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Intermediate checkin for safety -- now compiles 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1026 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-06-17 13:16:55 +00:00
parent 2250769a42
commit d1e25bfe88
5 changed files with 32 additions and 31 deletions
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3
java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java → java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/CovariateCounterWalker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers;
package org.broadinstitute.sting.playground.gatk.walkers.recalibration;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord;
@ -7,7 +7,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.playground.gatk.walkers.RecalData;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.QualityUtils;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java → java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/LogisticRecalibrationWalker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers;
package org.broadinstitute.sting.playground.gatk.walkers.recalibration;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.walkers.WalkerName;

53
java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/RecalData.java
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@ -1,7 +1,8 @@
package org.broadinstitute.sting.playground.gatk.walkers;
package org.broadinstitute.sting.playground.gatk.walkers.recalibration;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.BaseUtils;
public class RecalData {
long N;
@ -28,7 +29,7 @@ public class RecalData {
}
public void inc(char curBase, char ref) {
inc(1, nuc2num[curBase] == nuc2num[ref] ? 0 : 1);
inc(1, BaseUtils.simpleBaseToBaseIndex(curBase) == BaseUtils.simpleBaseToBaseIndex(ref) ? 0 : 1);
//out.printf("%s %s\n", curBase, ref);
}
@ -74,39 +75,39 @@ public class RecalData {
public static int bases2dinucIndex(char prevBase, char base, boolean Complement) {
if (!Complement) {
return nuc2num[prevBase] * 4 + nuc2num[base];
return BaseUtils.simpleBaseToBaseIndex(prevBase) * 4 + BaseUtils.simpleBaseToBaseIndex(base);
}else{
return (3 - nuc2num[prevBase]) * 4 + (3 - nuc2num[base]);
return (3 - BaseUtils.simpleBaseToBaseIndex(prevBase)) * 4 + (3 - BaseUtils.simpleBaseToBaseIndex(base));
}
}
public static String dinucIndex2bases(int index) {
char data[] = {num2nuc[index / 4], num2nuc[index % 4]};
char data[] = {BaseUtils.baseIndexToSimpleBase(index / 4), BaseUtils.baseIndexToSimpleBase(index % 4)};
return new String( data );
}
public static int string2dinucIndex(String s) {
return bases2dinucIndex(s.charAt(0), s.charAt(1), false);
}
private static int nuc2num[];
private static char num2nuc[];
static {
nuc2num = new int[128];
nuc2num['A'] = 0;
nuc2num['C'] = 1;
nuc2num['G'] = 2;
nuc2num['T'] = 3;
nuc2num['a'] = 0;
nuc2num['c'] = 1;
nuc2num['g'] = 2;
nuc2num['t'] = 3;
num2nuc = new char[4];
num2nuc[0] = 'A';
num2nuc[1] = 'C';
num2nuc[2] = 'G';
num2nuc[3] = 'T';
}
//
// private static int nuc2num[];
// private static char num2nuc[];
//
// static {
// nuc2num = new int[128];
// nuc2num['A'] = 0;
// nuc2num['C'] = 1;
// nuc2num['G'] = 2;
// nuc2num['T'] = 3;
// nuc2num['a'] = 0;
// nuc2num['c'] = 1;
// nuc2num['g'] = 2;
// nuc2num['t'] = 3;
//
// num2nuc = new char[4];
// num2nuc[0] = 'A';
// num2nuc[1] = 'C';
// num2nuc[2] = 'G';
// num2nuc[3] = 'T';
// }
}

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/RecalDataManager.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers;
package org.broadinstitute.sting.playground.gatk.walkers.recalibration;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -1,10 +1,11 @@
package org.broadinstitute.sting.playground.gatk.walkers;
package org.broadinstitute.sting.playground.gatk.walkers.recalibration;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.playground.gatk.walkers.recalibration.RecalData;
import org.apache.log4j.Logger;
import java.util.*;