this -1 made ALL the difference in the world. Minor bug fix.

Regular updates to the pbCalling pipeline.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5232 348d0f76-0448-11de-a6fe-93d51630548a

lua/remapAmplicons.lua

@@ -3,6 +3,8 @@ local samFile = arg[2]
 local headerFile = io.open(arg[2]:match("(.*).sam")..".header.sam", "w")
 local bodyFile = io.open(arg[2]:match("(.*).sam")..".body.sam", "w")
 
+
+-- These sizes are hardcoded for hg19, but future versions of this script should optionally take a .fai file to build this table.
 chrlength = {}
 chrlength["1"] =249250621
 chrlength["2"] =243199373
@@ -76,7 +78,7 @@ for l in io.lines(samFile) do
   if l:sub(1,1) == "@" then processSamHeaderLine(l, amplicons)
   else
     local before, amp, mapStart, after = l:match("(%d+%s+%d+%s+)ps%d+_([%w%p_]+)%s+(%d+)(.*)")
-    table.insert(reads, before..amplicons[amp].chr.."\t"..amplicons[amp].startPos + mapStart..after)
+    table.insert(reads, before..amplicons[amp].chr.."\t"..amplicons[amp].startPos + mapStart - 1 ..after)
   end
 end
 

scala/qscript/oneoffs/carneiro/pbCalling.scala

@@ -17,8 +17,6 @@ class pbCalling extends QScript {
   @Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=false)
   var noBAQ: Boolean = false
 
-  @Argument(shortName="noMASK", doc="turns off MASK calculation", required=false)
-  var noMASK: Boolean = false
 
 
 
@@ -184,10 +182,6 @@ class pbCalling extends QScript {
     this.filterName ++= List("HARD_TO_VALIDATE")
     this.filterExpression ++= List("\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\"")
     this.analysisName = t.name + "_VF"
-    if (!noMASK) {
-      this.rodBind :+= RodBind("mask", "Bed", t.maskFile)
-      this.maskName = "InDel"
-    }
   }
 
   // 3.) VQSR part1 Generate Gaussian clusters based on truth sites