gtf.h File Reference

Header file for the GTF module. More...

#include <Python.h>
#include <stdlib.h>
#include "../classes/GtfDict/GtfDict.h"
#include "../common.h"

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Macros
#define	DEFAULT_ATTR_SIZE    64
	How many attributes should be allocated by default.
#define	CORE_FIELD_COUNT   8
	The number of core fields in a GTF line.
#define	GFF3_FASTA_HEADER   "##FASTA"

Enumerations
enum	gtfFields {   SEQNAME = 0 , SOURCE = 1 , FEATURE = 2 , START = 3 ,   END = 4 , SCORE = 5 , REVERSE = 6 , FRAME = 7 ,   ATTRIBUTES = 8 }
	Enum containing the fields that a GTF line can contain. More...

Functions
GtfDict *	createGTFdict (const occurrence_t *restrict token, PyObject *attr_tp, hashmap_t *restrict attr_keys, hashmap_t *restrict attr_vals)
	Parses a singular GTF line into a Python dict.
bool	validGTFLineToParse (const char *line, size_t len)
	Determines if the provided line is a valid GTF line that can be parsed safely.
char *	write_owned (char *restrict buf, size_t *restrict len, size_t *alloc, const char *restrict in, size_t inLen)
	Writes a string to the output buffer, reallocing if necessary.
char *	GtfDict_dump (GtfDict *restrict const self, char *restrict in, size_t *restrict len, size_t *restrict alloc)
	Dumps the contents of a GtfDict to a string.
int	GtfDict_as_annotation (PyObject *restrict object, long *restrict start, long *restrict end)
	Converts a GtfDict or mapping object to an annotation.

Variables
const char *	keywords [CORE_FIELD_COUNT]
	Array containing the keywords of the GTF fields.
const uint8_t	keyword_sizes [CORE_FIELD_COUNT]
	Array containing the sizes of the keywords.
const PyTypeObject *	keyword_types [CORE_FIELD_COUNT]
	Array containing the types of the keywords.

Detailed Description

Header file for the GTF module.

Macro Definition Documentation

GFF3_FASTA_HEADER

#define GFF3_FASTA_HEADER   "##FASTA"

Function Documentation

GtfDict_as_annotation()

int GtfDict_as_annotation	(	PyObject *restrict	object,
		long *restrict	start,
		long *restrict	end
	)

Converts a GtfDict or mapping object to an annotation.

Parameters

object	the object to convert
start	a pointer to the start of the annotation
end	a pointer to the end of the annotation

Returns

0 on success, -1 on failure

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GtfDict_dump()

char * GtfDict_dump	(	GtfDict *restrict const	self,
		char *restrict	in,
		size_t *restrict	len,
		size_t *restrict	alloc
	)

Dumps the contents of a GtfDict to a string.

Parameters

self	the GtfDict to dump
in	the input buffer to write to
len	a pointer to the length of the output string
alloc	a pointer to the size of the allocated output string

Returns

the output buffer

Note

if no allocation is done, in is returned unchanged

Warning

this function takes ownership of in and will free it if necessary

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write_owned()

char * write_owned	(	char *restrict	buf,
		size_t *restrict	len,
		size_t *	alloc,
		const char *restrict	in,
		size_t	inLen
	)

Writes a string to the output buffer, reallocing if necessary.

Parameters

buf	The output buffer
len	The length of the output buffer
alloc	a pointer to the size of the allocated output buffer
in	The string to write
inLen	The length of the string to write

Returns

The updated output buffer

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