Represents NGS reads (FASTQ, etc. More...

Data Structures
struct	bioh5g_read_data
	Read data container. More...
Typedefs
typedef struct _bioh5g_reads *	bioh5g_reads
	BioHDF reads collection handle.
typedef struct _bioh5g_reads_iterator *	bioh5g_reads_iterator
	BioHDF reads iterator handle.
typedef struct _bioh5g_reads_properties *	bioh5g_reads_properties
	BioHDF reads creation properties.
Enumerations
enum	bioh5g_reads_type { BASE_SPACE, COLOR_SPACE }
	Describes the data "space" of the reads (base, color, etc.) More...
enum	bioh5g_reads_format { FASTQ_FORMAT, FASTA_FORMAT }
	The text file format for read I/O. More...
Functions
BIOHDF_API biohdf_error	BIOH5Gcheck_reads_presence (biohdf_file file, const char path, int presence)
	Test if a reads collection exists.
BIOHDF_API biohdf_error	BIOH5Gcreate_reads_collection (biohdf_file file, bioh5g_reads_properties properties, const char path, bioh5g_reads reads)
	Create (and open) a new reads collection.
BIOHDF_API biohdf_error	BIOH5Gopen_reads_collection (biohdf_file file, const char path, biohdf_open_mode mode, bioh5g_reads reads)
	Open an existing reads collection.
BIOHDF_API biohdf_error	BIOH5Gclose_reads_collection (bioh5g_reads *reads)
	Close an open reads collection.
BIOHDF_API biohdf_error	BIOH5Gget_reads_count (const bioh5g_reads reads, int64_t *count)
	Get the number of stored reads in a collection.
BIOHDF_API biohdf_error	BIOH5Gcreate_reads_iterator (const bioh5g_reads reads, bioh5g_reads_iterator *iter)
	Create an iterator for a reads collection.
BIOHDF_API biohdf_error	BIOH5Gdestroy_reads_iterator (bioh5g_reads_iterator *iter)
	Destroy an iterator for a reads collection.
BIOHDF_API biohdf_error	BIOH5Gadd_read (const bioh5g_reads reads, const bioh5g_read_data *data)
	Add a read to a collection.
BIOHDF_API biohdf_error	BIOH5Gget_index_of_last_added_read (const bioh5g_reads reads, int64_t *index)
	Get the index of the last read that was added.
BIOHDF_API biohdf_error	BIOH5Gget_next_read (bioh5g_reads_iterator iter, int64_t index, bioh5g_read_data *data)
	Get the next read from a reads collection.
BIOHDF_API biohdf_error	BIOH5Gget_read (const bioh5g_reads reads, int64_t index, bioh5g_read_data **data)
	Given a read index, get the read from a reads collection.
BIOHDF_API biohdf_error	BIOH5Gfree_read (bioh5g_read_data **data)
	Free read data that has been obtained from the library.
BIOHDF_API biohdf_error	BIOH5Gcreate_read_string (const bioh5g_read_data read, bioh5g_reads_format format, char *read_string)
	Create a read string in a given format (FASTQ, etc.)
BIOHDF_API biohdf_error	BIOH5Gwrite_read_to_stream (const bioh5g_read_data read, bioh5g_reads_format format, FILE stream)
	Output a read to a stream in a given format.
Functions: Data Accessors
BIOHDF_API biohdf_error	BIOH5Gcreate_read_data (bioh5g_read_data **data)
	Create a read data container.
BIOHDF_API biohdf_error	BIOH5Gget_read_identifier (bioh5g_read_data data, char *identifier)
	Get the read identifier.
BIOHDF_API biohdf_error	BIOH5Gset_read_identifier (bioh5g_read_data data, char identifier)
	Set the read identifier.
BIOHDF_API biohdf_error	BIOH5Gget_read_sequence (bioh5g_read_data data, char *sequence)
	Get the read sequence.
BIOHDF_API biohdf_error	BIOH5Gset_read_sequence (bioh5g_read_data data, char sequence)
	Set the read sequence.
BIOHDF_API biohdf_error	BIOH5Gget_read_quality_values (bioh5g_read_data data, char *quality_values)
	Get the read quality values.
BIOHDF_API biohdf_error	BIOH5Gset_read_quality_values (bioh5g_read_data data, char quality_values)
	Set the read quality values.
Functions: Collection Creation Properties
BIOHDF_API biohdf_error	BIOH5Gcreate_reads_properties (bioh5g_reads_properties *props)
	Create a reads properties container.
BIOHDF_API biohdf_error	BIOH5Gdestroy_reads_properties (bioh5g_reads_properties *props)
	Destroy a reads properties container.
BIOHDF_API biohdf_error	BIOH5Gset_reads_properties_reads_type (bioh5g_reads_properties props, bioh5g_reads_type reads_type)
	Set reads properties reads type.
BIOHDF_API biohdf_error	BIOH5Gset_reads_properties_chunk_size (bioh5g_reads_properties props, int64_t chunk_size)
	Set reads properties chunk size.
BIOHDF_API biohdf_error	BIOH5Gset_reads_properties_compression_level (bioh5g_reads_properties props, compression_level level)
	Set reads properties compression level.
BIOHDF_API biohdf_error	BIOH5Gset_reads_properties_sequences_scheme (bioh5g_reads_properties props, biohdf_string_storage_scheme scheme)
	Set reads properties sequences storage scheme.
BIOHDF_API biohdf_error	BIOH5Gset_reads_properties_identifiers_scheme (bioh5g_reads_properties props, biohdf_string_storage_scheme scheme)
	Set reads properties identifiers storage scheme.
BIOHDF_API biohdf_error	BIOH5Gset_reads_properties_sequences_length (bioh5g_reads_properties props, size_t length)
	Set reads properties sequences length.
BIOHDF_API biohdf_error	BIOH5Gset_reads_properties_identifiers_length (bioh5g_reads_properties props, size_t length)
	Set reads properties identifiers length.

