/* $Id: substring.h 207145 2017-06-10 00:20:06Z twu $ */ #ifndef SUBSTRING_INCLUDED #define SUBSTRING_INCLUDED typedef enum {GMAP_NOT_APPLICABLE, GMAP_VIA_SUBSTRINGS, GMAP_VIA_SEGMENTS, GMAP_VIA_REGION} GMAP_source_T; typedef enum {END, INS, DEL, FRAG, DON, ACC, AMB_DON, AMB_ACC, TERM} Endtype_T; typedef enum {NO_TRIM, PRE_TRIMMED, COMPUTE_TRIM} Trimaction_T; typedef struct Substring_T *Substring_T; #include #include "mode.h" #include "genomicpos.h" #include "types.h" #include "chrnum.h" #include "shortread.h" #include "genome.h" #include "compress.h" #include "iit-read-univ.h" #include "iit-read.h" #include "bool.h" #include "pairdef.h" #include "pairpool.h" #include "filestring.h" #include "junction.h" #include "intlist.h" #include "doublelist.h" #include "list.h" #ifdef LARGE_GENOMES #include "uint8list.h" #else #include "uintlist.h" #endif extern char * Endtype_string (Endtype_T endtype); extern char * Trimaction_string (Trimaction_T trimaction); extern void Substring_setup (bool print_nsnpdiffs_p_in, bool print_snplabels_p_in, bool show_refdiff_p_in, IIT_T snps_iit_in, int *snps_divint_crosstable_in, IIT_T genes_iit_in, int *genes_divint_crosstable_in, IIT_T splicesites_iit_in, int *splicesites_divint_crosstable_in, int donor_typeint_in, int acceptor_typeint_in, int trim_mismatch_score_in, bool novelsplicingp_in, bool knownsplicingp_in, bool output_sam_p_in, Mode_T mode_in, Univcoord_T genomelength_in); #define T Substring_T extern void Substring_alias_circular (T this); extern void Substring_unalias_circular (T this); extern T Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, Compress_T query_compress, Endtype_T start_endtype, Endtype_T end_endtype, int querystart, int queryend, int querylength, Univcoord_T alignstart, Univcoord_T alignend, bool exactp, bool plusp, int genestrand, Trimaction_T trim_left_action, Trimaction_T trim_right_action, int outofbounds_start, int outofbounds_end, int minlength, int orig_sensedir); extern T Substring_new_ambig_D (int querystart, int queryend, int splice_pos, int querylength, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, bool plusp, int genestrand, #ifdef LARGE_GENOMES Uint8list_T ambcoords, #else Uintlist_T ambcoords, #endif Intlist_T amb_knowni, Intlist_T amb_nmismatches, Doublelist_T amb_probs, double amb_common_prob, bool substring1p); extern T Substring_new_ambig_A (int querystart, int queryend, int splice_pos, int querylength, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, bool plusp, int genestrand, #ifdef LARGE_GENOMES Uint8list_T ambcoords, #else Uintlist_T ambcoords, #endif Intlist_T amb_knowni, Intlist_T amb_nmismatches, Doublelist_T amb_probs, double amb_common_prob, bool substring1p); extern Univcoord_T Substring_set_unambiguous (double *donor_prob, double *acceptor_prob, Univcoord_T *genomicstart, Univcoord_T *genomicend, T this, int bingoi); extern float Substring_compute_mapq (T this, Compress_T query_compress, char *quality_string, bool trim_terminals_p); extern int Substring_display_prep (T this, char *queryuc_ptr, int querylength, int extraleft, int extraright, Compress_T query_compress_fwd, Compress_T query_compress_rev, Genome_T genome); extern void Substring_free (T *old); extern bool Substring_contains_p (T this, int querypos); extern void Substring_print_ends (T this, int chrnum); extern int Substring_compare (T substring1, T substring2, int alias1, int alias2, Chrpos_T chrlength1, Chrpos_T chrlength2); extern bool Substring_overlap_p (T substring1, T substring2); extern Chrpos_T Substring_insert_length (T substring5, T substring3); extern bool Substring_overlap_point_trimmed_p (T substring, Univcoord_T endpos); extern Univcoord_T Substring_overlap_segment_trimmed (T substring1, T substring2); extern Univcoord_T Substring_left (T this); extern Univcoord_T Substring_splicecoord_A (T this); extern Univcoord_T Substring_splicecoord_D (T this); extern Chrpos_T Substring_chr_splicecoord_D (T this, char donor_strand); extern Chrpos_T