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notes for chartl 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1894 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-10-21 18:31:31 +00:00
parent 77863d4940
commit 15a1849758
1 changed files with 22 additions and 17 deletions
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39
java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
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@ -26,23 +26,23 @@ import net.sf.samtools.SAMRecord;
*/
@By(DataSource.REFERENCE)
public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<ReferenceContextWindow,Integer>{
@Argument(fullName="usePreviousBases", doc="Use previous bases of the reference as part of the calculation, uses the specified number, defaults to 0", required=false)
@Argument(fullName="usePreviousBases", doc="Use previous bases of the reference as part of the calculation, uses the specified number, defaults to 0", required=false)
int nPreviousBases = 0;
@Argument(fullName="useSecondaryBase",doc="Use the secondary base of a read as part of the calculation", required=false)
@Argument(fullName="useSecondaryBase",doc="Use the secondary base of a read as part of the calculation", required=false)
boolean useSecondaryBase = false;
@Argument(fullName="confidentRefThreshold",doc="Set the lod score that defines confidence in ref, defaults to 4", required=false)
@Argument(fullName="confidentRefThreshold",doc="Set the lod score that defines confidence in ref, defaults to 4", required=false)
int confidentRefThreshold = 5;
@Argument(fullName="maxNumMismatches",doc="Set the maximum number of mismatches at a locus before choosing not to use it in calculation. Defaults to 1.", required=false)
@Argument(fullName="maxNumMismatches",doc="Set the maximum number of mismatches at a locus before choosing not to use it in calculation. Defaults to 1.", required=false)
int maxNumMismatches = 1;
@Argument(fullName="minMappingQuality", doc ="Set the alignment quality below which to ignore reads; defaults to 30", required = false)
@Argument(fullName="minMappingQuality", doc ="Set the alignment quality below which to ignore reads; defaults to 30", required = false)
int minMappingQuality = 30;
@Argument(fullName="minQualityScore", doc = "Set the base quality score below which to ignore bases in the pileup, defaults to 20", required = false)
@Argument(fullName="minQualityScore", doc = "Set the base quality score below which to ignore bases in the pileup, defaults to 20", required = false)
int minQualityScore = 20;
@Argument(fullName="usePileupMismatches", doc = "Use the number of mismatches in the pileup as a condition for the table", required=false)
@Argument(fullName="usePileupMismatches", doc = "Use the number of mismatches in the pileup as a condition for the table", required=false)
boolean usePileupMismatches = false;
@Argument(fullName="usePreviousReadBases", doc="Use previous bases of the read as part of the calculation. Will ignore reads if there aren't this many previous bases. Uses the specified number. Defaults to 0", required=false)
@Argument(fullName="usePreviousReadBases", doc="Use previous bases of the read as part of the calculation. Will ignore reads if there aren't this many previous bases. Uses the specified number. Defaults to 0", required=false)
int nPreviousReadBases = 0;
@Argument(fullName="useReadGroup", doc="Use the group number of the read as a condition of the table.", required = false)
@Argument(fullName="useReadGroup", doc="Use the group number of the read as a condition of the table.", required = false)
boolean useReadGroup = false;
private UnifiedGenotyper ug;
@ -60,7 +60,10 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
return 0;
}
// todo -- emit table from map and reduce just sums
public ReferenceContextWindow map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
// todo -- change to use windowed reference itself
// todo -- move up calculations into map not reduce
ReadBackedPileup pileup = new ReadBackedPileup(ref.getBase(),context);
refWindow.update(ref,pileup,baseIsUsable(tracker,ref,pileup,context));
@ -242,13 +245,13 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
}
public boolean pileupContainsNoNs(ReadBackedPileup pileup) {
for ( char c : pileup.getBases().toCharArray() ) {
if ( c == 'N' ) {
return false;
}
}
for ( char c : pileup.getBases().toCharArray() ) {
if ( c == 'N' ) {
return false;
}
}
return true;
return true;
}
public boolean baseIsConfidentRef( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
@ -261,7 +264,6 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
}
class BaseTransitionTable implements Comparable {
private int[][] table;
@ -310,6 +312,7 @@ class BaseTransitionTable implements Comparable {
ListIterator<Comparable> thisIter = this.conditions.listIterator();
ListIterator<Comparable> thatIter = t.conditions.listIterator();
while ( thisIter.next() == thatIter.next() ) {
// todo -- compareTo
// do nothing
}
return thisIter.previous().compareTo(thatIter.previous());
@ -325,6 +328,8 @@ class BaseTransitionTable implements Comparable {
for ( char observedBase : BaseUtils.BASES ) {
for ( char refBase : BaseUtils.BASES ) {
// todo -- String.format please
// todo -- in these situations use StringBuilder
String outString = observedBase+"\t"+refBase;
for ( Comparable c : conditions ) {
outString = outString+"\t"+c.toString();
@ -338,7 +343,7 @@ class BaseTransitionTable implements Comparable {
//if ( observedBase == refBase ) {
// throw new StingException("BaseTransitionTable received equal observed and reference bases, which should not happen.");
//}
table[BaseUtils.simpleBaseToBaseIndex(observedBase)][BaseUtils.simpleBaseToBaseIndex(refBase)] ++;
table[BaseUtils.simpleBaseToBaseIndex(observedBase)][BaseUtils.simpleBaseToBaseIndex(refBase)]++;
}
public void update(byte observed, char ref) {