/* $Id: stage3hr.h 207311 2017-06-14 19:26:20Z twu $ */ #ifndef STAGE3HR_INCLUDED #define STAGE3HR_INCLUDED typedef struct Stage3end_T *Stage3end_T; #include #include "bool.h" #include "sense.h" #include "chrnum.h" #include "genomicpos.h" #include "intlist.h" #include "doublelist.h" #include "iit-read-univ.h" #include "iit-read.h" #include "shortread.h" #include "genome.h" #include "compress.h" #include "resulthr.h" #include "substring.h" #include "junction.h" #include "pair.h" #include "filestring.h" #include "dynprog.h" #include "diagpool.h" #include "cellpool.h" #include "oligoindex_hr.h" /* Should arrange in order of goodness, best to worst */ typedef enum {EXACT, SUB, INSERTION, DELETION, SUBSTRINGS, HALFSPLICE_DONOR, HALFSPLICE_ACCEPTOR, SPLICE, SAMECHR_SPLICE, TRANSLOC_SPLICE, ONE_THIRD_SHORTEXON, TWO_THIRDS_SHORTEXON, SHORTEXON, GMAP, TERMINAL} Hittype_T; #define T Stage3end_T typedef struct Stage3pair_T *Stage3pair_T; extern void Stage3hr_setup (bool invert_first_p_in, bool invert_second_p_in, Genome_T genome_in, Univ_IIT_T chromosome_iit_in, int nchromosomes_in, int circular_typeint_in, IIT_T genes_iit_in, int *genes_divint_crosstable_in, IIT_T tally_iit_in, int *tally_divint_crosstable_in, IIT_T runlength_iit_in, int *runlength_divint_crosstable_in, bool distances_observed_p, Chrpos_T pairmax_linear_in, Chrpos_T pairmax_circular_in, Chrpos_T expected_pairlength_in, Chrpos_T pairlength_deviation_in, int maxpeelback_in, int localsplicing_penalty_in, int indel_penalty_middle_in, int antistranded_penalty_in, bool favor_multiexon_p_in, int gmap_min_nconsecutive_in, int end_detail, int subopt_levels_in, int max_middle_insertions_in, int max_middle_deletions_in, bool novelsplicingp_in, Chrpos_T shortsplicedist_in, bool merge_samechr_p_in, bool *circularp_in, bool *altlocp_in, Univcoord_T *alias_starts_in, Univcoord_T *alias_ends_in, bool omit_concordant_uniq_p_in, bool omit_concordant_mult_p_in, char *failedinput_root_in, bool print_m8_p_in, bool want_random_p_in); extern char * Stage3end_deletion_string (T this); extern Hittype_T Stage3end_hittype (T this); extern char * Stage3end_hittype_string (T this); extern int Stage3end_genestrand (T this); extern bool Stage3end_sarrayp (T this); extern bool Stage3end_improved_by_gmap_p (T this); extern void Stage3end_set_improved_by_gmap (T this); extern bool Stage3end_anomalous_splice_p (T this); extern Chrnum_T Stage3end_chrnum (T this); extern Chrnum_T Stage3end_effective_chrnum (T this); extern Chrnum_T Stage3end_other_chrnum (T this); extern Univcoord_T Stage3end_chroffset (T this); extern Univcoord_T Stage3end_chrhigh (T this); extern Chrpos_T Stage3end_chrlength (T this); extern Univcoord_T Stage3end_genomicstart (T this); extern Univcoord_T Stage3end_genomicend (T this); extern int Stage3end_query_alignment_length (T this); extern Chrpos_T Stage3end_genomic_alignment_length (T this); extern Chrpos_T Stage3end_chrpos_low_trim (T this); extern int Stage3end_mapq_score (T this); extern int Stage3end_absmq_score (T this); extern int Stage3end_score (T this); extern int Stage3end_gmap_goodness (T this); extern int Stage3end_gmap_max_match_length (T this); extern int Stage3end_best_score (List_T hits); extern bool Stage3end_equiv_score_unpaired_p (List_T hits, int best_score); extern int Stage3end_best_score_paired (List_T hits); extern int Stage3end_nmatches_posttrim (T this); extern int Stage3end_nmatches (T this); extern int Stage3end_nmismatches_whole (T this); extern int Stage3end_nmismatches_bothdiff (T this); extern