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Changes to the BTTC scala walker: 

- Updated to use the unified genotyper rather than ssg
 - Fixed a minor issue where the Unified Genotyper returns null
   and SSG would still return an object. isDefinitelyHomRef() now
   checks for null Unified Genotyper <Call list, meta data> pairs.
 - Tables output survive a diff with previous tables




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1872 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-18 18:09:25 +00:00
parent bb180a23ef
commit f0021a3533
1 changed files with 12 additions and 6 deletions
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18
scala/src/BaseTransitionTableCalculator.scala
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@ -1,12 +1,14 @@
package org.broadinstitute.sting.scala
import gatk.walkers.genotyper.{SingleSampleGenotyper, SSGGenotypeCall}
import gatk.walkers.genotyper.{UnifiedGenotyper, GenotypeCall}
import java.io.File
import net.sf.samtools.SAMRecord
import org.broadinstitute.sting.gatk.walkers.LocusWalker
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker
import org.broadinstitute.sting.gatk.contexts.ReferenceContext
import org.broadinstitute.sting.gatk.contexts.AlignmentContext
import org.broadinstitute.sting.utils.Pair
import org.broadinstitute.sting.utils.genotype.GenotypeMetaData
import utils._
import cmdLine.Argument
@ -72,7 +74,7 @@ class BaseTransitionTableCalculator extends LocusWalker[Unit,Int] {
private var PRINT_FREQ = 1000000
private var CARE_ABOUT_STRAND = true
private val SSG = new SingleSampleGenotyper()
private val SSG = new UnifiedGenotyper()
private val table1 = new TransitionTable()
private val tableFWD = new TransitionTable()
private val tableREV = new TransitionTable()
@ -86,14 +88,15 @@ class BaseTransitionTableCalculator extends LocusWalker[Unit,Int] {
}
override def map(tracker: RefMetaDataTracker, ref: ReferenceContext, context: AlignmentContext): Unit = {
val call = SSG.map(tracker, ref, context)
val callPair = SSG.map(tracker, ref, context)
//val call = callPair.getFirst().get(0)
val pileup = new ReadBackedPileup(ref.getBase(), context)
def hasNoNs(): Boolean = {
return ! (pileup.getBases() exists ('N' ==))
}
if ( isDefinitelyHomRef(call) && hasNoNs() ) {
if ( isDefinitelyHomRef(callPair) && hasNoNs() ) {
var (refBases, nonRefBases) = splitBases(ref.getBase, pileup.getBases)
//printf("nonRefBases %s%n", nonRefBases)
@ -173,8 +176,11 @@ class BaseTransitionTableCalculator extends LocusWalker[Unit,Int] {
return (refBases, nonRefBases)
}
def isDefinitelyHomRef(call: SSGGenotypeCall): Boolean = {
return ! call.isVariation() && call.getBestNext() > MIN_LOD
def isDefinitelyHomRef(call: Pair[java.util.List[GenotypeCall],GenotypeMetaData]): Boolean = {
if ( call == null )
return false;
return ! call.getFirst().get(0).isVariant() && call.getFirst().get(0).getNegLog10PError() > MIN_LOD
}
def reduceInit(): Int = {