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Fix for expanded intervals in the case where the input file has overlapping intervals in it (seriously?) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5337 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-02-28 19:56:33 +00:00
parent 5ac9af472c
commit abab23350f
1 changed files with 17 additions and 5 deletions
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22
scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/ExpandIntervals.scala
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@ -56,8 +56,14 @@ class ExpandIntervals(in : File, start: Int, size: Int, out: File, ref: File, ip
curLoc = nextLoc
nextLoc = if ( xrl.hasNext ) parseGenomeInterval(xrl.next) else null
if ( curLoc != null ) {
intervalCache += refine(expandLeft(curLoc),prevLoc)
intervalCache += refine(expandRight(curLoc),nextLoc)
val left: GenomeLoc = refine(expandLeft(curLoc),prevLoc)
val right: GenomeLoc = refine(expandRight(curLoc),nextLoc)
if ( left != null ) {
intervalCache += left
}
if ( right != null ) {
intervalCache += right
}
}
linesProcessed += 1
if ( linesProcessed % LINES_TO_CACHE == 0 ) {
@ -83,14 +89,20 @@ class ExpandIntervals(in : File, start: Int, size: Int, out: File, ref: File, ip
def refine(newG: GenomeLoc, borderG: GenomeLoc) : GenomeLoc = {
if ( borderG == null || ! newG.overlapsP(borderG) ) {
newG
return newG
} else {
if ( newG.getStart < borderG.getStart ) {
parser.createGenomeLoc(newG.getContig,newG.getStart,borderG.getStart-startInt)
if ( borderG.getStart - startInt > newG.getStart ) {
return parser.createGenomeLoc(newG.getContig,newG.getStart,borderG.getStart-startInt)
}
} else {
parser.createGenomeLoc(newG.getContig,borderG.getStop+startInt,newG.getStop)
if ( borderG.getStop + startInt < newG.getStop ){
return parser.createGenomeLoc(newG.getContig,borderG.getStop+startInt,newG.getStop)
}
}
}
null
}
def repr(loc : GenomeLoc) : String = {