* samtools-0.1.3-7 (r246)

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index b607f96cc80ec4f3100380b051cb87a54675ac68..4045684230a7cba886a0ed0fa390db3340866f91 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -606,6 +606,35 @@ extern "C" {
        char bam_aux2A(const uint8_t *s);
        char *bam_aux2Z(const uint8_t *s);
 
+       /*!
+        @abstract     Get the color encoding the previous and current base
+        @param b      pointer to an alignment
+        @param i      The i-th position, 0-based
+        @return       color
+
+        @discussion   Returns 0 no color information is found.
+        */
+       char bam_aux_getCSi(bam1_t *b, int i);
+
+       /*!
+        @abstract     Get the color quality of the color encoding the previous and current base
+        @param b      pointer to an alignment
+        @param i      The i-th position, 0-based
+        @return       color quality
+
+        @discussion   Returns 0 no color information is found.
+        */
+       char bam_aux_getCQi(bam1_t *b, int i);
+
+       /*!
+        @abstract     Get the color error profile at the give position    
+        @param b      pointer to an alignment
+        @return       the original color if the color was an error, '-' (dash) otherwise
+
+        @discussion   Returns 0 no color information is found.
+        */
+       char bam_aux_getCEi(bam1_t *b, int i);
+
        /*!  
          @abstract Calculate the rightmost coordinate of an alignment on the
          reference genome.