Better accessors for dealing with second base prob pileups

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@785 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -8,7 +8,12 @@ package org.broadinstitute.sting.utils;
 public class BaseUtils {
     /** Private constructor.  No instantiating this class! */
     private BaseUtils() {}
-    
+
+    static public boolean basesAreEqual(byte base1, byte base2) {
+        return simpleBaseToBaseIndex((char)base1) == simpleBaseToBaseIndex((char)base2);
+    }
+
+
     /**
      * Converts a simple base to a base index
      *

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

@@ -68,15 +68,23 @@ abstract public class BasicPileup implements Pileup {
         return quals;
     }
 
-    public static String qualPileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
+    public static String mappingQualPileupAsString( List<SAMRecord> reads) {
-        StringBuilder quals = new StringBuilder();
+        return quals2String(mappingQualPileup(reads));
-        for ( int qual : qualPileup(reads, offsets)) {
+    }
+
+    public static String quals2String( List<Byte> quals ) {
+        StringBuilder qualStr = new StringBuilder();
+        for ( int qual : quals ) {
             qual = Math.min(qual, 63);              // todo: fixme, this isn't a good idea
             char qualChar = (char) (33 + qual);     // todo: warning, this is illegal for qual > 63
-            quals.append(qualChar);
+            qualStr.append(qualChar);
         }
 
-        return quals.toString();
+        return qualStr.toString();
+    }
+
+    public static String qualPileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
+        return quals2String(qualPileup(reads, offsets));
     }
 
     public static ArrayList<Byte> secondaryBasePileup( List<SAMRecord> reads, List<Integer> offsets ) {
@@ -153,17 +161,18 @@ abstract public class BasicPileup implements Pileup {
         return (hasAtLeastOneSQField ? quals2 : null);
     }
 
-    public static String secondaryQualPileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
+    public static String secondaryQualPileupAsString( List<SAMRecord> reads, List<Integer> offsets) {
         StringBuilder quals2 = new StringBuilder();
         ArrayList<Byte> sqquals = secondaryQualPileup(reads, offsets);
 
-        if (sqquals == null) { return null; }
+        if (sqquals == null) {
-
+            return null;
-        for (byte qual2 : secondaryQualPileup(reads, offsets)) {
+        } else {
-            quals2.append(qual2);
+            for (byte qual2 : secondaryQualPileup(reads, offsets)) {
+                quals2.append(qual2);
+            }
+            return quals2.toString();
         }
-
-        return quals2.toString();
     }
 
     public static double[][] probDistPileup( List<SAMRecord> reads, List<Integer> offsets ) {

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

@@ -23,6 +23,10 @@ public class QualityUtils {
         return 1.0 - qualToErrorProb(qual);
     }
 
+    static public double qualToProb(int qual) {
+        return 1.0 - Math.pow(10.0, ((double) qual)/-10.0);
+    }
+
     /**
      * Convert a quality score to a probability of error.  This is the Phred-style
      * conversion, *not* the Illumina-style conversion (though asymptotically, they're the same).

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

@@ -62,6 +62,10 @@ public class ReadBackedPileup extends BasicPileup {
         return Utils.join(",", mappingQualPileup(reads));
     }
 
+    public String getMappingQuals() {
+        return mappingQualPileupAsString(reads);
+    }
+
     public String getSecondaryBasePileup() {
         return secondaryBasePileupAsString(reads, offsets);
     }
@@ -76,6 +80,15 @@ public class ReadBackedPileup extends BasicPileup {
 
     public String getPileupString()
     {
-        return String.format("%s: %s %s %s", getLocation(), getRef(), getBases(), getQuals());
+        // In the pileup format, each line represents a genomic position, consisting of chromosome name,
+        // coordinate, reference base, read bases, read qualities and alignment mapping qualities.
+
+        //return String.format("%s %s %s %s", getLocation(), getRef(), getBases(), getQuals());
+        return String.format("%s %s %s %s %s %s",
+                getLocation().getContig(), getLocation().getStart(),    // chromosome name and coordinate
+                getRef(),                                               // reference base
+                getBases(),
+                getQuals(),
+                getMappingQuals());
     }
 }