int Stage3end_nmismatches_refdiff (T this); extern Endtype_T Stage3end_start_endtype (T this); extern Endtype_T Stage3end_end_endtype (T this); extern Endtype_T Stage3end_gmap_start_endtype (T this); extern Endtype_T Stage3end_gmap_end_endtype (T this); extern int Stage3end_nindels (T this); extern int Stage3end_querylength (T this); extern bool Stage3end_plusp (T this); extern bool Stage3end_paired_usedp (T this); extern int Stage3end_trim_left (T this); extern int Stage3end_trim_right (T this); extern int Stage3end_total_trim (T this); extern int Stage3end_circularpos (T this); extern Junction_T Stage3end_junctionD (T this); extern Junction_T Stage3end_junctionA (T this); extern List_T Stage3end_substrings_LtoH (T this); extern List_T Stage3end_junctions_LtoH (T this); extern Substring_T Stage3end_substring1 (T this); extern Substring_T Stage3end_substringN (T this); extern Substring_T Stage3end_substring_donor (T this); extern Substring_T Stage3end_substring_acceptor (T this); extern Substring_T Stage3end_substringD (T this); extern Substring_T Stage3end_substringA (T this); extern Substring_T Stage3end_substringS (T this); extern Substring_T Stage3end_substring_low (T this, int hardclip_low); extern Substring_T Stage3end_substring_containing (T this, int querypos); extern double Stage3end_min_evalue (T this); extern struct Pair_T * Stage3end_pairarray (T this); extern int Stage3end_npairs (T this); extern List_T Stage3end_cigar_tokens (T this); extern bool Stage3end_gmap_intronp (T this); extern Chrpos_T Stage3end_distance (T this); extern Chrpos_T Stage3end_shortexonA_distance (T this); extern Chrpos_T Stage3end_shortexonD_distance (T this); extern double Stage3end_chimera_prob (T this); extern double Stage3end_shortexon_prob (T this); extern Univcoord_T Stage3end_chimera_segmenti_left (T this); extern Univcoord_T Stage3end_chimera_segmentj_left (T this); extern int Stage3end_chimera_segmenti_cmp (const void *a, const void *b); extern int Stage3end_chimera_segmentj_cmp (const void *a, const void *b); extern int Stage3end_shortexon_substringD_cmp (const void *a, const void *b); extern int Stage3end_shortexon_substringA_cmp (const void *a, const void *b); extern int Stage3end_sensedir (T this); extern int Stage3end_sensedir_nonamb (T this); extern int Stage3end_cdna_direction (T this); extern int Stage3end_nintrons (T this); extern bool Stage3end_start_ambiguous_p (T this); extern bool Stage3end_end_ambiguous_p (T this); extern Univcoord_T * Stage3end_start_ambcoords (T this); extern Univcoord_T * Stage3end_end_ambcoords (T this); extern int Stage3end_start_nambcoords (T this); extern int Stage3end_end_nambcoords (T this); extern bool Stage3end_gmap_triedp (T this); extern void Stage3end_set_gmap_triedp (T this); extern int Stage3end_substrings_querystart (T this); extern int Stage3end_substrings_queryend (T this); extern int Stage3end_gmap_querystart (T this); extern int Stage3end_gmap_queryend (T this); extern int Stage3end_terminal_trim (T this); extern int Stage3end_trimlength (T this); extern void Stage3end_count_hits (int *npaths_primary, int *npaths_altloc, List_T hits); extern bool Stage3end_contains_known_splicesite (T this); extern bool Stage3end_indel_contains_known_splicesite (bool *leftp, bool *rightp, T this); extern bool Stage3end_genomicbound_from_start (Univcoord_T *genomicbound, T this, int overlap, Univcoord_T chroffset); extern bool Stage3end_genomicbound_from_end (Univcoord_T *genomicbound, T this, int overlap, Univcoord_T chroffset); extern