Substring_chr_splicecoord_A (T this, char acceptor_strand); extern int Substring_splicesitesD_knowni (T this); extern int Substring_splicesitesA_knowni (T this); extern bool Substring_plusp (T this); extern int Substring_genestrand (T this); extern char * Substring_genomic_bothdiff (T this); extern char * Substring_genomic_refdiff (T this); extern char * Substring_genomic_querydir (T this); extern int Substring_nmismatches_whole (T this); extern int Substring_nmismatches_bothdiff (T this); extern int Substring_nmismatches_refdiff (T this); extern int Substring_nmatches_posttrim (T this); extern int Substring_nmatches (T this); extern void Substring_set_nmismatches_terminal (T this, int nmismatches_whole, int nmismatches_bothdiff); extern Endtype_T Substring_start_endtype (T this); extern Endtype_T Substring_end_endtype (T this); extern void Substring_set_start_endtype (T this, Endtype_T start_endtype, int start_amb_length); extern void Substring_set_end_endtype (T this, Endtype_T end_endtype, int end_amb_length); extern float Substring_mapq_loglik (T this); extern int Substring_trim_left (T this); extern int Substring_trim_right (T this); extern bool Substring_trim_left_splicep (T this); extern bool Substring_trim_right_splicep (T this); extern int Substring_mandatory_trim_left (T this); extern int Substring_mandatory_trim_right (T this); extern int Substring_querystart (T this); extern int Substring_querystart_orig (T this); extern int Substring_queryend (T this); extern int Substring_queryend_orig (T this); extern int Substring_querylength (T this); extern int Substring_match_length (T this); extern int Substring_amb_length (T this); extern int Substring_start_amb_length (T this); extern int Substring_end_amb_length (T this); extern int Substring_match_length_orig (T this); extern Chrpos_T Substring_genomic_alignment_length (T this); extern Chrnum_T Substring_chrnum (T this); extern Univcoord_T Substring_chroffset (T this); extern Univcoord_T Substring_chrhigh (T this); extern Chrpos_T Substring_chrlength (T this); extern Univcoord_T Substring_alignstart (T this); extern Univcoord_T Substring_alignend (T this); extern Chrpos_T Substring_alignstart_chr (T this); extern Chrpos_T Substring_alignend_chr (T this); extern Univcoord_T Substring_alignstart_trim (T this); extern Univcoord_T Substring_alignend_trim (T this); extern Chrpos_T Substring_alignstart_trim_chr (T this); extern Chrpos_T Substring_alignend_trim_chr (T this); extern Univcoord_T Substring_left_genomicseg (T this); extern Univcoord_T Substring_genomicstart (T this); extern Chrpos_T Substring_genomicstart_chr (T this); extern Univcoord_T Substring_genomicstart_adj (T this); extern Univcoord_T Substring_genomicend (T this); extern Chrpos_T Substring_genomicend_chr (T this); extern double Substring_amb_donor_prob (T this); extern double Substring_amb_acceptor_prob (T this); extern double Substring_siteD_prob (T this); extern double Substring_siteA_prob (T this); extern int Substring_siteD_pos (T this); extern int Substring_siteA_pos (T this); extern int Substring_siteN_pos (T this); extern int Substring_sensedir (T this); extern bool Substring_ambiguous_p (T this); extern bool Substring_list_ambiguous_p (List_T list); extern int Substring_nambcoords (T this); extern Univcoord_T * Substring_ambcoords (T this); extern int * Substring_amb_knowni (T this); extern int * Substring_amb_nmismatches (T this); extern double * Substring_amb_probs (T this); extern int Substring_circularpos (T this); extern T Substring_copy (T old); extern T Substring_new_startfrag (Univcoord_T startfrag_coord, int splice_pos, int nmismatches, Univcoord_T left, Compress_T query_compress, int querylength, bool plusp, int genestrand, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength); extern T Substring_new_endfrag (Univcoord_T endfrag_coord, int splice_pos, int nmismatches, Univcoord_T left, Compress_T query_compress, int querylength, bool plusp, int