A quick hack to ensure that the sequence, qualities, and secondary qualities are in accordance with the strand flag.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@331 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/fourbasecaller/RepairBadlyCombinedSamFile.java

@@ -0,0 +1,70 @@
+package org.broadinstitute.sting.playground.fourbasecaller;
+
+import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
+import org.broadinstitute.sting.utils.QualityUtils;
+
+import java.io.File;
+
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMFileWriterFactory;
+
+public class RepairBadlyCombinedSamFile extends CommandLineProgram {
+    public static RepairBadlyCombinedSamFile Instance = null;
+
+    public File ASAM;
+    public File OSAM;
+
+    public static void main(String[] argv) {
+        Instance = new RepairBadlyCombinedSamFile();
+        start(Instance, argv);
+    }
+
+    protected void setupArgs() {
+        m_parser.addRequiredArg("aligned_sam",   "A", "Second input SAM file", "ASAM");
+        m_parser.addRequiredArg("sam_out",       "O", "Output SAM file",       "OSAM");
+    }
+
+    protected int execute() {
+        SAMFileReader asamr = new SAMFileReader(ASAM);
+        asamr.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
+
+        SAMFileWriter osamw = new SAMFileWriterFactory().makeSAMOrBAMWriter(asamr.getFileHeader(), false, OSAM);
+
+
+        for (SAMRecord samRecord : asamr) {
+            if (samRecord.getReadNegativeStrandFlag()) {
+                byte[] bases = samRecord.getReadBases();
+                byte[] quals = samRecord.getBaseQualities();
+                byte[] sq    = (byte[]) samRecord.getAttribute("SQ");
+
+                byte[] newbases = new byte[bases.length];
+                byte[] newquals = new byte[bases.length];
+                byte[] newsq    = new byte[bases.length];
+
+                for (int i = 0; i < bases.length; i++) {
+                    byte newbase;
+                    switch (bases[bases.length - i - 1]) {
+                        case 'A': newbase = 'T'; break;
+                        case 'C': newbase = 'G'; break;
+                        case 'G': newbase = 'C'; break;
+                        case 'T': newbase = 'A'; break;
+                        default: newbase = '.';
+                    }
+                    newbases[i] = newbase;
+                    newquals[i] = quals[bases.length - i - 1];
+                    newsq[i]    = QualityUtils.complementCompressedQuality(newquals[bases.length - i - 1]);
+                }
+
+                samRecord.setReadBases(newbases);
+                samRecord.setBaseQualities(newquals);
+                samRecord.setAttribute("SQ", newsq);
+            }
+            
+            osamw.addAlignment(samRecord);
+        }
+
+        return 0;
+    }
+}