X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam.h;h=4045684230a7cba886a0ed0fa390db3340866f91;hb=41586185b43962c1ffb3f82e93066a480254aa17;hp=92e7a36da97299d50aaa89e2576fb1242cf1576f;hpb=63e4e54189bc9e7f43852edf865f95e713b93dc4;p=samtools.git

diff --git a/bam.h b/bam.h
index 92e7a36..4045684 100644
--- a/bam.h
+++ b/bam.h
@@ -179,7 +179,6 @@ typedef struct {
   @field  data_len   current length of bam1_t::data
   @field  m_data     maximum length of bam1_t::data
   @field  data       all variable-length data, concatenated; structure: cigar-qname-seq-qual-aux
-  @field  hash       hash table for fast retrieval of tag-value pairs; private
 
   @discussion Notes:
  
@@ -191,7 +190,6 @@ typedef struct {
 	bam1_core_t core;
 	int l_aux, data_len, m_data;
 	uint8_t *data;
-	void *hash;
 } bam1_t;
 
 #define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
@@ -401,8 +399,8 @@ extern "C" {
 	  @abstract  Free the memory allocated for an alignment.
 	  @param  b  pointer to an alignment
 	 */
-#define bam_destroy1(b) do {						\
-		if ((b)->hash) free((b)->data); free(b);	\
+#define bam_destroy1(b) do {		\
+		free((b)->data); free(b);	\
 	} while (0)
 
 	/*!
@@ -608,6 +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.