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Searched refs:npaths_altloc (Results 1 – 20 of 20) sorted by relevance

/dports/biology/gmap/gmap-2020-09-12/src/
H A Dresulthr.c28 int npaths_altloc; member
106 *npaths_altloc = this->npaths_altloc; in Result_array()
117 *npaths_altloc = this->npaths2_altloc; in Result_array2()
135 if (npaths_primary + npaths_altloc == 0) { in Result_single_read_new()
150 if (npaths_primary + npaths_altloc > 1) { in Result_single_read_new()
165 new->npaths_altloc = npaths_altloc; in Result_single_read_new()
193 if (npaths_primary + npaths_altloc <= 1) { in Result_paired_read_new()
200 if (npaths_primary + npaths_altloc > 1) { in Result_paired_read_new()
219 new->npaths_altloc = npaths_altloc; in Result_paired_read_new()
281 new->npaths_altloc = npaths5_altloc; in Result_paired_as_singles_new()
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H A Doutput.c276 /*acc2*/NULL,pathnum,npaths_primary,npaths_altloc, in filestring_fromresult_sam()
688 if (npaths_primary + npaths_altloc == 0) { in Output_filestring_fromresult()
752 if (npaths_primary + npaths_altloc > 1) { in Output_filestring_fromresult()
776 if (npaths_primary + npaths_altloc > 1) { in Output_filestring_fromresult()
814 …(npaths_primary + npaths_altloc == 0 && quiet_if_excessive_p && npaths_primary + npaths_altloc > m… in Output_filestring_fromresult()
825 if (npaths_primary + npaths_altloc == 0) { in Output_filestring_fromresult()
870 if (npaths_primary + npaths_altloc == 0) { in Output_filestring_fromresult()
882 if (npaths_primary + npaths_altloc == 0) { in Output_filestring_fromresult()
974 if (npaths_primary + npaths_altloc == 0) { in Output_filestring_fromresult()
1031 if (npaths_primary + npaths_altloc > 0) { in Output_filestring_fromresult()
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H A Dresult.c29 int npaths_altloc; member
54 Result_array (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this)… in Result_array() argument
56 *npaths_altloc = this->npaths_altloc; in Result_array()
88 int npaths_primary, int npaths_altloc, int first_absmq, int second_absmq, in Result_new() argument
99 new->npaths_altloc = npaths_altloc; in Result_new()
134 for (i = 2; i < (*old)->npaths_primary + (*old)->npaths_altloc; i++) { in Result_free()
145 for (i = 0; i < (*old)->npaths_primary + (*old)->npaths_altloc; i++) { in Result_free()
H A Dsamprint.c452 if (npaths_primary + npaths_altloc > 0) { in SAM_print_nomapping()
453 FPRINTF(fp,"\tNH:i:%d",npaths_primary + npaths_altloc); in SAM_print_nomapping()
552 pathnum,npaths_primary,npaths_altloc,artificial_mate_p,npaths_mate, in print_substrings()
1353 if (npaths_primary + npaths_altloc == 0) { in SAM_print()
1374 acc1,acc2,pathnum,npaths_primary,npaths_altloc, in SAM_print()
1382 acc1,acc2,pathnum,npaths_primary,npaths_altloc, in SAM_print()
1391 acc1,acc2,pathnum,npaths_primary,npaths_altloc, in SAM_print()
1401 acc1,acc2,pathnum,npaths_primary,npaths_altloc, in SAM_print()
1409 acc1,acc2,pathnum,npaths_primary,npaths_altloc, in SAM_print()
1607 /*first_read_p*/true,/*pathnum*/1,npaths_primary,npaths_altloc, in SAM_print_paired()
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H A Dresulthr.h35 Result_array (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this);
37 Result_array2 (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this…
