From e4770885fdf00504c7bfffc1116e989b1288a2d4 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 14 May 2009 16:55:49 +0000
Subject: [PATCH] The four-probs for all bases in a single read.  Some utility
 functions for generating the primary and secondary base strings, as well as
 generating the SQ tag byte array in a manner that's consistent with the
 Bustard base calls (meaning the primary Bustard call and the secondary
 Four-Prob call are not permitted to be the same).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@704 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/secondarybase/FourProbRead.java     | 53 +++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/secondarybase/FourProbRead.java

diff --git a/java/src/org/broadinstitute/sting/secondarybase/FourProbRead.java b/java/src/org/broadinstitute/sting/secondarybase/FourProbRead.java
new file mode 100755
index 000000000..6b9fb09f0
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/secondarybase/FourProbRead.java
@@ -0,0 +1,53 @@
+package org.broadinstitute.sting.secondarybase;
+
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.QualityUtils;
+
+import java.util.ArrayList;
+
+public class FourProbRead extends ArrayList<FourProb> {
+    public FourProbRead(int initialCapacity) {
+        super(initialCapacity);
+    }
+
+    public String getBaseSequenceAtGivenRank(int rank) {
+        String pseq = "";
+
+        for (int cycle = 0; cycle < this.size(); cycle++) {
+            FourProb fp = this.get(cycle);
+
+            pseq += fp.baseAtRank(rank);
+        }
+
+        return pseq;
+    }
+
+    public String getPrimaryBaseSequence() {
+        return getBaseSequenceAtGivenRank(0);
+    }
+
+    public String getSecondaryBaseSequence() {
+        return getBaseSequenceAtGivenRank(1);
+    }
+
+    public byte[] getSQTag(RawRead rr) {
+        byte[] sqtag = new byte[this.size()];
+
+        for (int cycle = 0; cycle < this.size(); cycle++) {
+            FourProb fp = this.get(cycle);
+
+            int fpPrimaryBaseIndex = fp.indexAtRank(0);
+            int rawPrimaryBaseIndex = BaseUtils.simpleBaseToBaseIndex(rr.getSequenceAsString().charAt(cycle));
+
+            int fpSecondaryBaseIndex = (fpPrimaryBaseIndex == rawPrimaryBaseIndex) ? fp.indexAtRank(1) : fpPrimaryBaseIndex;
+
+            double qualdiff = -10.0*Math.log10(fp.probAtRank(2)/fp.probAtRank(1));
+
+            sqtag[cycle] = QualityUtils.baseAndProbDiffToCompressedQuality(fpSecondaryBaseIndex, qualdiff);
+
+            //System.out.println("SQTAG: " + qualdiff + " " + sqtag[cycle] + " " + QualityUtils.compressedQualityToProbDiff(sqtag[cycle]));
+        }
+
+        return sqtag;
+    }
+}