sam_header.h

Go to the documentation of this file.

/*
Copyright (c) 2013-2014 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>

Redistribution and use in source and binary forms, with or without 
modification, are permitted provided that the following conditions are met:

   1. Redistributions of source code must retain the above copyright notice, 
this list of conditions and the following disclaimer.

   2. Redistributions in binary form must reproduce the above copyright notice, 
this list of conditions and the following disclaimer in the documentation 
and/or other materials provided with the distribution.

   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
Institute nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/

/*
 * TODO.
 *
 * - Sort order (parse to struct, enum type, updating funcs)
 * - Removal of lines.
 * - Updating of lines
 */

#ifndef _SAM_HDR_H_
#define _SAM_HDR_H_

#ifdef __cplusplus
extern "C" {
#endif

#ifdef HAVE_CONFIG_H
#include "io_lib_config.h"
#endif

#include <stdarg.h>

#include "cram/string_alloc.h"
#include "cram/pooled_alloc.h"

#include "htslib/khash.h"
#include "htslib/kstring.h"

// For structure assignment. Eg kstring_t s = KS_INITIALIZER;
#define KS_INITIALIZER {0,0,0}

// For initialisation elsewhere. Eg KS_INIT(x->str);
#define KS_INIT(ks) ((ks)->l = 0, (ks)->m = 0, (ks)->s = NULL)

// Frees the string subfield only. Assumes 's' itself is static.
#define KS_FREE(ks) do { if ((ks)->s) free((ks)->s); } while(0)

/*
 * Proposed new SAM header parsing

1 @SQ ID:foo LN:100
2 @SQ ID:bar LN:200
3 @SQ ID:ram LN:300 UR:xyz
4 @RG ID:r ...
5 @RG ID:s ...

Hash table for 2-char @keys without dup entries.
If dup lines, we form a circular linked list. Ie hash keys = {RG, SQ}.

HASH("SQ")--\
            |
    (3) <-> 1 <-> 2 <-> 3 <-> (1)

HASH("RG")--\
            |
    (5) <-> 4 <-> 5 <-> (4)

Items stored in the hash values also form their own linked lists:
Ie SQ->ID(foo)->LN(100)
   SQ->ID(bar)->LN(200)
   SQ->ID(ram)->LN(300)->UR(xyz)
   RG->ID(r)
 */

typedef struct SAM_hdr_tag_s {
    struct SAM_hdr_tag_s *next;
    char *str;
    int   len;
} SAM_hdr_tag;

typedef struct SAM_hdr_item_s {
    struct SAM_hdr_item_s *next; // cirular
    struct SAM_hdr_item_s *prev;
    SAM_hdr_tag *tag;            // first tag
    int order;                   // 0 upwards
} SAM_hdr_type;

typedef struct {
    char *name;
    uint32_t len;
    SAM_hdr_type *ty;
    SAM_hdr_tag  *tag;
} SAM_SQ;

typedef struct {
    char *name;
    SAM_hdr_type *ty;
    SAM_hdr_tag  *tag;
    int name_len;
    int id;           // numerical ID
} SAM_RG;

typedef struct {
    char *name;
    SAM_hdr_type *ty;
    SAM_hdr_tag  *tag;
    int name_len;
    int id;           // numerical ID
    int prev_id;      // -1 if none
} SAM_PG;

KHASH_MAP_INIT_INT(sam_hdr, SAM_hdr_type*)
KHASH_MAP_INIT_STR(m_s2i, int)

typedef struct {
    kstring_t text;           
    khash_t(sam_hdr) *h;
    string_alloc_t *str_pool; 
    pool_alloc_t   *type_pool;
    pool_alloc_t   *tag_pool; 

    // @SQ lines / references
    int nref;                 
    SAM_SQ *ref;              
    khash_t(m_s2i) *ref_hash; 

    // @RG lines / read-groups
    int nrg;                  
    SAM_RG *rg;               
    khash_t(m_s2i) *rg_hash;  

    // @PG lines / programs
    int npg;                  
    int npg_end;              
    int npg_end_alloc;        
    SAM_PG *pg;         
    khash_t(m_s2i) *pg_hash;  
    int *pg_end;              

    // @cond internal
    char ID_buf[1024];  // temporary buffer
    int ID_cnt;
    int ref_count;      // number of uses of this SAM_hdr
    // @endcond
} SAM_hdr;

SAM_hdr *sam_hdr_new(void);

SAM_hdr *sam_hdr_parse_(const char *hdr, int len);


SAM_hdr *sam_hdr_dup(SAM_hdr *hdr);


void sam_hdr_incr_ref(SAM_hdr *hdr);


void sam_hdr_decr_ref(SAM_hdr *hdr);


void sam_hdr_free(SAM_hdr *hdr);

int sam_hdr_length(SAM_hdr *hdr);

char *sam_hdr_str(SAM_hdr *hdr);

int sam_hdr_add_lines(SAM_hdr *sh, const char *lines, int len);

int sam_hdr_add(SAM_hdr *sh, const char *type, ...);

int sam_hdr_vadd(SAM_hdr *sh, const char *type, va_list ap, ...);

SAM_hdr_type *sam_hdr_find(SAM_hdr *hdr, char *type,
         char *ID_key, char *ID_value);

char *sam_hdr_find_line(SAM_hdr *hdr, char *type,
      char *ID_key, char *ID_value);

SAM_hdr_tag *sam_hdr_find_key(SAM_hdr *sh,
            SAM_hdr_type *type,
            char *key,
            SAM_hdr_tag **prev);

int sam_hdr_update(SAM_hdr *hdr, SAM_hdr_type *type, ...);

int sam_hdr_rebuild(SAM_hdr *hdr);

int sam_hdr_name2ref(SAM_hdr *hdr, const char *ref);

SAM_RG *sam_hdr_find_rg(SAM_hdr *hdr, const char *rg);

int sam_hdr_link_pg(SAM_hdr *hdr);


int sam_hdr_add_PG(SAM_hdr *sh, const char *name, ...);

char *stringify_argv(int argc, char *argv[]);

#ifdef __cplusplus
}
#endif

#endif /* _SAM_HDR_H_ */