39 Result_single_read_new (int id, void **resultarray, int npaths_primary, int npaths_altloc,
42 Result_paired_read_new (int id, void **resultarray, int npaths_primary, int npaths_altloc,
H A Dresult.h22 Result_array (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this);
34 int npaths_primary, int npaths_altloc, int first_absmq, int second_absmq,
H A Dsamprint.h43 int pathnum, int npaths_primary, int npaths_altloc, bool artificial_mate_p, int npaths_mate,
49 … this, int querylength, char *acc1, char *acc2, int pathnum, int npaths_primary, int npaths_altloc,
H A Dstage1hr.h118 Stage1_single_read (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq,
129 Stage1_paired_read (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, P…
H A Dsimplepair.h60 int quality_shift, bool first_read_p, int pathnum, int npaths_primary, int npaths_altloc,
H A Dgmap.c971 *npaths_primary = *npaths_altloc = 0; in stage3array_from_list()
983 *npaths_altloc = norig_altloc; in stage3array_from_list()
1000 *npaths_altloc = norig_altloc; in stage3array_from_list()
1042 *npaths_altloc = i_altloc; in stage3array_from_list()
1075 *npaths_primary = *npaths_altloc = 0; in stage3array_from_list()
1081 (*npaths_altloc)++; in stage3array_from_list()
1131 *npaths_altloc = i_altloc; in stage3array_from_list()
1504 *npaths_primary = *npaths_altloc = 0; in stage3_from_usersegment()
5238 int npaths_primary, npaths_altloc, i;
5283 npaths_primary = npaths_altloc = 0;
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H A Dstage1hr.c1537 *npaths_primary = *npaths_altloc = 0; in Stage1_single_read()
1553 Stage3end_count_hits(&(*npaths_primary),&(*npaths_altloc),hits); in Stage1_single_read()
1555 stage3array = Stage3end_eval_and_sort(/*npaths*/(*npaths_primary) + (*npaths_altloc), in Stage1_single_read()
2638 *npaths_altloc = 1; in consolidate_paired_results()
2641 *npaths_altloc = 0; in consolidate_paired_results()
2658 Stage3pair_eval_and_sort(/*npaths*/(*npaths_primary) + (*npaths_altloc), in consolidate_paired_results()
2671 *npaths_primary = *npaths_altloc = 0; in consolidate_paired_results()
2745 *npaths_primary = *npaths_altloc = 0; in consolidate_paired_results()
2757 Stage3pair_count_hits(&(*npaths_primary),&(*npaths_altloc),result); in consolidate_paired_results()
2760 Stage3pair_privatize(stage3pairarray,/*npaths*/(*npaths_primary) + (*npaths_altloc)); in consolidate_paired_results()
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H A Dsimplepair.c1531 …int pathnum, int npaths_primary, int npaths_altloc, int absmq_score, int second_absmq, unsigned in… in print_overlap_sam_line() argument
1642 FPRINTF(fp,"\tNH:i:%d",npaths_primary + npaths_altloc); 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() argument
1783 flag = compute_sam_flag_nomate(npaths_primary + npaths_altloc,first_read_p,watsonp,sam_paired_p); in Simplepair_overlap_print_sam()
1817 querylength_given,quality_shift,pathnum,npaths_primary,npaths_altloc, in Simplepair_overlap_print_sam()
H A Dstage3hr.h244 Stage3end_count_hits (int *npaths_primary, int *npaths_altloc, List_T hits);
285 Stage3pair_count_hits (int *npaths_primary, int *npaths_altloc, List_T hitpairs);
H A Dstage3.h204 Stage3_count_paths (int *npaths_primary, int *npaths_altloc, List_T stage3list);
255 …int_sam (Filestring_T fp, char *abbrev, T this, int pathnum, int npaths_primary, int npaths_altloc,
