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/lib/bamFile.c src/lib/bamFile.c
index 1ef3588..94da58a 100644
--- src/lib/bamFile.c
+++ src/lib/bamFile.c
@@ -254,30 +254,36 @@
 {
 unsigned int *cigarPacked = bam1_cigar(bam);
 const bam1_core_t *core = &bam->core;
 int i;
 for (i = 0;  i < core->n_cigar;  i++)
     {
     char op;
     int n = bamUnpackCigarElement(cigarPacked[i], &op);
     if (i > 0)
 	printf(", ");
     switch (op)
 	{
 	case 'M': // match or mismatch (gapless aligned block)
 	    printf("%d (mis)Match", n);
 	    break;
+	case '=': // match
+	    printf("%d Match", n);
+	    break;
+	case 'X': // mismatch
+	    printf("%d Mismatch", n);
+	    break;
 	case 'I': // inserted in query
 	    printf("%d Insertion", n);
 	    break;
 	case 'S': // skipped query bases at beginning or end ("soft clipping")
 	    printf("%d Skipped", n);
 	    break;
 	case 'D': // deleted from query
 	    printf("%d Deletion", n);
 	    break;
 	case 'N': // long deletion from query (intron as opposed to small del)
 	    printf("%d deletioN", n);
 	    break;
 	case 'H': // skipped query bases not stored in record's query sequence ("hard clipping")
 	    printf("%d Hard clipped query", n);
 	    break;
@@ -328,30 +334,32 @@
 int bamGetTargetLength(const bam1_t *bam)
 /* Tally up the alignment's length on the reference sequence from
  * bam's packed-int CIGAR representation. */
 {
 unsigned int *cigarPacked = bam1_cigar(bam);
 const bam1_core_t *core = &bam->core;
 int tLength=0;
 int i;
 for (i = 0;  i < core->n_cigar;  i++)
     {
     char op;
     int n = bamUnpackCigarElement(cigarPacked[i], &op);
     switch (op)
 	{
 	case 'M': // match or mismatch (gapless aligned block)
+	case '=': // match
+	case 'X': // mismatch
 	    tLength += n;
 	    break;
 	case 'I': // inserted in query
 	    break;
 	case 'D': // deleted from query
 	case 'N': // long deletion from query (intron as opposed to small del)
 	    tLength += n;
 	    break;
 	case 'S': // skipped query bases at beginning or end ("soft clipping")
 	case 'H': // skipped query bases not stored in record's query sequence ("hard clipping")
 	case 'P': // P="silent deletion from padded reference sequence" -- ignore these.
 	    break;
 	default:
 	    errAbort("bamGetTargetLength: unrecognized CIGAR op %c -- update me", op);
 	}