io_add_* commands and io_allocate

A set of Tcl functions exists for allocating new gap4 database structures. Each function allocates the next sequentially numbered structure. In the case of annotations it is preferable to reuse items stored on the annotation free list before allocating new structures.

io_add_reading io

Creates a new reading numbered NumReadings(io)+1. The name, trace_name and trace_type fields are all allocated and written as "uninitialised". No other items are allocated and all other fields are set to 0. The database num_readings and Nreadings fields are also updated. Returns the new reading number.

io_add_contig io

Creates a new contig numbered NumContigs(io)+1. The contig structure fields are all set to 0. The contig_order array is updated with the new contig as the last (right most) one. The database num_contigs and Ncontigs fields are also updated. Returns the new contig number.

io_add_annotation io

Creates a new annotation. The structure fields initialised to 0. The database Nannotations field is also updated. Returns the new annotation number.

io_add_template io

Creates a new template. The template name is allocated and set to "uninitialised"; strand is set to 1; vector is set to the "unknown" vector (1) if present or creates a new blank vector to reference; and the clone, insert_size_min and insert_size_max are set to 0. The database Ntemplates field is also updated. Returns the new template number.

io_add_vector io

Creates a new vector. The vector name is allocated and set to "uninitialised". The level is set to 0. The database Nvectors field is also updated. Returns the new vector number.

io_add_clone io

Creates a new clone. The clone name is allocated and set to "uninitialised". The vector is set to the "unknown" vector(1) or creates a new blank vector to reference. The database Nclones field is also updated. Returns the new template number.

io_allocate io type

Allocates a new record of the specified type. Currently only the text type is supported. The new record number is returned.

Utility Commands

• db_info
• edid_to_editor
• add_tags
• get_read_names