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More robust error handling with parallelization + usePreviousBase. Added forceReadBasesToMatchRef to use in conjunction with nPreviousReadBases as a less stringent approximation of usePreviousBases (requiring previous pileups only had mismatches, and that read mapping quality be high was throwing everything away) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1916 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-27 17:20:44 +00:00
parent 31d5df2859
commit 4192b093b8
1 changed files with 34 additions and 5 deletions
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39
java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
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@ -47,6 +47,8 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
boolean useReadGroup = false;
@Argument(fullName="outputFile", shortName="of", doc="Output to this file rather than standard out. Must be used with -nt.", required = false)
String outFilePath = null;
@Argument(fullName="forcePreviousReadBasesToMatchRef", doc="Forces previous read bases to match the reference", required = false)
boolean readBasesMustMatchRef = false;
private UnifiedGenotyper ug;
// private ReferenceContextWindow refWindow;
@ -55,7 +57,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
private List<GenomeLoc> previousBaseLoci;
public void initialize() {
if ( nPreviousBases > 3 ) {
if ( nPreviousBases > 3 || ( nPreviousReadBases > 3 && readBasesMustMatchRef ) ) {
throw new StingException("You have opted to use a number of previous bases in excess of 3. In order to do this you must change the reference window size in the walker itself.");
}
ug = new UnifiedGenotyper();
@ -116,6 +118,13 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
}
public Set<BaseTransitionTable> treeReduce( Set<BaseTransitionTable> reduce1, Set<BaseTransitionTable> reduce2 ) {
// check to see if this is a truly tree-reducable calculation
if ( nPreviousBases >= 1 ) {
String errMsg = "Parallelization cannot be used with UsePreviousBases due to the fact that internal walker data specifies whether a previous reference base is usable or not.";
String errMsg2 = " This can cause cause concurrency issues and unpredictable behavior when used with parallelization. Either do not specify -nt, or try a the conjunction of ";
String errMsg3 = "--usePreviousReadBases and --forcePreviousReadBasesToMatchRef.";
throw new StingException(errMsg+errMsg2+errMsg3);
}
return reduce(reduce1,reduce2);
}
@ -215,11 +224,15 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
return false;
} else if ( read.getBaseQualities()[offset] <= minQualityScore ) {
return false;
} else if ( useSecondaryBase && read.getAttribute("SQ") == null )
} else if ( useSecondaryBase && read.getAttribute("SQ") == null ) {
return false;
else if ( nPreviousBases >= 1 && previousReadBasesMismatchRef(read, offset, ref) )
} else if ( nPreviousBases >= 1 && previousReadBasesMismatchRef(read, offset, ref) ) {
return false;
else {
} else if ( nPreviousReadBases >= 1 && readLacksPreviousBases(read,offset,nPreviousReadBases) ) {
return false;
} else if ( nPreviousReadBases >= 1 && readBasesMustMatchRef && previousReadBasesMismatchRef(read, offset, ref) ) {
return false;
} else {
return true;
}
}
@ -241,6 +254,14 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
return false;
}
public boolean readLacksPreviousBases( SAMRecord read, int offset, int prevBases ) {
if ( ! read.getReadNegativeStrandFlag() ) {
return offset - prevBases < 0;
} else {
return offset + prevBases + 1 >= read.getReadLength();
}
}
public List<Comparable> buildConditions( SAMRecord read, int offset, ReferenceContext ref, ReadBackedPileup pileup ) {
ArrayList<Comparable> conditions = new ArrayList<Comparable>();
@ -254,7 +275,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
}
if ( nPreviousReadBases > 0 ) {
conditions.add(read.getReadString().substring(offset-nPreviousReadBases,offset));
conditions.add(buildReadString(read, offset, nPreviousReadBases));
}
if ( usePileupMismatches ) {
@ -276,6 +297,14 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
}
}
public String buildReadString( SAMRecord read, int offset, int nPreviousReadBases ) {
if ( ! read.getReadNegativeStrandFlag() ) {
return read.getReadString().substring(offset-nPreviousReadBases,offset);
} else {
return BaseUtils.simpleReverseComplement( read.getReadString().substring(offset+1,offset+nPreviousReadBases+1) );
}
}
public String createHeaderFromConditions() {
String header = "Observed_base\tTrue_base";