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sam_header.c File Reference
#include <string.h>
#include <assert.h>
#include "cram/sam_header.h"
#include "cram/string_alloc.h"

Go to the source code of this file.

Macros

#define K(a)   (((a)[0]<<8)|((a)[1]))
 

Functions

void sam_hdr_dump (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_typesam_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_tagsam_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)
 
SAM_hdrsam_hdr_new ()
 
SAM_hdrsam_hdr_parse (const char *hdr, int len)
 
SAM_hdrsam_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_name2ref (SAM_hdr *hdr, const char *ref)
 
SAM_RGsam_hdr_find_rg (SAM_hdr *hdr, const char *rg)
 
int sam_hdr_link_pg (SAM_hdr *hdr)
 
const char * sam_hdr_PG_ID (SAM_hdr *sh, const char *name)
 
int sam_hdr_add_PG (SAM_hdr *sh, const char *name,...)
 
char * stringify_argv (int argc, char *argv[])
 

Macro Definition Documentation

#define K (   a)    (((a)[0]<<8)|((a)[1]))

Definition at line 746 of file sam_header.c.

Function Documentation

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

Adds a single line to a SAM header.

Specify type and one or more key,value pairs, ending with the NULL key. Eg. sam_hdr_add(h, "SQ", "ID", "foo", "LN", "100", NULL).

Returns
Returns 0 on success; -1 on failure

Definition at line 416 of file sam_header.c.

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

Appends a formatted line to an existing SAM header.

Line is a full SAM header record, eg "@SQ\tSN:foo\tLN:100", with optional new-line. If it contains more than 1 line then multiple lines will be added in order.

Len is the length of the text data, or 0 if unknown (in which case it should be null terminated).

Returns
Returns 0 on success; -1 on failure

Definition at line 276 of file sam_header.c.

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

Add an line.

If we wish complete control over this use sam_hdr_add() directly. This function uses that, but attempts to do a lot of tedious house work for you too.

  • It will generate a suitable ID if the supplied one clashes.
  • It will generate multiple records if we have multiple PG chains.

Call it as per sam_hdr_add() with a series of key,value pairs ending in NULL.

Returns
Returns 0 on success; -1 on failure

Definition at line 1147 of file sam_header.c.

void sam_hdr_decr_ref ( SAM_hdr hdr)

Increments a reference count on hdr.

This permits multiple files to share the same header, all calling sam_hdr_free when done, without causing errors for other open files.

If the reference count hits zero then the header is automatically freed. This makes it a synonym for sam_hdr_free().

Definition at line 948 of file sam_header.c.

void sam_hdr_dump ( SAM_hdr hdr)

Definition at line 53 of file sam_header.c.

SAM_hdr* sam_hdr_dup ( SAM_hdr hdr)

Produces a duplicate copy of hdr and returns it.

Returns
Returns NULL on failure

Definition at line 924 of file sam_header.c.

SAM_hdr_type* sam_hdr_find ( SAM_hdr hdr,
char *  type,
char *  ID_key,
char *  ID_value 
)
Returns
Returns the first header item matching 'type'. If ID is non-NULL it checks for the tag ID: and compares against the specified ID.

Returns NULL if no type/ID is found

Definition at line 565 of file sam_header.c.

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

Looks for a specific key in a single sam header line.

If prev is non-NULL it also fills this out with the previous tag, to permit use in key removal. *prev is set to NULL when the tag is the first key in the list. When a tag isn't found, prev (if non NULL) will be the last tag in the existing list.

Returns
Returns the tag pointer on success; NULL on failure

Definition at line 672 of file sam_header.c.

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

As per SAM_hdr_type, but returns a complete line of formatted text for a specific head type/ID combination. If ID is NULL then it returns the first line of the specified type.

The returned string is malloced and should be freed by the calling function with free().

Returns
Returns NULL if no type/ID is found.

Definition at line 635 of file sam_header.c.

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

Looks up a read-group by name and returns a pointer to the start of the associated tag list.

Returns
Returns NULL on failure

Definition at line 1044 of file sam_header.c.

void sam_hdr_free ( SAM_hdr hdr)

Deallocates all storage used by a SAM_hdr struct.

This also decrements the header reference count. If after decrementing it is still non-zero then the header is assumed to be in use by another caller and the free is not done.

This is a synonym for sam_hdr_dec_ref().

Definition at line 960 of file sam_header.c.

void sam_hdr_incr_ref ( SAM_hdr hdr)

Increments a reference count on hdr.

This permits multiple files to share the same header, all calling sam_hdr_free when done, without causing errors for other open files.

Definition at line 936 of file sam_header.c.

int sam_hdr_length ( SAM_hdr hdr)

Returns the current length of the SAM_hdr in text form.

Call sam_hdr_rebuild() first if editing has taken place.

Definition at line 1021 of file sam_header.c.

int sam_hdr_link_pg ( SAM_hdr hdr)

Fixes any PP links in headers.

If the entries are in order then this doesn't need doing, but incase our header is out of order this goes through the sh->pg[] array setting the prev_id field.

Returns
Returns 0 on sucess; -1 on failure (indicating broken PG/PP records)

Definition at line 1065 of file sam_header.c.

int sam_hdr_name2ref ( SAM_hdr hdr,
const char *  ref 
)

Looks up a reference sequence by name and returns the numerical ID.

Returns
Returns -1 if unknown reference.

Definition at line 1033 of file sam_header.c.

SAM_hdr* sam_hdr_new ( void  )

Creates an empty SAM header, ready to be populated.

Returns
Returns a SAM_hdr struct on success (free with sam_hdr_free()) NULL on failure

Definition at line 822 of file sam_header.c.

SAM_hdr* sam_hdr_parse ( const char *  hdr,
int  len 
)

Tokenises a SAM header into a hash table.

Also extracts a few bits on specific data types, such as lines.

Returns
Returns a SAM_hdr struct on success (free with sam_hdr_free()); NULL on failure

Definition at line 891 of file sam_header.c.

const char* sam_hdr_PG_ID ( SAM_hdr sh,
const char *  name 
)

Definition at line 1118 of file sam_header.c.

int sam_hdr_rebuild ( SAM_hdr hdr)

Reconstructs the kstring from the header hash table.

Returns
Returns 0 on success; -1 on failure

Definition at line 753 of file sam_header.c.

char* sam_hdr_str ( SAM_hdr hdr)

Returns the string form of the SAM_hdr.

Call sam_hdr_rebuild() first if editing has taken place.

Definition at line 1025 of file sam_header.c.

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

Adds or updates tag key,value pairs in a header line.

Eg for adding M5 tags to lines or updating sort order for the line (although use the sam_hdr_sort_order() function for HD manipulation, which is a wrapper around this funuction).

Specify multiple key,value pairs ending in NULL.

Returns
Returns 0 on success; -1 on failure

Definition at line 704 of file sam_header.c.

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

Adds a single line to a SAM header.

This is much like sam_hdr_add() but with the additional va_list argument. This is followed by specifying type and one or more key,value pairs, ending with the NULL key.

Eg. sam_hdr_vadd(h, "SQ", args, "ID", "foo", "LN", "100", NULL).

The purpose of the additional va_list parameter is to permit other varargs functions to call this while including their own additional parameters; an example is in sam_hdr_add_PG().

Returns
Returns 0 on success; -1 on failure

Definition at line 422 of file sam_header.c.

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

A function to help with construction of CL tags in records. Takes an argc, argv pair and returns a single space-separated string. This string should be deallocated by the calling function.

Returns
Returns malloced char * on success; NULL on failure

Definition at line 1194 of file sam_header.c.