* samtools-0.1.4-8 (r338)

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index b607f96cc80ec4f3100380b051cb87a54675ac68..c635e72767e31852ddf8b2759a3d9493d13e58bc 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -100,7 +100,7 @@ typedef struct {
        int32_t n_targets;
        char **target_name;
        uint32_t *target_len;
-       void *hash;
+       void *hash, *rg2lib;
        int l_text;
        char *text;
 } bam_header_t;
@@ -315,8 +315,18 @@ extern "C" {
         */
        bam_header_t *sam_header_read2(const char *fn_list);
 
+       bam_header_t *sam_header_read(tamFile fp);
+       int sam_header_parse(bam_header_t *h);
+       int sam_header_parse_rg(bam_header_t *h);
+
 #define sam_write1(header, b) bam_view1(header, b)
 
+       int bam_strmap_put(void *strmap, const char *rg, const char *lib);
+       const char *bam_strmap_get(const void *strmap, const char *rg);
+       void *bam_strmap_dup(const void*);
+       void *bam_strmap_init();
+       void bam_strmap_destroy(void *strmap);
+
        /*!
          @abstract Initialize a header structure.
          @return   the pointer to the header structure
@@ -404,11 +414,12 @@ extern "C" {
        } while (0)
 
        /*!
-         @abstract       Print an alignment to the standard output in TAM format.
+         @abstract       Format a BAM record in the SAM format
          @param  header  pointer to the header structure
          @param  b       alignment to print
+         @return         a pointer to the SAM string
         */
-       void bam_view1(const bam_header_t *header, const bam1_t *b);
+       char *bam_format1(const bam_header_t *header, const bam1_t *b);
 
        /*!
          @abstract    Merge multiple sorted BAM.
@@ -511,17 +522,6 @@ extern "C" {
         */
        int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
 
-       /*!
-         @abstract         A more convenient interface to bam_plbuf_push()
-         @param  fp        BAM file handler
-         @param  func      user defined function
-         @param  func_data user provided data
-
-         @discussion The file position indicator must be placed right
-         before the start of an alignment. See also bam_plbuf_push().
-        */
-       int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);
-
        struct __bam_lplbuf_t;
        typedef struct __bam_lplbuf_t bam_lplbuf_t;
 
@@ -599,13 +599,43 @@ extern "C" {
        void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
 
        void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
-       uint8_t *bam_aux_get(bam1_t *b, const char tag[2]);
+       // uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get()
+       uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]);
        int32_t bam_aux2i(const uint8_t *s);
        float bam_aux2f(const uint8_t *s);
        double bam_aux2d(const uint8_t *s);
        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.