mrf.c File Reference

Module to parse mapped read format. More...

#include "log.h"
#include "format.h"
#include "linestream.h"
#include "common.h"
#include "bits.h"
#include "mrf.h"

Go to the source code of this file.

Functions
int	getReadLength (MrfRead *currRead)
	Compute and return the length of the read.
void	mrf_addNewColumnType (char *columnName)
	Add a new column type.
void	mrf_deInit (void)
	Deinitialize the mrf module.
void	mrf_init (char *fileName)
	Initialize the module module from a file.
void	mrf_initFromPipe (char *cmd)
	Initialize the module from a command.
MrfEntry *	mrf_nextEntry (void)
	Returns a pointer to next MrfEntry.
Array	mrf_parse (void)
	Returns an Array of MrfEntries.
char *	mrf_writeEntry (MrfEntry *currEntry)
	Write an MrfEntry.
char *	mrf_writeHeader (void)
	Write the mrf header preceeded by comments, if any.

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Detailed Description

Module to parse mapped read format.

Definition in file mrf.c.

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Function Documentation

void mrf_addNewColumnType

(

char *

columnName

)

Add a new column type.

Parameters:

[in]

columnName

Name of the new column

Definition at line 123 of file mrf.c.

void mrf_init

(

char *

fileName

)

Initialize the module module from a file.

Parameters:

[in]

fileName

File name, use "-" to denote stdin

Definition at line 101 of file mrf.c.

void mrf_initFromPipe

(

char *

cmd

)

Initialize the module from a command.

Parameters:

[in]

cmd

command to be executed

Definition at line 112 of file mrf.c.

MrfEntry* mrf_nextEntry

(

void

)

Returns a pointer to next MrfEntry.

Precondition:

The module has been initialized using mrf_init().

Definition at line 311 of file mrf.c.

Array mrf_parse

(

void

)

Returns an Array of MrfEntries.

Precondition:

The module has been initialized using mrf_init().

Note:

The memory belongs to this routine.

Definition at line 323 of file mrf.c.

char* mrf_writeEntry

(

MrfEntry *

currEntry

)

Write an MrfEntry.

Precondition:

The module has been initialized using mrf_init().

Definition at line 406 of file mrf.c.

char* mrf_writeHeader

(

void

)

Write the mrf header preceeded by comments, if any.

Precondition:

The module has been initialized using mrf_init().

Definition at line 368 of file mrf.c.