/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | resulthr.c | 28 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() [all …]
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H A D | output.c | 276 /*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() [all …]
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H A D | result.c | 29 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()
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H A D | samprint.c | 452 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() [all …]
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H A D | resulthr.h | 35 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,
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H A D | result.h | 22 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,
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H A D | samprint.h | 43 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,
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H A D | stage1hr.h | 118 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…
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H A D | simplepair.h | 60 int quality_shift, bool first_read_p, int pathnum, int npaths_primary, int npaths_altloc,
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H A D | gmap.c | 971 *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; [all …]
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H A D | stage1hr.c | 1537 *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() [all …]
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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() 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()
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H A D | stage3hr.h | 244 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);
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H A D | stage3.h | 204 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,
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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 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()
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H A D | stage3hr.c | 1472 *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() [all …]
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H A D | pair.h | 223 int quality_shift, bool first_read_p, int pathnum, int npaths_primary, int npaths_altloc,
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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() 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()
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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() 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()
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/dports/biology/gmap/gmap-2020-09-12/ |
H A D | ChangeLog | 617 * gmap.c: Setting npaths_primary and npaths_altloc when stage3list is NULL 4033 * resulthr.c: Using npaths_primary and npaths_altloc 4365 npaths_altloc
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