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-use the getReadGroup() function that was added to picard for us 

-clean up some include lines


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1808 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-12 01:39:32 +00:00
parent d844d1c496
commit cf7a26759d
4 changed files with 2 additions and 14 deletions
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5
java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
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@ -36,9 +36,6 @@ import net.sf.samtools.SAMRecord;
public class MissingReadGroupFilter implements SamRecordFilter { public class MissingReadGroupFilter implements SamRecordFilter {
public boolean filterOut(SAMRecord rec) { public boolean filterOut(SAMRecord rec) {
String RG = (String)(rec.getAttribute("RG")); return rec.getReadGroup() == null;
return RG == null ||
rec.getHeader() == null ||
rec.getHeader().getReadGroup(RG) == null;
} }
} }

3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionGenotypeLikelihoods.java
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@ -56,8 +56,7 @@ public class EmpiricalSubstitutionGenotypeLikelihoods extends GenotypeLikelihood
public static SequencerPlatform getReadSequencerPlatform( SAMRecord read ) { public static SequencerPlatform getReadSequencerPlatform( SAMRecord read ) {
if ( lastReadForPL != read ) { if ( lastReadForPL != read ) {
lastReadForPL = read; lastReadForPL = read;
final String readGroupString = ((String)read.getAttribute("RG")); SAMReadGroupRecord readGroup = read.getReadGroup();
SAMReadGroupRecord readGroup = readGroupString == null ? null : read.getHeader().getReadGroup(readGroupString);
final String platformName = readGroup == null ? null : (String)readGroup.getAttribute(SAM_PLATFORM_TAG); final String platformName = readGroup == null ? null : (String)readGroup.getAttribute(SAM_PLATFORM_TAG);
plOfLastRead = standardizeSequencerPlatform(platformName); plOfLastRead = standardizeSequencerPlatform(platformName);
} }

5
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/OneStateErrorGenotypeLikelihoods.java
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@ -3,12 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import static java.lang.Math.log10;
import java.util.TreeMap;
import java.util.EnumMap;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord;
/** /**
* This implements the old style CRD calculation of the chance that a base being a true chromBase given * This implements the old style CRD calculation of the chance that a base being a true chromBase given

3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ThreeStateErrorGenotypeLikelihoods.java
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@ -4,11 +4,8 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import static java.lang.Math.log10; import static java.lang.Math.log10;
import java.util.TreeMap;
import java.util.EnumMap;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord;
public class ThreeStateErrorGenotypeLikelihoods extends GenotypeLikelihoods { public class ThreeStateErrorGenotypeLikelihoods extends GenotypeLikelihoods {
// //