sim4b1.h File Reference

Go to the source code of this file.

Functions
void	link_to_data_list (Pointer, ValNodePtr *, ValNodePtr *)
void	ValNodeFreeData (ValNodePtr)
int	good_ratio (int)
void	flip_list (Exon **, Exon **)
void	free_list (Exon *)
void	free_table (void)
void	free_align (edit_script_list *)
void	complement_exons (Exon **, int, int)
void	print_exons (const Exon *)
void	print_pipmaker_exons (Exon *, edit_script_list *, const char *, int, int, int, int, const char *, const char *, int)
void	bld_table (const char *s, int len, int in_W, int type)
edit_script_list *	SIM4 (const kzseq &so1, const kzseq &so2, const sim4Args &cmd, int *, Exon **, sim4_stats_t *)
Variables
const char *	seq1
const char *	seq2
int	M
int	N
int	encoding [NACHARS]
comparisonType	file_type
coords	last_GT
coords	last_CT
coords	last_AG
coords	last_AC
sim4Args	command

---

Function Documentation

void bld_table	(	const char *	s,
		int	len,
		int	in_W,
		int	type
	)

References add_word(), ckalloc(), hash_node::ecode, encoding, HASH_SIZE, INIT, L, mask, NACHARS, next_pos, PERM, and pnext_pos.

Referenced by exon_cores(), and main().

void complement_exons	(	Exon **	,
		int	,
		int
	)

References fatal(), flip_list(), exon::from1, exon::from2, exon::next_exon, exon::ori, exon::to1, and exon::to2.

Referenced by main().

void flip_list	(	Exon **	,
		Exon **
	)

References exon::next_exon.

Referenced by complement_exons(), print_pipmaker_exons(), and SIM4().

void free_align

(

edit_script_list *

)

References Free_script(), edit_script_list::next_script, and edit_script_list::script.

Referenced by main(), and SIM4().

void free_list

(

Exon *

)

References exon::next_exon.

Referenced by main(), and SIM4().

void free_table

(

void

)

References hash_node::link, and pnext_pos.

Referenced by main().

int good_ratio

(

int

)

References sim4Args::cutoff, P, and W.

Referenced by extend_bw(), extend_fw(), Xextend_bw(), and Xextend_fw().

void link_to_data_list	(	Pointer	,
		ValNodePtr *	,
		ValNodePtr *
	)

References ckalloc(), ValNode::data, and ValNode::next.

Referenced by greedy(), Xextend_bw(), and Xextend_fw().

void print_exons

(

const Exon *

)

References EST_GEN, fatal(), file_type, exon::from1, exon::from2, exon::match, exon::next_exon, exon::ori, exon::to1, and exon::to2.

Referenced by main().

void print_pipmaker_exons	(	Exon *	,
		edit_script_list *	,
		const char *	,
		int	,
		int	,
		int	,
		int	,
		const char *	,
		const char *	,
		int
	)

References BWD, check_consistency_intron_ori(), dispatch_find_ends(), fatal(), flip_list(), FREE_BOTH_ENDS, FREE_END, FREE_START, exon::from1, FWD, exon::next_exon, OK, exon::to1, and while().

Referenced by main().

edit_script_list* SIM4	(	const kzseq &	so1,
		const kzseq &	so2,
		const sim4Args &	cmd,
		int *	,
		Exon **	,
		sim4_stats_t *
	)

References sim4Args::acc_flag, sim4Args::ali_flag, bmatch(), sim4Args::C, C_score, compact_list(), END_SIG, exon_cores(), EXTEND_BW, EXTEND_FW, FALSE, find_previous(), flip_list(), fmatch(), free_align(), free_list(), free_msps(), exon::from1, exon::from2, G_score, get_match_quality(), get_stats(), get_sync_flag(), greedy(), I, sim4Args::K, exon::length, M, max, MAX_GRINIT, merge(), min, N, new_exon(), exon::next_exon, sim4_stats::nmatches, numMSPs, exon::ori, P, PERM, pluri_align(), sim4Args::poly_flag, kzseq::polyATsize(), coordinates::pos1, coordinates::pos2, relink(), resolve_overlap(), seq1, seq2, kzseq::seqchar(), kzseq::seqlen(), sim4Args::set_C, sim4Args::set_K, SLIDE_INTRON, START_SIG, TEMP, exon::to1, exon::to2, sim4Args::W, W, sim4Args::X, and X.

Referenced by main().

void ValNodeFreeData

(

ValNodePtr

)

References ValNode::data, and ValNode::next.

Referenced by greedy(), Xextend_bw(), and Xextend_fw().

---

Variable Documentation

sim4Args command

Referenced by main().

int encoding[NACHARS]

comparisonType file_type

coords last_AC

Referenced by Xextend_bw().

coords last_AG

Referenced by Xextend_bw().

coords last_CT

Referenced by Xextend_fw().

coords last_GT

Referenced by Xextend_fw().

int M

Referenced by align_path(), pluri_align(), print_align(), and SIM4().

int N

Referenced by ChisquareAndRatio(), get_stats(), main(), pluri_align(), print_align(), and SIM4().

const char* seq1

Referenced by main(), mgsaln(), pluri_align(), print_align_blk(), print_align_lat(), rsnake(), SIM4(), snake(), and storeBadInTable().

const char * seq2

Referenced by main(), mgsaln(), pluri_align(), print_align_blk(), print_align_lat(), rsnake(), SIM4(), and snake().