Release samtools-0.1.17

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index 4594ac477e33be12fc023ac0e18c2cfe3dc7962e..246b020d679a07f073cfbae8dc40a8d57b501d25 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -33,13 +33,15 @@
 
   BAM library provides I/O and various operations on manipulating files
   in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map)
-  format. It now supports importing from or exporting to TAM, sorting,
+  format. It now supports importing from or exporting to SAM, sorting,
   merging, generating pileup, and quickly retrieval of reads overlapped
   with a specified region.
 
   @copyright Genome Research Ltd.
  */
 
+#define BAM_VERSION "0.1.17 (r973:277)"
+
 #include <stdint.h>
 #include <stdlib.h>
 #include <string.h>
@@ -262,6 +264,12 @@ typedef struct __bam_iter_t *bam_iter_t;
  */
 extern int bam_is_be;
 
+/*!
+  @abstract Verbose level between 0 and 3; 0 is supposed to disable all
+  debugging information, though this may not have been implemented.
+ */
+extern int bam_verbose;
+
 /*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
 extern unsigned char bam_nt16_table[256];
 
@@ -495,7 +503,7 @@ extern "C" {
                bam1_t *b;
                int32_t qpos;
                int indel, level;
-               uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1;
+               uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1, aux:28;
        } bam_pileup1_t;
 
        typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);
@@ -738,4 +746,13 @@ 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