From d748c85dc44d66e88b9fc92e5562433115ae42d3 Mon Sep 17 00:00:00 2001 From: depristo Date: Thu, 18 Jun 2009 22:28:34 +0000 Subject: [PATCH] Cleaned code and reorganized -- moving in the right direction for v2 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1052 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/recalibration/CovariateCounterWalker.java | 11 +++++++---- .../recalibration/LogisticRecalibrationWalker.java | 2 +- .../sting/gatk/walkers/recalibration/RecalData.java | 4 ++-- .../gatk/walkers/recalibration/RecalDataManager.java | 2 +- .../recalibration/TableRecalibrationWalker.java | 3 +-- .../org/broadinstitute/sting/utils/QualityUtils.java | 4 +++- 6 files changed, 15 insertions(+), 11 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java index c614ad20d..c7bbfdb75 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.recalibration; +package org.broadinstitute.sting.gatk.walkers.recalibration; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMReadGroupRecord; @@ -43,8 +43,9 @@ public class CovariateCounterWalker extends LocusWalker { @Argument(fullName="MAX_READ_GROUPS", shortName="mrg", required=false, doc="Abort if number of read groups in input file exceeeds this count.") public int MAX_READ_GROUPS = 100; - @Argument(fullName="PLATFORM", shortName="pl", required=false, doc="Only calibrate read groups generated from the given platform (default = Illumina)") - public List platforms = Collections.singletonList("ILLUMINA"); + @Argument(fullName="PLATFORM", shortName="pl", required=false, doc="Only calibrate read groups generated from the given platform (default = * for all platforms)") + public List platforms = Collections.singletonList("*"); + //public List platforms = Collections.singletonList("ILLUMINA"); @Argument(fullName="rawData", shortName="raw", required=false, doc="If true, raw mismatch observations will be output to a file") public boolean outputRawData = true; @@ -380,7 +381,9 @@ public class CovariateCounterWalker extends LocusWalker { private boolean isSupportedReadGroup( SAMReadGroupRecord readGroup ) { for( String platform: platforms ) { platform = platform.trim(); - if( readGroup.getAttribute("PL") == null || readGroup.getAttribute("PL").toString().equalsIgnoreCase(platform) ) + if( readGroup.getAttribute("PL") == null || + platform.equals("*") || + readGroup.getAttribute("PL").toString().equalsIgnoreCase(platform) ) return true; } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/LogisticRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/LogisticRecalibrationWalker.java index 118c2713b..43d29a6bb 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/LogisticRecalibrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/LogisticRecalibrationWalker.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.recalibration; +package org.broadinstitute.sting.gatk.walkers.recalibration; import net.sf.samtools.*; import org.broadinstitute.sting.gatk.walkers.WalkerName; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalData.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalData.java index 9f4b408d7..7007b5c6d 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalData.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalData.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.recalibration; +package org.broadinstitute.sting.gatk.walkers.recalibration; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.BaseUtils; @@ -38,7 +38,7 @@ public class RecalData { public double empiricalQualDouble() { double empiricalQual = -10 * Math.log10((double)B / N); - if (empiricalQual > QualityUtils.MAX_QUAL_SCORE) empiricalQual = QualityUtils.MAX_QUAL_SCORE; + if (empiricalQual > QualityUtils.MAX_REASONABLE_Q_SCORE) empiricalQual = QualityUtils.MAX_REASONABLE_Q_SCORE; return empiricalQual; } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java index 775271f46..b37b65e49 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.recalibration; +package org.broadinstitute.sting.gatk.walkers.recalibration; import org.broadinstitute.sting.utils.QualityUtils; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java index cc7cdbb2c..30af5e8ff 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.recalibration; +package org.broadinstitute.sting.gatk.walkers.recalibration; import net.sf.samtools.*; import org.broadinstitute.sting.gatk.walkers.WalkerName; @@ -7,7 +7,6 @@ import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.DataSource; 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.*; diff --git a/java/src/org/broadinstitute/sting/utils/QualityUtils.java b/java/src/org/broadinstitute/sting/utils/QualityUtils.java index fc451aec3..ce684902c 100755 --- a/java/src/org/broadinstitute/sting/utils/QualityUtils.java +++ b/java/src/org/broadinstitute/sting/utils/QualityUtils.java @@ -8,6 +8,8 @@ package org.broadinstitute.sting.utils; */ public class QualityUtils { public final static byte MAX_QUAL_SCORE = 63; + public final static double MIN_REASONABLE_ERROR = 0.0001; + public final static byte MAX_REASONABLE_Q_SCORE = 40; /** * Private constructor. No instantiating this class! @@ -47,7 +49,7 @@ public class QualityUtils { * @return a quality score (0-40) */ static public byte probToQual(double prob) { - return probToQual(prob, 0.0001); + return probToQual(prob, MIN_REASONABLE_ERROR); //return (byte) Math.round(-10.0*Math.log10(1.0 - prob + 0.0001)); }