalibration"
     this.jobName = queueLogDir + outBam + ".recalibration"
-    this.scatterCount = nContigs
+    this.scatterCount = threads
   }
 
   case class analyzeCovariates (inRecalFile: File, outPath: String) extends AnalyzeCovariates {

public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala

@@ -22,15 +22,15 @@ object QScriptUtils {
    * to have empty lines and comment lines (lines starting with #).
    */
   def createListFromFile(in: File):List[File] = {
-    // If the file provided ends with .bam, it is not a bam list, we treat it as a single file.
+    // If the file provided ends with .bam, .fasta or .fq, it is not a bam list, we treat it as a single file.
     // and return a list with only this file.
-    if (in.toString.endsWith(".bam"))
+    if (in.toString.endsWith(".bam") || in.toString.endsWith(".fasta") || in.toString.endsWith(".fq"))
       return List(in)
 
     var list: List[File] = List()
-    for (bam <- fromFile(in).getLines)
+    for (file <- fromFile(in).getLines)
-      if (!bam.startsWith("#") && !bam.isEmpty )
+      if (!file.startsWith("#") && !file.isEmpty )
-        list :+= new File(bam.trim())
+        list :+= new File(file.trim())
     list.sortWith(_.compareTo(_) < 0)
   }