Holds raw intensities, sequence, and quality scores.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@701 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/secondarybase/RawRead.java

@@ -0,0 +1,67 @@
+package org.broadinstitute.sting.secondarybase;
+
+import org.broadinstitute.sting.utils.BaseUtils;
+
+public class RawRead {
+    private byte lane;
+    private short tile;
+    private short x;
+    private short y;
+    
+    private byte[] sequence;
+    private byte[] quals;
+    private short[][] intensities;
+
+    public RawRead(String[][] pastedReadString, int cycleBegin, int cycleEnd) {
+        lane = Byte.valueOf(pastedReadString[0][0]);
+        tile = Short.valueOf(pastedReadString[0][1]);
+        x = Short.valueOf(pastedReadString[0][2]);
+        y = Short.valueOf(pastedReadString[0][3]);
+
+        sequence = pastedReadString[1][4].substring(cycleBegin, cycleEnd).getBytes();
+
+        quals = new byte[sequence.length];
+        intensities = new short[sequence.length][4];
+
+        for (int cycle = 0; cycle < sequence.length; cycle++) {
+            byte maxQual = -50;
+
+            for (int fullReadIndex = 4*cycle; fullReadIndex < 4*cycle + 4; fullReadIndex++) {
+                byte qual = Byte.valueOf(pastedReadString[2][fullReadIndex]);
+
+                if (qual > maxQual) { maxQual = qual; }
+            }
+
+            quals[cycle] = maxQual >= 0 ? maxQual : 0;
+
+            for (int fullReadIndex = 4*cycle + 4, channel = 0; fullReadIndex < 4*cycle + 8; fullReadIndex++, channel++) {
+                double doubleChannelIntensity = Double.valueOf(pastedReadString[0][fullReadIndex]);
+                short shortChannelIntensity = (short) doubleChannelIntensity;
+
+                intensities[cycle][channel] = shortChannelIntensity;
+            }
+        }
+    }
+
+    public byte getLane() { return lane; }
+    public int getTile() { return tile; }
+    public int getXCoordinate() { return x; }
+    public int getYCoordinate() { return y; }
+
+    public String getReadKey() { return String.format("%d:%d:%d:%d", lane, tile, x, y); }
+
+    public byte[] getSequence() { return sequence; }
+    public void setSequence(byte[] sequence) { this.sequence = sequence; }
+
+    public String getSequenceAsString() {
+        return new String(getSequence());
+    }
+
+    public byte[] getQuals() { return quals; }
+    public void setQuals(byte[] quals) { this.quals = quals; }
+
+    public short[][] getIntensities() { return intensities; }
+    public void setIntensities(short[][] intensities) { this.intensities = intensities; }
+
+    public int getReadLength() { return sequence.length; }
+}