H/profiledist.h File Reference

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Functions
float	profile_edit_distance (const float *T1, const float *T2)
	Align the 2 probability profiles T1, T2 .
float *	Make_bp_profile_bppm (FLT_OR_DBL *bppm, int length)
	condense pair probability matrix into a vector containing probabilities for upstream paired, downstream paired and unpaired.
void	print_bppm (const float *T)
	print string representation of probability profile
void	free_profile (float *T)
	free space allocated in Make_bp_profile
float *	Make_bp_profile (int length)

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Detailed Description

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Function Documentation

float profile_edit_distance	(	const float *	T1,
		const float *	T2
	)

Align the 2 probability profiles T1, T2
.

This is like a Needleman-Wunsch alignment, we should really use affine gap-costs ala Gotoh

float* Make_bp_profile_bppm	(	FLT_OR_DBL *	bppm,
		int	length
	)

condense pair probability matrix into a vector containing probabilities for upstream paired, downstream paired and unpaired.

This resulting probability profile is used as input for profile_edit_distance

Parameters:

	bppm	A pointer to the base pair probability matrix
	length	The length of the sequence

Returns:

The bp profile

void free_profile

(

float *

T

)

free space allocated in Make_bp_profile

Backward compatibility only. You can just use plain free()

float* Make_bp_profile

(

int

length

)

Note:

This function is NOT threadsafe

See also:

Make_bp_profile_bppm()

Deprecated:

This function is deprecated and will be removed soon! See Make_bp_profile_bppm() for a replacement