All walkers now use read.getReadGroup()

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1839 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java

@@ -25,11 +25,8 @@ public class PlatformUnitFilter implements SamRecordFilter {
         Object pu_attr = samRecord.getAttribute("PU");
 
         if ( pu_attr == null ) {
-            // no platform unit in the record, go get the header if we have at least read group
+            // no platform unit in the record, go get from read group
-            final String rgId = (String)samRecord.getAttribute("RG");
+            SAMReadGroupRecord rgr = samRecord.getReadGroup();
-            if (rgId == null) return false; // we do not have read group either, can not filter
-
-            SAMReadGroupRecord rgr = samRecord.getHeader().getReadGroup(rgId);
 
             pu_attr = rgr.getAttribute("PU") ;
         }

java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java

@@ -97,14 +97,13 @@ public class SplitSamFileWalker extends ReadWalker<SAMRecord, Map<String, SAMFil
      * Write out the read
      */
     public Map<String, SAMFileWriter> reduce(SAMRecord read, Map<String, SAMFileWriter> outputs) {
-        final String readGroup = read.getAttribute("RG").toString();
+        final String sample = read.getReadGroup().getSample();
-        final String sample = read.getHeader().getReadGroup(readGroup).getSample();
         SAMFileWriter output = outputs.get(sample);
 
         if ( output != null ) {
             output.addAlignment(read);
         } else {
-            throw new RuntimeException(String.format("Read group %s not present in header but found in read %s", readGroup, read.getReadName()));
+            throw new RuntimeException(String.format("Read group %s not present in header but found in read %s", read.getReadGroup().getReadGroupId(), read.getReadName()));
         }
 
         return outputs;

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EMGenotypeCalculationModel.java

@@ -203,8 +203,7 @@ public abstract class EMGenotypeCalculationModel extends GenotypeCalculationMode
             if ( POOLED_INPUT ) {
                 sample = "POOL";
             } else {
-                String readGroup = read.getAttribute("RG").toString(); // can't be null because those are filtered out
+                sample = read.getReadGroup().getSample();
-                sample = read.getHeader().getReadGroup(readGroup).getSample();
             }
 
             // create a new context object if this is the first time we're seeing a read for this sample

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperWalker.java

@@ -819,16 +819,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
             	indels.set(pos, indelsAtSite);
             }
             
-            String sample = null;
+            String sample = r.getReadGroup().getSample();
-            Object readGroupAttr = r.getAttribute("RG");
-            if ( readGroupAttr != null ) {
-                SAMReadGroupRecord readGroup = r.getHeader().getReadGroup(readGroupAttr.toString());
-                if ( readGroup != null ) {
-                    Object readSampleAttr = readGroup.getAttribute("SM");
-                    if ( readSampleAttr != null )
-                        sample = readSampleAttr.toString();
-                }
-            }
 
             boolean found = false;
             for ( IndelVariant v : indelsAtSite ) {

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java

@@ -119,17 +119,16 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
                     throw new RuntimeException("Expectedly long read, please increase maxium read len with maxReadLen parameter: " + read.format());
                 }
 
-                final String readGroupString = ((String)read.getAttribute("RG"));
+                SAMReadGroupRecord readGroup = read.getReadGroup();
-                SAMReadGroupRecord readGroup = read.getHeader().getReadGroup(readGroupString);
 
-                if ( readGroupString == null ) {
+                if ( readGroup == null ) {
                     throw new RuntimeException("No read group annotation found for read " + read.format());
                 }
 
                 if ((read.getMappingQuality() >= MIN_MAPPING_QUALITY && isSupportedReadGroup(readGroup) )) {
                     int offset = offsets.get(i);
                     if ( offset > 0 && offset < (read.getReadLength() - 1) ) { // skip first and last bases because they suck and they don't have a dinuc count
-                        counted_bases += covariateCounter.updateDataFromRead(readGroupString, read, offset, ref.getBase(), useOriginalQuals);
+                        counted_bases += covariateCounter.updateDataFromRead(readGroup.getReadGroupId(), read, offset, ref.getBase(), useOriginalQuals);
                     }
                 }
             }

java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageBySample.java

@@ -95,8 +95,7 @@ public class CoverageBySample extends LocusWalker<String, String>
         for (int i = 0; i < context.getReads().size(); i++)
         {
             SAMRecord read = context.getReads().get(i);
-            String RG = (String)(read.getAttribute("RG"));
+            String sample = read.getReadGroup().getSample();
-            String sample = header.getReadGroup(RG).getSample();
 			counts.put(sample, counts.get(sample)+1); 
         }
         return counts;
@@ -124,12 +123,11 @@ public class CoverageBySample extends LocusWalker<String, String>
         {
             SAMRecord read = context.getReads().get(i);
             Integer offset = context.getOffsets().get(i);
-            String RG = (String)(read.getAttribute("RG"));
 
             assert(header != null);
-            assert(header.getReadGroup(RG) != null);
+            assert(read.getReadGroup() != null);
 
-            String sample = header.getReadGroup(RG).getSample();
+            String sample = read.getReadGroup().getSample();
 			//if (SAMPLE_NAME_REGEX != null) { sample = sample.replaceAll(SAMPLE_NAME_REGEX, "$1"); }
             reads[index.get(sample)].add(read); 
             offsets[index.get(sample)].add(offset); 

java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java

@@ -35,9 +35,7 @@ public class ListSampleIds extends LocusWalker<Boolean, Boolean>
         for ( int i = 0; i < reads.size(); i++ )
         {
             SAMRecord read = reads.get(i);
-            String rg = (String) read.getAttribute("RG");
+            SAMReadGroupRecord readGroup = read.getReadGroup();
-            SAMFileHeader header = read.getHeader();
-            SAMReadGroupRecord readGroup = header.getReadGroup(rg);
             if (readGroup == null) { System.out.printf("."); return false; }
             String sample = readGroup.getSample();
             System.out.printf("FROM_MAP %s\n", sample);

java/src/org/broadinstitute/sting/utils/Utils.java

@@ -203,14 +203,11 @@ public class Utils {
     }
 
     public static boolean is454Read(SAMRecord read) {
-        Object readGroupAttr = read.getAttribute("RG");
+        SAMReadGroupRecord readGroup = read.getReadGroup();
-        if ( readGroupAttr != null ) {
+        if ( readGroup != null ) {
-            SAMReadGroupRecord readGroup = read.getHeader().getReadGroup(readGroupAttr.toString());
-            if ( readGroup != null ) {
             Object readPlatformAttr = readGroup.getAttribute("PL");
             if ( readPlatformAttr != null )
                 return readPlatformAttr.toString().toUpperCase().contains("454");
-            }
         }
         return false;
     }