Detailed Description

Represents NGS reads (FASTQ, etc.

entries).

Enumeration Type Documentation

enum bioh5g_reads_format

The text file format for read I/O.

BioHDF stores the FASTQ quality values verbatim and does no attempt to convert or normalize them between quality score schemes.

Enumerator:

FASTQ_FORMAT	FASTQ format.
FASTA_FORMAT	FASTA (or CSFASTA) format.

enum bioh5g_reads_type

Describes the data "space" of the reads (base, color, etc.)

Reads are stored verbatim and not converted between spaces.

Enumerator:

BASE_SPACE	Base/sequence space reads.
COLOR_SPACE	Color space (SOLiD) reads.

Function Documentation

BIOHDF_API biohdf_error BIOH5Gadd_read	(	const bioh5g_reads	reads,
		const bioh5g_read_data *	data
	)

Add a read to a collection.

Parameters:

reads	A BioHDF reads handle
data	A BioHDF read

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

CHECK*PARAMETERS

CODE

SUCCESS

FAILURE

BIOHDF_API biohdf_error BIOH5Gcheck_reads_presence	(	biohdf_file	file,
		const char *	path,
		int *	presence
	)

Test if a reads collection exists.

This function will return TRUE if a collection of the same type exists at the named location. If any other HDF5 or BioHDF object with that same name exists, TRUE will be returned as well as an error code, the assumption being that Bad Code(tm) that does not check return values will be more likely to attempt to open code (and fail), rather than create things (which my partially succeed, making a mess).

Parameters:

	file	A BioHDF file handle
	path	The BioHDF path to the collection
[out]	presence	TRUE if the collection exists, FALSE if it does not.

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

CHECK*PARAMETERS

CODE

SUCCESS

FAILURE

BIOHDF_API biohdf_error BIOH5Gclose_reads_collection ( bioh5g_reads * reads )

Close an open reads collection.

This function will set the collection handle to NULL after freeing it.

Parameters:

[in,out] reads A BioHDF reads handle

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

CHECK*PARAMETERS

CODE

SUCCESS

FAILURE

BIOHDF_API biohdf_error BIOH5Gcreate_read_string	(	const bioh5g_read_data *	read,
		bioh5g_reads_format	format,
		char **	read_string
	)

Create a read string in a given format (FASTQ, etc.)

The read sequence and identifier must not be NULL. If the format is FASTQ, the quality values must not be NULL. The sequence and quality values must also have the same length for FASTQ output.

Parameters:

	read	The BioHDF read
	format	The format for the output string
[out]	read_string	The output string

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

CHECK*PARAMETERS

CODE

SUCCESS

FAILURE

BIOHDF_API biohdf_error BIOH5Gcreate_reads_collection	(	biohdf_file	file,
		bioh5g_reads_properties	properties,
		const char *	path,
		bioh5g_reads *	reads
	)

Create (and open) a new reads collection.