H A Dgsnap.c943 …int npaths_primary, npaths_altloc, npaths5_primary, npaths5_altloc, npaths3_primary, npaths3_altlo… in process_request() local
969 stage3array = Stage1_single_read(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq, in process_request()
973 …result = Result_single_read_new(jobid,(void **) stage3array,npaths_primary,npaths_altloc,first_abs… in process_request()
979 …} else if ((stage3pairarray = Stage1_paired_read(&npaths_primary,&npaths_altloc,&first_absmq,&seco… in process_request()
985 …result = Result_paired_read_new(jobid,(void **) stage3pairarray,npaths_primary,npaths_altloc,first… in process_request()
1014 …if ((stage3pairarray = Stage1_paired_read(&npaths_primary,&npaths_altloc,&first_absmq,&second_absm… in process_request()
1020 …result = Result_paired_read_new(jobid,(void **) stage3pairarray,npaths_primary,npaths_altloc,first… in process_request()
H A Dstage3hr.c1472 *npaths_primary = *npaths_altloc = 0; in Stage3end_count_hits()
1477 *npaths_altloc += 1; in Stage3end_count_hits()
1707 *npaths_primary = *npaths_altloc = 0; in Stage3pair_count_hits()
1712 *npaths_altloc += 1; in Stage3pair_count_hits()
1714 *npaths_altloc += 1; in Stage3pair_count_hits()
10074 FPRINTF(fp,"\t%d %s",npaths_primary + npaths_altloc,CONCORDANT_TEXT); in Stage3pair_print_end()
10093 FPRINTF(fp,"\t%d %s",npaths_primary + npaths_altloc,CONCORDANT_TEXT); in Stage3pair_print_end()
10143 FPRINTF(fp,"\t%d %s",npaths_primary + npaths_altloc,CONCORDANT_TEXT); in Stage3pair_print_end()
10162 FPRINTF(fp,"\t%d %s",npaths_primary + npaths_altloc,CONCORDANT_TEXT); in Stage3pair_print_end()
10258 FPRINTF(fp,"\t%d %s",npaths_primary + npaths_altloc,PAIRED_TEXT); in Stage3pair_print_end()
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H A Dpair.h223 int quality_shift, bool first_read_p, int pathnum, int npaths_primary, int npaths_altloc,
H A Dpair.c5850 …int pathnum, int npaths_primary, int npaths_altloc, int absmq_score, int second_absmq, unsigned in… in print_sam_line() argument
5948 FPRINTF(fp,"\tNH:i:%d",npaths_primary + npaths_altloc); in print_sam_line()
6333 int quality_shift, bool first_read_p, int pathnum, int npaths_primary, int npaths_altloc, in Pair_print_sam() argument
6355 flag = compute_sam_flag_nomate(npaths_primary + npaths_altloc,first_read_p,watsonp,sam_paired_p); in Pair_print_sam()
6389 querylength_given,chimera,quality_shift,pathnum,npaths_primary,npaths_altloc, in Pair_print_sam()
H A Dstage3.c5470 Stage3_count_paths (int *npaths_primary, int *npaths_altloc, List_T stage3list) { in Stage3_count_paths() argument
5473 *npaths_primary = *npaths_altloc = 0; in Stage3_count_paths()
5478 (*npaths_altloc) += 1; in Stage3_count_paths()
6631 …int_sam (Filestring_T fp, char *abbrev, T this, int pathnum, int npaths_primary, int npaths_altloc, in Stage3_print_sam() argument
6656 pathnum,npaths_primary,npaths_altloc,absmq_score,second_absmq,chrpos,this->chrlength, in Stage3_print_sam()
6664 pathnum,npaths_primary,npaths_altloc,absmq_score,second_absmq,/*chrpos*/1,this->chrlength, in Stage3_print_sam()
6673 pathnum,npaths_primary,npaths_altloc,absmq_score,second_absmq,chrpos,this->chrlength, in Stage3_print_sam()
/dports/biology/gmap/gmap-2020-09-12/
H A DChangeLog617 * gmap.c: Setting npaths_primary and npaths_altloc when stage3list is NULL
4033 * resulthr.c: Using npaths_primary and npaths_altloc
4365 npaths_altloc