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Gamgee
You miserable little maggot. I'll stove your head in!
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Gamgee
You miserable little maggot. I'll stove your head in!
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#include <sam_header.h>
Public Member Functions | |
| khash_t (sam_hdr)*h | |
| khash_t (m_s2i)*ref_hash | |
| Maps SQ SN field to sq[] index. More... | |
| khash_t (m_s2i)*rg_hash | |
| Maps RG ID field to rg[] index. More... | |
| khash_t (m_s2i)*pg_hash | |
| Maps PG ID field to pg[] index. More... | |
Public Attributes | |
| kstring_t | text |
| concatenated text, indexed by SAM_hdr_tag More... | |
| string_alloc_t * | str_pool |
| Pool of SAM_hdr_tag->str strings. More... | |
| pool_alloc_t * | type_pool |
| Pool of SAM_hdr_type structs. More... | |
| pool_alloc_t * | tag_pool |
| Pool of SAM_hdr_tag structs. More... | |
| int | nref |
| Number of @SQ lines. More... | |
| SAM_SQ * | ref |
| Array of parsed @SQ lines. More... | |
| int | nrg |
| Number of @RG lines. More... | |
| SAM_RG * | rg |
| Array of parsed @RG lines. More... | |
| int | npg |
| Number of @PG lines. More... | |
| int | npg_end |
| Number of terminating @PG lines. More... | |
| int | npg_end_alloc |
| Size of pg_end field. More... | |
| SAM_PG * | pg |
| Array of parsed @PG lines. More... | |
| int * | pg_end |
| @PG chain termination IDs More... | |
Primary structure for header manipulation
The initial header text is held in the text kstring_t, but is also parsed out into SQ, RG and PG arrays. These have a hash table associated with each to allow lookup by ID or SN fields instead of their numeric array indices. Additionally PG has an array to hold the linked list start points (the last in a PP chain).
Use the appropriate sam_hdr_* functions to edit the header, and call sam_hdr_rebuild() any time the textual form needs to be updated again.
| SAM_hdr::khash_t | ( | sam_hdr | ) |
| SAM_hdr::khash_t | ( | m_s2i | ) |
Maps SQ SN field to sq[] index.
| SAM_hdr::khash_t | ( | m_s2i | ) |
Maps RG ID field to rg[] index.
| SAM_hdr::khash_t | ( | m_s2i | ) |
Maps PG ID field to pg[] index.
| int SAM_hdr::npg |
Number of @PG lines.
| int SAM_hdr::npg_end |
Number of terminating @PG lines.
| int SAM_hdr::npg_end_alloc |
Size of pg_end field.
| int SAM_hdr::nref |
Number of @SQ lines.
| int SAM_hdr::nrg |
Number of @RG lines.
| SAM_PG* SAM_hdr::pg |
Array of parsed @PG lines.
| int* SAM_hdr::pg_end |
@PG chain termination IDs
| SAM_SQ* SAM_hdr::ref |
Array of parsed @SQ lines.
| SAM_RG* SAM_hdr::rg |
Array of parsed @RG lines.
| string_alloc_t* SAM_hdr::str_pool |
Pool of SAM_hdr_tag->str strings.
| pool_alloc_t* SAM_hdr::tag_pool |
Pool of SAM_hdr_tag structs.
| kstring_t SAM_hdr::text |
concatenated text, indexed by SAM_hdr_tag
| pool_alloc_t* SAM_hdr::type_pool |
Pool of SAM_hdr_type structs.
1.8.8