void Stage3end_free (T *old); extern void Stage3end_list_free (List_T *values); extern bool Stage3pair_anomalous_splice_p (Stage3pair_T this); extern int Stage3pair_genestrand (Stage3pair_T this); extern Stage3end_T Stage3pair_hit5 (Stage3pair_T this); extern Stage3end_T Stage3pair_hit3 (Stage3pair_T this); extern int Stage3pair_mapq_score (Stage3pair_T this); extern int Stage3pair_absmq_score (Stage3pair_T this); extern Chrpos_T Stage3pair_pairlength (Stage3pair_T this); extern int Stage3pair_total_trim (Stage3pair_T this); extern int Stage3pair_nmatches_posttrim (int *nmatches5, int *nmatches3, Stage3pair_T this); extern bool Stage3pair_concordantp (List_T hitpairs); extern void Stage3pair_count_hits (int *npaths_primary, int *npaths_altloc, List_T hitpairs); extern List_T Stage3pair_filter_nonconcordant (List_T hitpairs); extern int Stage3pair_overlap (int *hardclip5_low, int *hardclip5_high, int *hardclip3_low, int *hardclip3_high, Stage3pair_T this); extern void Stage3pair_set_private5p (Stage3pair_T this); extern void Stage3pair_clear_private5p (Stage3pair_T this); extern void Stage3pair_set_private3p (Stage3pair_T this); extern void Stage3pair_clear_private3p (Stage3pair_T this); extern void Stage3pair_free (Stage3pair_T *old); extern T Stage3end_copy (T old); extern T Stage3end_new_substrings (int *found_score, Intlist_T endpoints, #ifdef LARGE_GENOMES Uint8list_T lefts, #else Uintlist_T lefts, #endif Intlist_T nmismatches_list, List_T junctions, int querylength, Compress_T query_compress, Substring_T right_ambig, Substring_T left_ambig, bool plusp, int genestrand, int sensedir, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, bool sarrayp); extern T Stage3end_substrings_run_gmap_plus (T *hit2, T this, char *queryuc_ptr, int querylength, int genestrand, int maxpeelback, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR, Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, bool extend_ends_p); extern T Stage3end_substrings_run_gmap_minus (T *hit2, T this, char *queryuc_ptr, int querylength, int genestrand, int maxpeelback, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR, Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool, bool extend_ends_p); extern T Stage3end_gmap_run_gmap_plus (T *hit2, T this, char *queryuc_ptr, int querylength, int genestrand, int maxpeelback, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR, Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool); extern T Stage3end_gmap_run_gmap_minus (T *hit2, T this, char *queryuc_ptr, int querylength, int genestrand, int maxpeelback, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR, Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool); extern T Stage3end_new_exact (int *found_score, Univcoord_T left, int genomiclength, Compress_T query_compress, bool plusp, int genestrand, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, bool sarrayp); extern T Stage3end_new_substitution (int *found_score, int nmismatches, Univcoord_T left, int genomiclength, Compress_T query_compress, bool plusp, int genestrand, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, bool sarrayp); extern T Stage3end_new_insertion (int *found_score, int nindels, int indel_pos, int nmismatches1, int nmismatches2, 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, int indel_penalty, bool sarrayp); extern T Stage3end_new_deletion (int *found_score, int nindels, int indel_pos, int nmismatches1, int nmismatches2, 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, int indel_penalty, bool