From 9bc763a835431d4981f03fc6c4bf4bccb9f4aa27 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 9 Apr 2009 20:51:37 +0000
Subject: [PATCH] A better (aka 'working') tool for combining four-base probs
 with an aligned sam file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@350 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../CombineSamAndFourProbs.java               | 118 ++++++++++++++++++
 1 file changed, 118 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/playground/fourbasecaller/CombineSamAndFourProbs.java

diff --git a/java/src/org/broadinstitute/sting/playground/fourbasecaller/CombineSamAndFourProbs.java b/java/src/org/broadinstitute/sting/playground/fourbasecaller/CombineSamAndFourProbs.java
new file mode 100755
index 000000000..723d518b4
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/fourbasecaller/CombineSamAndFourProbs.java
@@ -0,0 +1,118 @@
+package org.broadinstitute.sting.playground.fourbasecaller;
+
+import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
+import org.broadinstitute.sting.utils.QualityUtils;
+
+import java.io.*;
+import java.util.HashMap;
+
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMFileWriterFactory;
+
+public class CombineSamAndFourProbs extends CommandLineProgram {
+    public static CombineSamAndFourProbs Instance = null;
+
+    public File SAM;
+    public File FOURPROBS;
+    public File SAM_OUT;
+
+    public static void main(String[] argv) {
+        Instance = new CombineSamAndFourProbs();
+        start(Instance, argv);
+    }
+
+    protected void setupArgs() {
+        m_parser.addRequiredArg("sam",      "S", "Input SAM file",                        "SAM");
+        m_parser.addRequiredArg("fourprob", "F", "Input text file := read_name sq_field", "FOURPROBS");
+        m_parser.addRequiredArg("sam_out",  "O", "Output SAM file",                       "SAM_OUT");
+    }
+
+    protected int execute() {
+        BufferedReader fpreader = null;
+
+        try {
+            fpreader = new BufferedReader(new FileReader(FOURPROBS));
+
+            HashMap fourprobMap = new HashMap(27000000);
+
+            String fourprobLine;
+            int processed = 0;
+            while ((fourprobLine = fpreader.readLine()) != null) {
+                String[] fourprobPieces = fourprobLine.split("\\s+");
+                String[] sqfield = fourprobPieces[1].split(":");
+                byte[] sq = hexStringToBytes(sqfield[2]);
+
+                fourprobMap.put(fourprobPieces[0], sq);
+
+                if (processed % 1000000 == 0) {
+                    System.out.println("Processed " + processed);
+                }
+                processed++;
+            }
+
+            fpreader.close();
+
+            SAMFileReader sf = new SAMFileReader(SAM);
+            sf.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
+
+            SAMFileWriter sw = new SAMFileWriterFactory().makeSAMOrBAMWriter(sf.getFileHeader(), true, SAM_OUT);
+
+            for (SAMRecord sr : sf) {
+                String readname = sr.getReadName();
+                byte[] sq = (byte[]) fourprobMap.get(readname);
+
+                if (sr.getReadNegativeStrandFlag()) {
+                    sq = QualityUtils.reverseComplementCompressedQualityArray(sq);
+                }
+                
+                sr.setAttribute("SQ", sq);
+
+                sw.addAlignment(sr);
+            }
+
+            sf.close();
+            sw.close();
+        } catch (IOException e) {
+            System.err.println("There was an error.");
+            System.exit(1);
+        }
+
+        return 0;
+    }
+
+    static String bytesToHexString(final byte[] data) {
+        final char[] chars = new char[2 * data.length];
+        for (int i = 0; i < data.length; i++) {
+            final byte b = data[i];
+            chars[2*i] = toHexDigit((b >> 4) & 0xF);
+            chars[2*i+1] = toHexDigit(b & 0xF);
+        }
+        return new String(chars);
+    }
+    
+    static byte[] hexStringToBytes(final String s)  throws NumberFormatException {
+        if (s.length() % 2 != 0) {
+            throw new NumberFormatException("Hex representation of byte string does not have even number of hex chars: " + s);
+        }
+        final byte[] ret = new byte[s.length() / 2];
+        for (int i = 0; i < ret.length; ++i) {
+            ret[i] = (byte) ((fromHexDigit(s.charAt(i * 2)) << 4) | fromHexDigit(s.charAt(i * 2 + 1)));
+        }
+        return ret;
+    }
+
+    private static char toHexDigit(final int value) {
+        return (char) ((value < 10) ? ('0' + value) : ('A' + value - 10));
+    }
+    
+    private static int fromHexDigit(final char c) throws NumberFormatException {
+        final int ret = Character.digit(c, 16);
+        if (ret == -1) {
+            throw new NumberFormatException("Not a valid hex digit: " + c);
+        }
+        return ret;
+    }
+}
+