| /dports/biology/gmap/gmap-2020-09-12/src/ |
| H A D | resulthr.c | 29 int first_absmq; member
104 Result_array (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this)… in Result_array() argument
107 *first_absmq = this->first_absmq; in Result_array()
115 Result_array2 (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this… in Result_array2() argument
118 *first_absmq = this->first_absmq2; in Result_array2()
131 int first_absmq, int second_absmq) { in Result_single_read_new() argument
166 new->first_absmq = first_absmq; in Result_single_read_new()
174 int first_absmq, int second_absmq, Pairtype_T final_pairtype) { in Result_paired_read_new() argument
220 new->first_absmq = first_absmq; in Result_paired_read_new()
282 new->first_absmq = first_absmq5; in Result_paired_as_singles_new()
|
| H A D | result.c | 30 int first_absmq; member
54 Result_array (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this)… in Result_array() argument
57 *first_absmq = this->first_absmq; in Result_array()
88 int npaths_primary, int npaths_altloc, int first_absmq, int second_absmq, in Result_new() argument
100 new->first_absmq = first_absmq; in Result_new()
|
| 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…
40 int first_absmq, int second_absmq);
43 int first_absmq, int second_absmq,
|
| 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,
|
| H A D | output.c | 159 int npaths_primary, npaths_altloc, pathnum, first_absmq, second_absmq; in filestring_fromresult_sam() local
202 …stage3array = (Stage3end_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_abs… in filestring_fromresult_sam()
223 …/*pathnum*/1,npaths_primary,npaths_altloc,Stage3end_absmq_score(stage3array[0]),first_absmq,second… in filestring_fromresult_sam()
241 …stage3array = (Stage3end_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_abs… in filestring_fromresult_sam()
277 Stage3end_absmq_score(stage3array[pathnum-1]),first_absmq,second_absmq, in filestring_fromresult_sam()
295 …stage3array = (Stage3end_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_abs… in filestring_fromresult_sam()
333 Stage3end_absmq_score(stage3array[pathnum-1]),first_absmq,second_absmq, in filestring_fromresult_sam()
400 int npaths_primary, npaths_altloc, pathnum, first_absmq, second_absmq; in filestring_fromresult_gsnap() local
466 …stage3array = (Stage3end_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_abs… in filestring_fromresult_gsnap()
663 int npaths_primary, npaths_altloc, pathnum, effective_maxpaths, first_absmq, second_absmq; in Output_filestring_fromresult() local
[all …]
|
| H A D | samprint.c | 204 } else if (absmq_score != first_absmq) { in compute_flag()
580 absmq_score,first_absmq,invertp,invert_mate_p,supplementaryp); in print_substrings()
1651 Stage3pair_absmq_score(stage3pair),first_absmq,second_absmq, in SAM_print_paired()
1663 Stage3pair_absmq_score(stage3pair),first_absmq,second_absmq, in SAM_print_paired()
1735 Stage3pair_absmq_score(stage3pair),first_absmq,second_absmq, in SAM_print_paired()
1747 Stage3pair_absmq_score(stage3pair),first_absmq,second_absmq, in SAM_print_paired()
1782 Stage3pair_absmq_score(stage3pair),first_absmq,/*invertp*/false, in SAM_print_paired()
1849 Stage3pair_absmq_score(stage3pair),first_absmq,/*second_absmq*/0, in SAM_print_paired()
1861 Stage3pair_absmq_score(stage3pair),first_absmq,/*second_absmq*/0, in SAM_print_paired()
1911 Stage3pair_absmq_score(stage3pair),first_absmq,second_absmq, in SAM_print_paired()
[all …]
|
| 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…
|
| H A D | stage3hr.h | 363 Stage3end_eval_and_sort (int npaths, int *first_absmq, int *second_absmq,
367 Stage3end_eval_and_sort_guided (int npaths, int *first_absmq, int *second_absmq, Stage3end_T guide,
465 Stage3pair_eval_and_sort (int npaths, int *first_absmq, int *second_absmq,
|
| H A D | samprint.h | 50 int absmq_score, int first_absmq, int second_absmq, int mapq_score, Univ_IIT_T chromosome_iit,
|
| 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() argument
1556 &(*first_absmq),&(*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() argument
2659 &(*first_absmq),&(*second_absmq),stage3pairarray, in consolidate_paired_results()
2763 &(*first_absmq),&(*second_absmq), 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() argument
2919 …consolidate_paired_results(&(*npaths_primary),&(*npaths_altloc),&(*first_absmq),&(*second_absmq),&… in Stage1_paired_read()
2980 …consolidate_paired_results(&(*npaths_primary),&(*npaths_altloc),&(*first_absmq),&(*second_absmq),&… in Stage1_paired_read()
|
| H A D | gmap.c | 969 *first_absmq = 0; in stage3array_from_list()
980 *first_absmq = 0; in stage3array_from_list()
992 *first_absmq = Stage3_absmq_score(array0[0]); in stage3array_from_list()
1043 *first_absmq = Stage3_absmq_score(array0[0]); in stage3array_from_list()
1132 *first_absmq = Stage3_absmq_score(array1[0]); in stage3array_from_list()
4437 int npaths_primary, npaths_altloc, first_absmq, second_absmq; in process_request() local
4506 first_absmq,second_absmq,diagnostic,NO_FAILURE); in process_request()
4551 stage3array = stage3array_from_list(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq, in process_request()
4555 first_absmq,second_absmq,diagnostic,NO_FAILURE); in process_request()
4557 stage3array = stage3array_from_list(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq, in process_request()
[all …]
|
| H A D | gsnap.c | 944 int first_absmq, second_absmq, first_absmq5, second_absmq5, first_absmq3, second_absmq3; in process_request() local
969 stage3array = Stage1_single_read(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq, in process_request()
973 …single_read_new(jobid,(void **) stage3array,npaths_primary,npaths_altloc,first_absmq,second_absmq); in process_request()
979 …} else if ((stage3pairarray = Stage1_paired_read(&npaths_primary,&npaths_altloc,&first_absmq,&seco… in process_request()
985 …red_read_new(jobid,(void **) stage3pairarray,npaths_primary,npaths_altloc,first_absmq,second_absmq, in process_request()
1014 …if ((stage3pairarray = Stage1_paired_read(&npaths_primary,&npaths_altloc,&first_absmq,&second_absm… in process_request()
1020 …red_read_new(jobid,(void **) stage3pairarray,npaths_primary,npaths_altloc,first_absmq,second_absmq, in process_request()
|
| H A D | stage3hr.c | 6273 Stage3end_eval_and_sort (int npaths, int *first_absmq, int *second_absmq, in Stage3end_eval_and_sort() argument
6285 *first_absmq = 0; in Stage3end_eval_and_sort()
6297 *first_absmq = hit->absmq_score; in Stage3end_eval_and_sort()
6361 *first_absmq = stage3array[0]->absmq_score; in Stage3end_eval_and_sort()
6522 *first_absmq = 0; in Stage3end_eval_and_sort_guided()
6534 *first_absmq = hit->absmq_score; in Stage3end_eval_and_sort_guided()
6603 *first_absmq = stage3array[0]->absmq_score; in Stage3end_eval_and_sort_guided()
9999 int first_absmq, second_absmq; in Stage3pair_print_end() local
13794 *first_absmq = 0; in Stage3pair_eval_and_sort()
13809 *first_absmq = hitpair->absmq_score; in Stage3pair_eval_and_sort()
[all …]
|
| /dports/biology/gmap/gmap-2020-09-12/ |
| H A D | ChangeLog | 10897 first_absmq as an argument
|