| /dports/lang/mit-scheme/mit-scheme-9.2/src/microcode/ |
| H A D | os2cthrd.h | 40 unsigned int first_read_p : 1; member
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| /dports/biology/gmap/gmap-2020-09-12/src/ |
| H A D | samprint.c | 124 bool first_read_p, int pathnum, int npaths, bool artificial_mate_p, int npaths_mate, in compute_flag()
351 Univ_IIT_T chromosome_iit, Resulttype_T resulttype, bool first_read_p, in SAM_print_nomapping()
488 Resulttype_T resulttype, bool first_read_p, bool artificial_mate_p, int npaths_mate, in print_substrings()
984 Resulttype_T resulttype, bool first_read_p, bool artificial_mate_p, int npaths_mate, in print_splice()
1344 Resulttype_T resulttype, bool first_read_p, bool artificial_mate_p, int npaths_mate, in SAM_print()
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| H A D | extension-search.c | 1399 bool plusp, int genestrand, bool paired_end_p, bool first_read_p, in process_seed()
1592 bool plusp, int genestrand, bool paired_end_p, bool first_read_p, in extend_seeds()
1708 int genestrand, bool paired_end_p, bool first_read_p, int level) { in Extension_search()
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| H A D | distant-dna.c | 82 int querylength, bool first_read_p, in Distant_dna_solve()
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| H A D | cigar.c | 2015 Stage3end_T stage3end, int querylength, bool first_read_p, Stage3end_T mate, in Cigar_compute_main()
2203 Stage3end_T stage3end, int querylength, bool first_read_p, Stage3end_T mate, in Cigar_compute_supplemental()
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| H A D | distant-rna.c | 1201 int querylength, int nmismatches_allowed, bool first_read_p, in find_splicepairs_rna()
1944 int genestrand, bool first_read_p, Listpool_T listpool, in Distant_rna_solve()
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| H A D | transcript.c | 479 Univ_IIT_T transcript_iit, bool concordantp, bool first_read_p, in Transcript_concordance_print()
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| H A D | segment-search.c | 1105 bool plusp, int genestrand, bool paired_end_p, bool first_read_p, in solve_all()
1354 int genestrand, bool paired_end_p, bool first_read_p, in Segment_search_all()
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| H A D | simplepair.c | 1535 Stage3pair_T stage3pair, Stage3end_T stage3hit, bool first_read_p, in print_overlap_sam_line()
1734 int quality_shift, bool first_read_p, int pathnum, int npaths_primary, int npaths_altloc, in Simplepair_overlap_print_sam()
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| H A D | stage3hr.c | 890 Stage3end_substring_for_concordance (T this, bool first_read_p) { in Stage3end_substring_for_concordance()
899 Stage3end_substring_other (T this, bool first_read_p) { in Stage3end_substring_other()
909 Stage3end_donor_concordant_p (T this, bool first_read_p) { in Stage3end_donor_concordant_p()
5276 bool copy_donor_p, bool copy_acceptor_p, bool first_read_p, int orig_sensedir, in Stage3end_new_splice()
5612 bool first_read_p, Listpool_T listpool, int level) { in Stage3end_new_distant()
6052 Stage3end_display_prep (Stage3end_T this, char *queryuc_ptr, bool first_read_p) { in Stage3end_display_prep()
9731 int pairscore, Pairtype_T pairtype, int mapq_score, bool first_read_p) { in print_substrings()
9940 int pairscore, Pairtype_T pairtype, int mapq_score, bool first_read_p) { in Stage3end_print()
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| H A D | pair.c | 4965 compute_sam_flag_nomate (int npaths, bool first_read_p, bool watsonp, bool sam_paired_p) { in compute_sam_flag_nomate()
4998 bool first_read_p, bool sam_paired_p, char *sam_read_group_id) { in Pair_print_sam_nomapping()
6333 int quality_shift, bool first_read_p, int pathnum, int npaths_primary, int npaths_altloc, in Pair_print_sam()
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| H A D | stage1hr.c | 1060 bool paired_end_p, bool first_read_p) { in single_read_search()
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| H A D | path-solve.c | 3459 bool paired_end_p, bool first_read_p, in Path_solve_from_diagonals()
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