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Updating HomopolymerCovariate to only count the consecutive previous bases. I left in the code but commented out for if somebody wants to worry about carry forward homopolymer problems. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2391 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2009-12-17 18:25:09 +00:00
parent b863fffdf6
commit aa86f3710d
3 changed files with 29 additions and 9 deletions
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34
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java
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@ -32,15 +32,15 @@ import net.sf.samtools.SAMRecord;
* User: rpoplin
* Date: Dec 4, 2009
*
* The Homopolymer Run Covariate. This is the number of bases in the previous N that match the current base.
* The Homopolymer Run Covariate. This is the number of consecutive bases in the previous N that match the current base.
* For example, if N = 10:
* ATTGCCCCGTAAAAAAAAAA
* 00100123121123456789
* ATTGCCCCGTAAAAAAAAATA
* 001001230001234567800
*/
public class HomopolymerCovariate implements ExperimentalCovariate {
int numBack = 8;
int numBack = 7;
// Initialize any member variables using the command-line arguments passed to the walkers
public void initialize( final RecalibrationArgumentCollection RAC ) {
@ -50,6 +50,10 @@ public class HomopolymerCovariate implements ExperimentalCovariate {
// Used to pick out the covariate's value from attributes of the read
public final Comparable getValue( final SAMRecord read, final int offset ) {
// This block of code is for if you don't want to only count consecutive bases
// ATTGCCCCGTAAAAAAAAATA
// 001001231211234567819
/*
int numAgree = 0; // The number of bases that agree with you in the previous numBack bases of the read
int startPos = 0;
int stopPos = 0;
@ -57,15 +61,31 @@ public class HomopolymerCovariate implements ExperimentalCovariate {
byte thisBase = bases[offset];
if( !read.getReadNegativeStrandFlag() ) { // Forward direction
startPos = Math.max(offset - numBack, 0);
stopPos = offset;
stopPos = Math.max(offset - 1, 0);
} else { // Negative direction
startPos = offset + 1;
stopPos = Math.min(offset + numBack + 1, read.getReadLength());
startPos = Math.min(offset + 2, bases.length);
stopPos = Math.min(offset + numBack + 1, bases.length);
}
for( int iii = startPos; iii < stopPos; iii++ ) {
if( bases[iii] == thisBase ) { numAgree++; }
}
*/
int numAgree = 0; // The number of consecutive bases that agree with you in the previous numBack bases of the read
byte[] bases = read.getReadBases();
int iii = offset;
if( !read.getReadNegativeStrandFlag() ) { // Forward direction
while( iii <= bases.length-2 && bases[iii] == bases[iii+1] && numAgree < numBack ) {
numAgree++;
iii++;
}
} else { // Negative direction
while( iii >= 1 && bases[iii] == bases[iii-1] && numAgree < numBack ) {
numAgree++;
iii--;
}
}
return numAgree;
}

2
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
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@ -58,7 +58,7 @@ public class RecalibrationArgumentCollection {
@Argument(fullName = "window_size_nqs", shortName="nqs", doc="The window size used by MinimumNQSCovariate for its calculation", required=false)
public int WINDOW_SIZE = 5;
@Argument(fullName = "homopolymer_nback", shortName="nback", doc="The number of previous bases to look at in HomopolymerCovariate", required=false)
public int HOMOPOLYMER_NBACK = 8;
public int HOMOPOLYMER_NBACK = 7;
public boolean checkSolidRecalMode() {
return ( SOLID_RECAL_MODE.equalsIgnoreCase("DO_NOTHING") || SOLID_RECAL_MODE.equalsIgnoreCase("SET_Q_ZERO") ||

2
packages/GenomeAnalysisTK.xml
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@ -24,7 +24,7 @@
<class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
<!-- Local realignment around indels -->
<class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>