Starting the work on next package update.

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index 87e3de326fea144e10323ad8229309b6b31136a4..346c750c8c807c44ea32804eeb1bb93411d0b71a 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -40,7 +40,7 @@
   @copyright Genome Research Ltd.
  */
 
-#define BAM_VERSION "0.1.15 (r949:203)"
+#define BAM_VERSION "0.1.18 (r982:295)"
 
 #include <stdint.h>
 #include <stdlib.h>
@@ -134,20 +134,25 @@ typedef struct {
 /*
   CIGAR operations.
  */
-/*! @abstract CIGAR: match */
+/*! @abstract CIGAR: M = match or mismatch*/
 #define BAM_CMATCH      0
-/*! @abstract CIGAR: insertion to the reference */
+/*! @abstract CIGAR: I = insertion to the reference */
 #define BAM_CINS        1
-/*! @abstract CIGAR: deletion from the reference */
+/*! @abstract CIGAR: D = deletion from the reference */
 #define BAM_CDEL        2
-/*! @abstract CIGAR: skip on the reference (e.g. spliced alignment) */
+/*! @abstract CIGAR: N = skip on the reference (e.g. spliced alignment) */
 #define BAM_CREF_SKIP   3
-/*! @abstract CIGAR: clip on the read with clipped sequence present in qseq */
+/*! @abstract CIGAR: S = clip on the read with clipped sequence
+  present in qseq */
 #define BAM_CSOFT_CLIP  4
-/*! @abstract CIGAR: clip on the read with clipped sequence trimmed off */
+/*! @abstract CIGAR: H = clip on the read with clipped sequence trimmed off */
 #define BAM_CHARD_CLIP  5
-/*! @abstract CIGAR: padding */
+/*! @abstract CIGAR: P = padding */
 #define BAM_CPAD        6
+/*! @abstract CIGAR: equals = match */
+#define BAM_CEQUAL        7
+/*! @abstract CIGAR: X = mismatch */
+#define BAM_CDIFF        8
 
 /*! @typedef
   @abstract Structure for core alignment information.
@@ -746,4 +751,13 @@ static inline bam1_t *bam_dup1(const bam1_t *src)
        return b;
 }
 
+static inline int bam_aux_type2size(int x)
+{
+       if (x == 'C' || x == 'c' || x == 'A') return 1;
+       else if (x == 'S' || x == 's') return 2;
+       else if (x == 'I' || x == 'i' || x == 'f') return 4;
+       else return 0;
+}
+
+
 #endif