From d1e25bfe88926299d071580130514437cecb9879 Mon Sep 17 00:00:00 2001 From: depristo Date: Wed, 17 Jun 2009 13:16:55 +0000 Subject: [PATCH] Intermediate checkin for safety -- now compiles git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1026 348d0f76-0448-11de-a6fe-93d51630548a --- .../CovariateCounterWalker.java | 3 +- .../LogisticRecalibrationWalker.java | 2 +- .../gatk/walkers/recalibration/RecalData.java | 53 ++++++++++--------- .../recalibration/RecalDataManager.java | 2 +- .../TableRecalibrationWalker.java | 3 +- 5 files changed, 32 insertions(+), 31 deletions(-) rename java/src/org/broadinstitute/sting/playground/gatk/walkers/{ => recalibration}/CovariateCounterWalker.java (99%) rename java/src/org/broadinstitute/sting/playground/gatk/walkers/{ => recalibration}/LogisticRecalibrationWalker.java (99%) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/CovariateCounterWalker.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/CovariateCounterWalker.java index 841eaa7b7..a12836050 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/CovariateCounterWalker.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/LogisticRecalibrationWalker.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/LogisticRecalibrationWalker.java index 7835eaecf..696e9cb78 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/LogisticRecalibrationWalker.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/RecalData.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/RecalData.java index eedea5c74..662fe3a49 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/RecalData.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/RecalData.java @@ -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'; +// } } \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/RecalDataManager.java index 1d9a6d909..c6fc3f4e1 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/RecalDataManager.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/RecalDataManager.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/TableRecalibrationWalker.java index aa773a1c0..59495ed00 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/TableRecalibrationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/recalibration/TableRecalibrationWalker.java @@ -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.*;