From bd1e679bc5a3994c4fe5b6aadb3327fc1e6ecd1f Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 27 Aug 2009 20:23:41 +0000
Subject: [PATCH] @ Fixed issues with AnalyzePowerWalker which depended on
 CoverageAndPowerWalker. The latter was changed but not the former. Now fixed

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1464 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/poolseq/AnalyzePowerWalker.java   | 22 ++++++++++++-------
 .../poolseq/CoverageAndPowerWalker.java       |  7 ++++++
 2 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/AnalyzePowerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/AnalyzePowerWalker.java
index 79db22fdd..9af1731e0 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/AnalyzePowerWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/AnalyzePowerWalker.java
@@ -6,6 +6,7 @@ import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.playground.utils.PoolUtils;
 
 import java.io.FileNotFoundException;
 import java.io.FileReader;
@@ -13,8 +14,11 @@ import java.io.BufferedReader;
 import java.io.IOException;
 import java.util.StringTokenizer;
 import java.util.NoSuchElementException;
+import java.util.List;
 import java.rmi.NoSuchObjectException;
 
+import net.sf.samtools.SAMRecord;
+
 /**
  * Created by IntelliJ IDEA.
  * User: chartl
@@ -29,8 +33,6 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{
         String pathToSyzygyFile = null;
     @Argument(fullName = "ColumnOffset", shortName = "co", doc = "Offset of column containing the power in the pf", required = true)
         int colOffset = 0;
-    @Argument(fullName = "linesToClear", shortName="clr", doc = "Clear so many lines from the read file before starting (default - just the header line)", required = false)
-        int clrLines = 1;
 
     BufferedReader syzyFileReader;
     final String pfFileDelimiter = " ";
@@ -42,9 +44,7 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{
         super.initialize();
         try {
             syzyFileReader = new BufferedReader(new FileReader(pathToSyzygyFile));
-            for(int clear = 0; clear < clrLines; clear++) {
-                syzyFileReader.readLine();
-            }
+            syzyFileReader.readLine();
         } catch (FileNotFoundException e) {
             String newErrMsg = "Syzygy input file " + pathToSyzygyFile + " could be incorrect. File not found.";
             throw new StingException(newErrMsg,e);
@@ -56,11 +56,13 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{
     }
 
     @Override
-    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context)
+    public Pair<Integer,Integer> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context)
     {
+
+        Pair<Pair<List<SAMRecord>, List<SAMRecord>>,Pair<List<Integer>,List<Integer>>> splitReads = PoolUtils.splitReadsByReadDirection(context.getReads(),context.getOffsets());
         if ( !super.suppress_printing )
         {
-            Pair<Double,Byte> powpair = super.boostrapSamplingPowerCalc(context);
+            Pair<double[],byte[]> powpair = super.calculatePower(splitReads,false,context);
 
             boolean syzyFileIsReady;
             try {
@@ -80,7 +82,7 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{
             }
         }
 
-        return context.getReads().size();
+        return new Pair(splitReads.getFirst().getFirst().size(), splitReads.getFirst().getFirst().size());
     }
 
     public Pair<Double,String> getSyzyPowFromFile() {
@@ -107,4 +109,8 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{
             throw new StingException(errMsg);
         }
     }
+
+    public String createHeaderString() {
+        return (super.createHeaderString() + "  PowSyz");
+    }
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/CoverageAndPowerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/CoverageAndPowerWalker.java
index e44210f4e..040765d5e 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/CoverageAndPowerWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/CoverageAndPowerWalker.java
@@ -43,6 +43,9 @@ public class CoverageAndPowerWalker extends LocusWalker<Pair<Integer, Integer>,
     }
 
     public Pair<Long,Long> reduceInit() {
+        if ( ! suppress_printing ) { // print header
+            out.printf("%s%n",createHeaderString());
+        }
         return new Pair(0l,0l);
     }
 
@@ -154,6 +157,10 @@ public class CoverageAndPowerWalker extends LocusWalker<Pair<Integer, Integer>,
         return power;
     }
 
+    public String createHeaderString() {
+        return "Chrom:Pos  CvgF  CvgR  CvgC  QmedF  QmedR  QmedC  PowF  PowR  PowC";
+    }
+
     // class methods
 
     public static Pair<Pair<List<SAMRecord>,List<SAMRecord>>,Pair<List<Integer>,List<Integer>>> coinTossPartition(List<SAMRecord> reads, List<Integer> offsets, double snpProb) {