If the first base of a read is 'N', and the alignment cigar says every base matches, samtools calls shennanigans. Now I just output an A, but the real way to do this is to modify the cigar string accordingly.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@337 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -50,7 +50,7 @@ public class RepairBadlyCombinedSamFile extends CommandLineProgram {
                         case 'C': newbase = 'G'; break;
                         case 'G': newbase = 'C'; break;
                         case 'T': newbase = 'A'; break;
-                        default: newbase = '.';
+                        default: newbase = 'A'; // hack.  This is so downstream applications don't barf on an ambiguous base 'matching' the reference
                     }
                     newbases[i] = newbase;
                     newquals[i] = quals[bases.length - i - 1];