c709a48585f153d6aab69081cbc5ff3fee7b6b3f
angie
  Mon Sep 26 15:21:34 2011 -0700
Samtools CIGAR strings have two new opcodes: '=' for exactly matchingbases, 'X' for mismatching bases.  These are more explicit versions of
the 'M' opcode for matching and/or mismatching bases.

diff --git src/inc/bamFile.h src/inc/bamFile.h
index 2c876c7..01ce1e8 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -52,32 +52,32 @@
  * The pSamFile parameter is optional.  If non-NULL it will be filled in, just for
  * the benefit of the callback function, with the open samFile.  */
 
 void bamClose(samfile_t **pSamFile);
 /* Close down a samefile_t */
 
 boolean bamIsRc(const bam1_t *bam);
 /* Return TRUE if alignment is on - strand. */
 
 INLINE int bamUnpackCigarElement(unsigned int packed, char *retOp)
 /* Given an unsigned int containing a number of bases and an offset into an
  * array of BAM-enhanced-CIGAR ASCII characters (operations), store operation 
  * char into *retOp (retOp must not be NULL) and return the number of bases. */
 {
 #ifdef USE_BAM
-// decoding lifted from samtools bam.c bam_format1(), long may it remain stable:
-#define BAM_DOT_C_OPCODE_STRING "MIDNSHP"
+// decoding lifted from samtools bam.c bam_format1_core(), long may it remain stable:
+#define BAM_DOT_C_OPCODE_STRING "MIDNSHP=X"
 int n = packed>>BAM_CIGAR_SHIFT;
 int opcode = packed & BAM_CIGAR_MASK;
 if (opcode >= strlen(BAM_DOT_C_OPCODE_STRING))
     errAbort("bamUnpackCigarElement: unrecognized opcode %d. "
 	     "(I only recognize 0..%lu [" BAM_DOT_C_OPCODE_STRING "])  "
 	     "Perhaps samtools bam.c's bam_format1 encoding changed?  If so, update me.",
 	     opcode, (unsigned long)(strlen(BAM_DOT_C_OPCODE_STRING)-1));
 *retOp = BAM_DOT_C_OPCODE_STRING[opcode];
 return n;
 #else // no USE_BAM
 errAbort(COMPILE_WITH_SAMTOOLS, "bamUnpackCigarElement");
 return 0;
 #endif// USE_BAM
 }