genestrand, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength); extern T Substring_new_donor (Univcoord_T donor_coord, int donor_knowni, int donor_pos, int substring_querystart, int substring_queryend, int donor_nmismatches, double donor_prob, Univcoord_T left, Compress_T query_compress, int querylength, bool plusp, int genestrand, int sensedir, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength); extern T Substring_new_acceptor (Univcoord_T acceptor_coord, int acceptor_knowni, int acceptor_pos, int substring_querystart, int substring_queryend, int acceptor_nmismatches, double acceptor_prob, Univcoord_T left, Compress_T query_compress, int querylength, bool plusp, int genestrand, int sensedir, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength); extern T Substring_new_shortexon (Univcoord_T acceptor_coord, int acceptor_knowni, Univcoord_T donor_coord, int donor_knowni, int acceptor_pos, int donor_pos, int nmismatches, double acceptor_prob, double donor_prob, Univcoord_T left, Compress_T query_compress, int querylength, bool plusp, int genestrand, int sensedir, bool acceptor_ambp, bool donor_ambp, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength); extern List_T Substring_sort_siteD_halves (List_T hitlist, bool ascendingp); extern List_T Substring_sort_siteA_halves (List_T hitlist, bool ascendingp); extern List_T Substring_sort_siteN_halves (List_T hitlist, bool ascendingp); extern Chrpos_T Substring_compute_chrpos (T this, int hardclip_low, int hardclip_high, bool hide_soft_clips_p); extern double Substring_evalue (T substring); extern void Substring_print_m8 (Filestring_T fp, T substring, Shortread_T headerseq, char *acc_suffix, char *chr, bool invertp); extern void Substring_print_alignment (Filestring_T fp, Junction_T pre_junction, T substring, Junction_T post_junction, Shortread_T queryseq, Genome_T genome, char *chr, bool invertp); extern void Substring_print_gmap (Filestring_T fp, struct Pair_T *pairs, int npairs, int nsegments, bool invertedp, Endtype_T start_endtype, Endtype_T end_endtype, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, int querylength, bool watsonp, int cdna_direction, int score, int insertlength, int pairscore, int mapq_score, Univ_IIT_T chromosome_iit, bool pairedp, GMAP_source_T gmap_source); extern bool Substring_contains_known_splicesite (T this); extern Overlap_T Substring_gene_overlap (T this, bool favor_multiexon_p); extern long int Substring_tally (T this, IIT_T tally_iit, int *tally_divint_crosstable); extern bool Substring_runlength_p (T this, IIT_T runlength_iit, int *runlength_divint_crosstable); extern int Substring_count_mismatches_region (T this, int trim_left, int trim_right, Compress_T query_compress_fwd, Compress_T query_compress_rev); extern List_T Substring_convert_to_pairs (List_T pairs, T substring, char *queryuc_ptr, Chrpos_T chrlength, Pairpool_T pairpool); extern List_T Substring_convert_to_pairs_out (List_T pairs, T substring, int querylength, Shortread_T queryseq, int hardclip_low, int hardclip_high, int queryseq_offset); extern List_T Substring_add_insertion (List_T pairs, T substringA, T substringB, int insertionlength, char *queryuc_ptr, Pairpool_T pairpool); extern List_T Substring_add_deletion (List_T pairs, T substringA, T substringB, char *deletion, int deletionlength, Pairpool_T pairpool); extern List_T Substring_add_intron (List_T pairs, T substringA, T substringB, Pairpool_T pairpool); extern List_T Substring_add_insertion_out (List_T pairs, T substringA, T substringB, int querylength, int insertionlength, Shortread_T queryseq, int hardclip_low, int hardclip_high, int queryseq_offset); extern List_T Substring_add_deletion_out (List_T pairs, T substringA, T substringB, int querylength, char *deletion, int deletionlength, int hardclip_low, int hardclip_high, int queryseq_offset); extern List_T Substring_add_intron_out (List_T pairs, T substringA, T substringB, int querylength, int hardclip_low, int hardclip_high, int queryseq_offset); #undef T #endif