Commiting a simple merge IPF for use with qscripts (currently use a long grep, awk, pipe command, which can be unsafe and is hard to extend). Tests for all these functions coming soon. Also, IntelliJ + intermittent VPN connection = botched repository.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5179 348d0f76-0448-11de-a6fe-93d51630548a

scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala

@@ -0,0 +1,78 @@
+package org.broadinstitute.sting.queue.library.ipf.vcf
+
+import collection.JavaConversions._
+import org.broadinstitute.sting.queue.function.InProcessFunction
+import org.broadinstitute.sting.commandline._
+import org.broadinstitute.sting.utils.text.XReadLines
+import java.io.{PrintStream, PrintWriter, File}
+import net.sf.samtools.{SAMSequenceRecord, SAMSequenceDictionary}
+import org.broadinstitute.sting.utils.{GenomeLocParser, GenomeLoc}
+
+class VCFSimpleMerge extends InProcessFunction {
+  @Input(doc="VCFs to be merged") var vcfs: List[File] = Nil
+  @Input(doc="The reference fasta index") var fasta: File = _
+  @Output(doc="The final VCF to write to") var outVCF : File = _
+
+  class PeekableXRL(f : File ) {
+    var xrl : XReadLines = new XReadLines(f)
+    var cur : String = if ( xrl.hasNext ) xrl.next else null
+
+    def hasNext : Boolean = xrl.hasNext || cur != null
+    def next : String = {
+      var toRet : String = cur
+      if ( xrl.hasNext ) {
+        cur = xrl.next
+      } else {
+        cur = null
+      }
+
+      return toRet
+    }
+
+    def peek : String = cur
+
+  }
+
+  def readHeader( xrl : PeekableXRL ) : List[String] = {
+    var toRet : List[String] = Nil
+    while ( xrl.hasNext && xrl.peek.startsWith("#") ) {
+      toRet :+= xrl.next
+    }
+
+    return toRet
+  }
+
+  def genomeLoc(xrl : PeekableXRL, p : GenomeLocParser ) : GenomeLoc = {
+    var slp = xrl.peek.split("\t",3)
+    return p.parseGenomeLoc(slp(0),Integer.parseInt(slp(1)),Integer.parseInt(slp(1)))
+  }
+
+  def run = {
+    var ssd : SAMSequenceDictionary = new SAMSequenceDictionary
+    for ( line <- (new XReadLines(fasta)).readLines ) {
+      val spl = line.split("\\s+")
+      val ctig = spl(0)
+      val pos = Integer.parseInt(spl(1))
+      ssd.addSequence(new SAMSequenceRecord(ctig,pos))
+    }
+
+    var xrls : List[PeekableXRL] = vcfs.map( new PeekableXRL(_) )
+
+    var w : PrintWriter = new PrintWriter(new PrintStream(outVCF))
+
+    readHeader(xrls(0)).foreach(u => w.println(u) )
+
+    xrls.foreach(readHeader(_))
+
+    val glp : GenomeLocParser = new GenomeLocParser(ssd)
+
+    while ( ! xrls.forall( u => ! u.hasNext ) ) {
+      val first = xrls.filter( u => u.hasNext).reduceLeft( (a,b) => if ( genomeLoc(a,glp).isBefore(genomeLoc(b,glp))) a else b )
+      w.println(first.next)
+    }
+
+    w.close
+
+  }
+
+}