intervalFind.h File Reference

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Data Structures
struct	Interval
	Interval. More...
struct	SubInterval
	SubInterval. More...
Functions
void	intervalFind_addIntervalsToSearchSpace (char *fileName, int source)
	Add intervals to the search space.
Array	intervalFind_getAllIntervals (void)
	Retrieve all the intervals that have been added to the search space.
int	intervalFind_getNumberOfIntervals (void)
	Get the total number of intervals that have been added to the search space.
Array	intervalFind_getOverlappingIntervals (char *chromosome, int start, int end)
	Get the intervals that overlap with the query interval.

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Detailed Description

Author:

Lukas Habegger (lukas.habegger@yale.edu)

Definition in file intervalFind.h.

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Function Documentation

void intervalFind_addIntervalsToSearchSpace	(	char *	fileName,
		int	source
	)

Add intervals to the search space.

Parameters:

[in]

fileName

File name of the file that contains the interval and subintervals to search against. This tab-delimited file must have the following format:

   Column:   Description:
   1         Name of the interval
   2         Chromosome 
   3         Strand
   4         Interval start
   5         Interval end
   6         Number of subintervals
   7         Subinterval starts (comma-delimited)
   8         Subinterval end (comma-delimited)
   

This is an example:

   uc001aaw.1      chr1    +       357521  358460  1       357521  358460
   uc001aax.1      chr1    +       410068  411702  3       410068,410854,411258    410159,411121,411702
   uc001aay.1      chr1    -       552622  554252  3       552622,553203,554161    553066,553466,554252
   uc001aaz.1      chr1    +       556324  557910  1       556324  557910
   uc001aba.1      chr1    +       558011  558705  1       558011  558705
   

Note in this example the intervals represent a transcripts, while the subintervals denote exons.

Parameters:

[in]

source

An integer that specifies the source. This is useful when multiple files are used.

Definition at line 107 of file intervalFind.c.

Array intervalFind_getAllIntervals

(

void

)

Retrieve all the intervals that have been added to the search space.

Returns:

An Array of type Interval.

Note:

This function generates a copy of the intervals Array. The user can modify the returned Array.

Precondition:

Intervals were added to the search space using intervalFind_addIntervalsToSearchSpace().

Definition at line 54 of file intervalFind.c.

int intervalFind_getNumberOfIntervals

(

void

)

Get the total number of intervals that have been added to the search space.

Returns:

The total number of intervals in the search space.

Precondition:

Intervals were added to the search space using intervalFind_addIntervalsToSearchSpace()

Definition at line 40 of file intervalFind.c.

Array intervalFind_getOverlappingIntervals	(	char *	chromosome,
		int	start,
		int	end
	)

Get the intervals that overlap with the query interval.

Parameters:

[in]	chromosome	Chromosome of the query interval
[in]	start	Start of the query interval
[in]	end	End of the query interval

Returns:

An Array of Interval pointers. If no overlapping intervals are found, then an empty Array is returned

Precondition:

Intervals were added to the search space, see intervalFind_addIntervalsToSearchSpace()

Definition at line 252 of file intervalFind.c.