The collection handle returned by this function will be ready to accept I/O.

Parameters:

	file	A BioHDF file handle
	properties	Collection creation properties
	path	The BioHDF path to the collection
[out]	reads	A BioHDF reads handle

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

CHECK*PARAMETERS

CODE

SUCCESS

FAILURE

BIOHDF_API biohdf_error BIOH5Gcreate_reads_iterator	(	const bioh5g_reads	reads,
		bioh5g_reads_iterator *	iter
	)

Create an iterator for a reads collection.

Parameters:

	reads	A BioHDF reads handle
[out]	iter	An iterator for a reads collection

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

CHECK*PARAMETERS

CODE

SUCCESS

FAILURE

BIOHDF_API biohdf_error BIOH5Gdestroy_reads_iterator ( bioh5g_reads_iterator * iter )

Destroy an iterator for a reads collection.

The iterator is set to NULL as a part of deletion.

Parameters:

[in,out] iter An iterator for a reads collection

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

BIOHDF_API biohdf_error BIOH5Gfree_read ( bioh5g_read_data ** data )

Free read data that has been obtained from the library.

The data is set to NULL as a part of deletion.

Parameters:

[in,out] data The BioHDF read

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

BIOHDF_API biohdf_error BIOH5Gget_index_of_last_added_read	(	const bioh5g_reads	reads,
		int64_t *	index
	)

Get the index of the last read that was added.

Useful for adding SAM lines where a link to a given read must be created.

Parameters:

	reads	A BioHDF reads handle
[out]	index	The index of the last read that was added

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

CHECK*PARAMETERS

CODE

SUCCESS

FAILURE

BIOHDF_API biohdf_error BIOH5Gget_next_read	(	bioh5g_reads_iterator	iter,
		int64_t *	index,
		bioh5g_read_data **	data
	)

Get the next read from a reads collection.

When the iterator has finished traversing the collection, data will be NULL, index will be -1 and the return value will be BIOHDF_NO_ERROR.

Parameters:

	iter	An iterator for a reads collection
[out]	index	The index of this read
[out]	data	The BioHDF read

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

CHECK*PARAMETERS

CODE

SUCCESS

FAILURE

BIOHDF_API biohdf_error BIOH5Gget_read	(	const bioh5g_reads	reads,
		int64_t	index,
		bioh5g_read_data **	data
	)

Given a read index, get the read from a reads collection.

Parameters:

	reads	A BioHDF reads handle
	index	The index of this read
[out]	data	The BioHDF read

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

CHECK*PARAMETERS

CODE

SUCCESS

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BIOHDF_API biohdf_error BIOH5Gget_reads_count	(	const bioh5g_reads	reads,
		int64_t *	count
	)

Get the number of stored reads in a collection.

Parameters:

	reads	A BioHDF reads handle
[out]	count	The number of reads in the collection

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

CHECK*PARAMETERS

CODE

SUCCESS

FAILURE

BIOHDF_API biohdf_error BIOH5Gopen_reads_collection	(	biohdf_file	file,
		const char *	path,
		biohdf_open_mode	mode,
		bioh5g_reads *	reads
	)

Open an existing reads collection.

Parameters:

	file	A BioHDF file handle
	path	The BioHDF path to the collection
	mode	The access mode (read-only \| read-write)
[out]	reads	A BioHDF reads handle

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

CHECK*PARAMETERS

CODE

SUCCESS

FAILURE

BIOHDF_API biohdf_error BIOH5Gwrite_read_to_stream	(	const bioh5g_read_data *	read,
		bioh5g_reads_format	format,
		FILE *	stream
	)

Output a read to a stream in a given format.

This saves you from having to create temp strings that will just be dumped to a stream.

The read sequence and identifier must not be NULL. If the format is FASTQ, the quality values must not be NULL. The sequence and quality values must also have the same length for FASTQ output.

Parameters:

read	The BioHDF read
format	The format for the output string
stream	The output stream (can be STDOUT)

Returns:: BIOHDF_NO_ERROR on success, a BioHDF error code on failure

CHECK*PARAMETERS

CODE

SUCCESS

FAILURE

Data Structures

Typedefs

Enumerations

Functions

Functions: Data Accessors

Functions: Collection Creation Properties

Detailed Description

Enumeration Type Documentation

Function Documentation