sarrayp); extern T Stage3end_new_terminal (int querystart, int queryend, Univcoord_T left, Compress_T query_compress, int querylength, bool plusp, int genestrand, Endtype_T start_endtype, Endtype_T end_endtype, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, int max_mismatches_allowed, bool sarrayp); extern T Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches, Substring_T donor, Substring_T acceptor, double donor_prob, double acceptor_prob, Chrpos_T distance, bool shortdistancep, int splicing_penalty, int querylength, #ifdef LARGE_GENOMES Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, #else Uintlist_T ambcoords_donor, Uintlist_T ambcoords_acceptor, #endif Intlist_T amb_knowni_donor, Intlist_T amb_knowni_acceptor, Intlist_T amb_nmismatches_donor, Intlist_T amb_nmismatches_acceptor, Doublelist_T amb_probs_donor, Doublelist_T amb_probs_acceptor, bool copy_donor_p, bool copy_acceptor_p, bool first_read_p, int sensedir, bool sarrayp); extern T Stage3end_new_shortexon (int *found_score, Substring_T donor, Substring_T acceptor, Substring_T shortexon, double donor_prob, double shortexonA_prob, double shortexonD_prob, double acceptor_prob, int amb_length_donor, int amb_length_acceptor, #ifdef LARGE_GENOMES Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, #else Uintlist_T ambcoords_donor, Uintlist_T ambcoords_acceptor, #endif Intlist_T amb_knowni_donor, Intlist_T amb_knowni_acceptor, Intlist_T amb_nmismatches_donor, Intlist_T amb_nmismatches_acceptor, Doublelist_T amb_probs_donor, Doublelist_T amb_probs_acceptor, bool copy_donor_p, bool copy_acceptor_p, bool copy_shortexon_p, int splicing_penalty, int querylength, int sensedir, bool sarrayp); extern T Stage3end_new_gmap (int nmismatches_whole, int nmatches_posttrim, int max_match_length, int ambig_end_length_5, int ambig_end_length_3, Splicetype_T ambig_splicetype_5, Splicetype_T ambig_splicetype_3, double avg_splice_score, int goodness, struct Pair_T *pairarray, int npairs, int nsegments, int nintrons, int nindelbreaks, Univcoord_T left, int genomiclength, bool plusp, int genestrand, char *accession, int querylength, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, int cdna_direction, int sensedir, bool sensedir_knownp, GMAP_source_T gmap_source); extern List_T Stage3end_sort_bymatches (List_T hits); extern List_T Stage3end_sort_by_paired_seenp (List_T hits); extern List_T Stage3end_filter_coverage (List_T hits, int min_coverage); extern Stage3end_T * Stage3end_eval_and_sort (int npaths, int *first_absmq, int *second_absmq, Stage3end_T *stage3array, int maxpaths, Shortread_T queryseq, char *queryuc_ptr, Compress_T query_compress_fwd, Compress_T query_compress_rev, char *quality_string, bool displayp); extern Stage3end_T * Stage3end_eval_and_sort_guided (int npaths, int *first_absmq, int *second_absmq, Stage3end_T guide, Stage3end_T *stage3array, int maxpaths, Shortread_T queryseq, char *queryuc_ptr, Compress_T query_compress_fwd, Compress_T query_compress_rev, char *quality_string, bool displayp); extern List_T Stage3pair_remove_excess_terminals (List_T hitpairlist); extern List_T Stage3end_optimal_score (List_T hitlist, Compress_T query_compress_fwd, Compress_T query_compress_rev, int querylength, bool keep_gmap_p, bool finalp); extern bool Stage3pair_sense_consistent_p (List_T hitpairlist); extern List_T Stage3end_linearize_5 (List_T hitlist); extern List_T Stage3end_linearize_3 (List_T hitlist); extern List_T Stage3end_remove_circular_alias (List_T hitlist); extern List_T Stage3end_remove_duplicates (List_T hitlist); extern List_T Stage3end_reject_trimlengths (List_T hits); extern List_T Stage3end_remove_overlaps (List_T hitlist, bool finalp); extern List_T Stage3end_resolve_multimapping (List_T hitlist); extern Pairtype_T Stage3_determine_pairtype (T hit5, T hit3); /* If hit5 and hit3 are not NULL, then we know this is part of a pair */ extern void Stage3end_print (Filestring_T fp, T this, int score, Univ_IIT_T chromosome_iit, Shortread_T queryseq, Shortread_T headerseq, char *acc_suffix, bool invertp, T hit5, T hit3, int pairedlength, int pairscore, Pairtype_T pairtype, int mapq_score); extern Pairtype_T Stage3pair_pairtype (Stage3pair_T this); extern Pairtype_T Stage3pair_determine_pairtype (Stage3pair_T this); extern bool Stage3pair_circularp (Stage3pair_T this); extern bool Stage3pair_altlocp (Stage3pair_T this); extern void Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput, Result_T result, Resulttype_T resulttype, char initchar, bool firstp, Univ_IIT_T chromosome_iit, Shortread_T queryseq, Shortread_T headerseq1, Shortread_T headerseq2, int maxpaths, bool quiet_if_excessive_p, bool invertp, int quality_shift); extern List_T Stage3pair_resolve_insides (List_T hitpairlist, char *queryuc_ptr_5, char *queryuc_ptr_3, Compress_T query5_compress_fwd, Compress_T query5_compress_rev, Compress_T query3_compress_fwd, Compress_T query3_compress_rev, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR, Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool); extern Stage3pair_T Stage3pair_new (T hit5, T hit3, int genestrand, Pairtype_T pairtype, bool private5p, bool private3p, bool expect_concordant_p); struct Pair_T * Stage3pair_merge (int *npairs, int *querylength_merged, char **queryseq_merged, char **quality_merged, Stage3pair_T this, Shortread_T queryseq5, Shortread_T queryseq3, int querylength_5, int querylength_3, int clipdir, int hardclip5_low, int hardclip5_high, int hardclip3_low, int hardclip3_high); extern void Stage3pair_privatize (Stage3pair_T *array, int npairs); extern List_T Stage3pair_sort_bymatches (List_T hits); extern List_T Stage3pair_remove_overlaps (List_T hitpairlist, bool translocp, bool finalp); extern List_T Stage3pair_resolve_multimapping (List_T hitpairs); extern List_T Stage3pair_filter_coverage (List_T hits, int min_coverage_5, int min_coverage_3); extern Stage3pair_T * Stage3pair_eval_and_sort (int npaths, int *first_absmq, int *second_absmq, Stage3pair_T *stage3pairarray, int maxpaths, Shortread_T queryseq1, Shortread_T queryseq2, char *queryuc_ptr_5, char *queryuc_ptr_3, Compress_T query5_compress_fwd, Compress_T query5_compress_rev, Compress_T query3_compress_fwd, Compress_T query3_compress_rev, char *quality_string_5, char *quality_string_3); extern List_T Stage3pair_optimal_score (List_T hitpairlist, Compress_T query5_compress_fwd, Compress_T query5_compress_rev, Compress_T query3_compress_fwd, Compress_T query3_compress_rev, int querylength5, int querylength3, bool keep_gmap_p, bool finalp); #if 0 extern List_T Stage3end_unalias_circular (List_T hitlist); #endif extern List_T Stage3pair_remove_circular_alias (List_T hitpairlist); extern List_T Stage3_pair_up_concordant (bool *abort_pairing_p, int *found_score, int *nconcordant, int *nsamechr, List_T *samechr, List_T *conc_transloc, List_T *terminals, List_T hitpairs, List_T *hitarray5, int narray5, List_T *hitarray3, int narray3, int cutoff_level_5, int cutoff_level_3, int querylength5, int querylength3, int maxpairedpaths, int genestrand); #undef T #endif