works

[samtools.git] / bam.h

diff --git a/bam.h b/bam.h
index 41f8d95d5b642c5e5f683e34cfbaf12764d1ac78..a3305e3cf4b758edaaeaf201ea4fbc87ab8f919b 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -33,14 +33,14 @@
 
   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 "0.1.12-r924:126"
+#define BAM_VERSION "0.1.18-r580"
 
 #include <stdint.h>
 #include <stdlib.h>
@@ -89,7 +89,7 @@ typedef struct {
        char **target_name;
        uint32_t *target_len;
        void *dict, *hash, *rg2lib;
-       size_t l_text, n_text;
+       uint32_t l_text, n_text;
        char *text;
 } bam_header_t;
 
@@ -134,26 +134,40 @@ 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
+#define BAM_CBACK       9
+
+#define BAM_CIGAR_STR  "MIDNSHP=XB"
+#define BAM_CIGAR_TYPE 0x3C1A7
+
+#define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
+#define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT)
+#define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)])
+#define bam_cigar_gen(l, o) ((l)<<BAM_CIGAR_SHIFT|(o))
+#define bam_cigar_type(o) (BAM_CIGAR_TYPE>>((o)<<1)&3) // bit 1: consume query; bit 2: consume reference
 
 /*! @typedef
   @abstract Structure for core alignment information.
   @field  tid     chromosome ID, defined by bam_header_t
   @field  pos     0-based leftmost coordinate
-  @field  strand  strand; 0 for forward and 1 otherwise
   @field  bin     bin calculated by bam_reg2bin()
   @field  qual    mapping quality
   @field  l_qname length of the query name
@@ -178,13 +192,15 @@ typedef struct {
   @field  l_aux      length of auxiliary data
   @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  data       all variable-length data, concatenated; structure: qname-cigar-seq-qual-aux
 
   @discussion Notes:
  
    1. qname is zero tailing and core.l_qname includes the tailing '\0'.
    2. l_qseq is calculated from the total length of an alignment block
       on reading or from CIGAR.
+   3. cigar data is encoded 4 bytes per CIGAR operation.
+   4. seq is nybble-encoded according to bam_nt16_table.
  */
 typedef struct {
        bam1_core_t core;
@@ -240,7 +256,10 @@ typedef struct __bam_iter_t *bam_iter_t;
   @param  i  The i-th position, 0-based
   @return    4-bit integer representing the base.
  */
-#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
+//#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
+#define bam1_seqi(s, i) ((s)[(i)>>1] >> ((~(i)&1)<<2) & 0xf)
+
+#define bam1_seq_seti(s, i, c) ( (s)[(i)>>1] = ((s)[(i)>>1] & 0xf<<(((i)&1)<<2)) | (c)<<((~(i)&1)<<2) )
 
 /*! @function
   @abstract  Get query sequence and quality
@@ -264,6 +283,14 @@ 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;
+
+extern int bam_no_B;
+
 /*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
 extern unsigned char bam_nt16_table[256];
 
@@ -409,6 +436,8 @@ extern "C" {
         */
        int bam_read1(bamFile fp, bam1_t *b);
 
+       int bam_remove_B(bam1_t *b);
+
        /*!
          @abstract Write an alignment to BAM.
          @param  fp       BAM file handler
@@ -740,4 +769,25 @@ 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' || x == 'F') return 4;
+       else return 0;
+}
+
+/*********************************
+ *** Compatibility with htslib ***
+ *********************************/
+
+typedef bam_header_t bam_hdr_t;
+
+#define bam_get_qname(b) bam1_qname(b)
+#define bam_get_cigar(b) bam1_cigar(b)
+
+#define bam_hdr_read(fp) bam_header_read(fp)
+#define bam_hdr_write(fp, h) bam_header_write(fp, h)
+#define bam_hdr_destroy(fp) bam_header_destroy(fp)
+
 #endif