| /dports/biology/gmap/gmap-2020-09-12/src/ |
| H A D | resulthr.c | 27 int npaths_primary; member
104 Result_array (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this)… in Result_array()
115 Result_array2 (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this… in Result_array2()
130 Result_single_read_new (int id, void **resultarray, int npaths_primary, int npaths_altloc, in Result_single_read_new()
173 Result_paired_read_new (int id, void **resultarray, int npaths_primary, int npaths_altloc, in Result_paired_read_new()
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| H A D | result.c | 28 int npaths_primary; member
54 Result_array (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this)… in Result_array()
88 int npaths_primary, int npaths_altloc, int first_absmq, int second_absmq, in Result_new()
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| H A D | output.c | 159 int npaths_primary, npaths_altloc, pathnum, first_absmq, second_absmq; in filestring_fromresult_sam() local
363 print_header_singleend (Filestring_T fp, Request_T request, bool translocationp, int npaths_primary… in print_header_singleend()
400 int npaths_primary, npaths_altloc, pathnum, first_absmq, second_absmq; in filestring_fromresult_gsnap() local
663 int npaths_primary, npaths_altloc, pathnum, effective_maxpaths, first_absmq, second_absmq; in Output_filestring_fromresult() local
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| H A D | samprint.c | 352 int pathnum, int npaths_primary, int npaths_altloc, bool artificial_mate_p, int npaths_mate, in SAM_print_nomapping()
481 char *acc1, char *acc2, int pathnum, int npaths_primary, int npaths_altloc, in print_substrings()
977 char *acc1, char *acc2, int pathnum, int npaths_primary, int npaths_altloc, in print_splice()
1337 …Stage3end_T this, int querylength, char *acc1, char *acc2, int pathnum, int npaths_primary, int np… in SAM_print()
1428 int npaths_primary, npaths_altloc, npaths_max, npaths_primary_max, npaths_altloc_max, in SAM_print_paired() local
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| H A D | simplepair.c | 1531 …int pathnum, int npaths_primary, int npaths_altloc, int absmq_score, int second_absmq, unsigned in… 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 | stage1hr.c | 1420 Stage1_single_read (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, in Stage1_single_read()
2392 consolidate_paired_results (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_… in consolidate_paired_results()
2780 Stage1_paired_read (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, P… in Stage1_paired_read()
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| H A D | gmap.c | 954 stage3array_from_list (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, in stage3array_from_list()
1435 stage3_from_usersegment (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_abs… in stage3_from_usersegment()
4437 int npaths_primary, npaths_altloc, first_absmq, second_absmq; in process_request() local
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| H A D | gsnap.c | 943 …int npaths_primary, npaths_altloc, npaths5_primary, npaths5_altloc, npaths3_primary, npaths3_altlo… in process_request() local
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| H A D | stage3hr.c | 1469 Stage3end_count_hits (int *npaths_primary, int *npaths_altloc, List_T hits) { in Stage3end_count_hits()
1704 Stage3pair_count_hits (int *npaths_primary, int *npaths_altloc, List_T hitpairs) { in Stage3pair_count_hits()
9998 int npaths_primary, npaths_altloc, npaths_mate_primary, npaths_mate_altloc, pathnum; in Stage3pair_print_end() local
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| H A D | pair.c | 5850 …int pathnum, int npaths_primary, int npaths_altloc, int absmq_score, int second_absmq, unsigned in… in print_sam_line()
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 | stage3.c | 5470 Stage3_count_paths (int *npaths_primary, int *npaths_altloc, List_T stage3list) { in Stage3_count_paths()
6631 Stage3_print_sam (Filestring_T fp, char *abbrev, T this, int pathnum, int npaths_primary, int npath… in Stage3_print_sam()
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