/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | pairpool.c | 228 pair->queryjump = 0; in Pairpool_push() 342 pair->queryjump = 0; in Pairpool_push_gapalign() 428 pair->queryjump = queryjump; in Pairpool_push_gapholder() 465 pair,pair->queryjump,pair->genomejump); in Pairpool_push_existing() 513 (*x)->queryjump,(*x)->genomejump); in Pairpool_pop() 691 int queryjump, genomejump; in Pairpool_clean_join() local 759 pair->queryjump,pair->genomejump)); in Pairpool_remove_gapholders() 805 int queryjump = -1, genomejump = -1; in Pairpool_join_end3() local 866 queryjump,genomejump)); in Pairpool_join_end3() 895 int queryjump = -1, genomejump = -1; in Pairpool_join_end5() local [all …]
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H A D | dynprog_cdna.c | 842 int queryjump, genomejump; in Dynprog_cdna_gap() local 889 queryjump = rev_roffsetR - roffsetL + 1; in Dynprog_cdna_gap() 891 pairs = Pairpool_push_gapholder(NULL,pairpool,queryjump,genomejump, in Dynprog_cdna_gap() 902 queryjump = rev_roffsetR - roffsetL + 1; in Dynprog_cdna_gap() 904 pairs = Pairpool_push_gapholder(NULL,pairpool,queryjump,genomejump, in Dynprog_cdna_gap() 1018 queryjump = (rev_roffsetR-bestrR) - (roffsetL+bestrL) + 1; in Dynprog_cdna_gap() 1023 if (queryjump == INSERT_PAIRS && genomejump == INSERT_PAIRS) { in Dynprog_cdna_gap() 1146 queryjump = (rev_roffsetR-bestrR) - (roffsetL+bestrL) + 1; in Dynprog_cdna_gap() 1151 if (queryjump == INSERT_PAIRS && genomejump == INSERT_PAIRS) { in Dynprog_cdna_gap() 1249 queryjump = (rev_roffsetR-bestrR) - (roffsetL+bestrL) + 1; in Dynprog_cdna_gap() [all …]
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H A D | stage3.c | 1285 if (pair->queryjump != queryjump) { 1288 leftpair->querypos,rightpair->querypos,pair->queryjump,queryjump)); 1291 leftpair->querypos,rightpair->querypos,pair->queryjump,queryjump)); 1613 queryjump = 0; in insert_gapholders() 1775 queryjump = pair->queryjump; in assign_gap_types() 2057 queryjump = pair->queryjump; in assign_intron_probs() 2325 queryjump = pair->queryjump; in remove_indel_gaps() 9289 if (queryjump > 0 && queryjump <= genomejump + MININTRONLEN) { in traverse_cdna_gap() 9313 /*length1L*/queryjump,/*length1R*/queryjump,/*length2*/genomejump, in traverse_cdna_gap() 9460 if (queryjump == 0) { in traverse_genome_gap() [all …]
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H A D | pairdef.h | 17 int queryjump; /* Used only for gaps */ member
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H A D | pairpool.h | 33 Pairpool_push_gapholder (List_T list, T this, int queryjump, int genomejump,
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H A D | smooth.c | 76 } else if (pair->genomejump > pair->queryjump) { in big_gap_p() 77 return (pair->genomejump - pair->queryjump) > BIGGAP ? true : false; in big_gap_p() 282 if (pair->genomejump > pair->queryjump) { in get_intronlengths() 285 list = Intlist_push(list,pair->queryjump); in get_intronlengths() 288 if ((length = pair->genomejump - pair->queryjump) < 0) { in get_intronlengths()
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H A D | stage2.c | 5292 int querypos, lastquerypos, queryjump, genomejump, fill, default_fill; in convert_to_nucleotides() local 5411 queryjump = lastquerypos - 1 - querypos; in convert_to_nucleotides() 5414 if (queryjump == 0 && genomejump == 0) { in convert_to_nucleotides() 5442 queryjump -= fill; in convert_to_nucleotides() 5445 if (include_gapholders_p == true && (genomejump > 0 || queryjump > 0)) { in convert_to_nucleotides() 5447 pairs = Pairpool_push_gapholder(pairs,pairpool,queryjump,genomejump, in convert_to_nucleotides() 5451 if (queryjump == 0) { in convert_to_nucleotides() 5686 queryjump = lastquerypos - 1 - querypos; in convert_to_nucleotides_snps() 5689 if (queryjump == 0 && genomejump == 0) { in convert_to_nucleotides_snps() 5717 queryjump -= fill; in convert_to_nucleotides_snps() [all …]
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H A D | gmap.c | 2492 int queryjump; in find_breakpoint() local 2512 queryjump = Stage3_querystart(to) - Stage3_queryend(from) - 1; in find_breakpoint() 2514 max_extend_p = ((int) genomejump == queryjump) ? false : true; in find_breakpoint() 2515 … exists: genomejump = %u, queryjump = %d, max_extend_p = %d\n",genomejump,queryjump,max_extend_p)); in find_breakpoint() 2517 queryjump = Stage3_querystart(to) - Stage3_queryend(from) - 1; in find_breakpoint() 2519 max_extend_p = ((int) genomejump == queryjump) ? false : true; in find_breakpoint() 2520 … exists: genomejump = %u, queryjump = %d, max_extend_p = %d\n",genomejump,queryjump,max_extend_p)); in find_breakpoint() 2542 queryjump = Stage3_queryend(from) - Stage3_querystart(to) - 1; in find_breakpoint() 2544 max_extend_p = (genomejump == queryjump) ? false : true; in find_breakpoint() 2546 queryjump = Stage3_queryend(from) - Stage3_querystart(to) - 1; in find_breakpoint() [all …]
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H A D | pair.c | 1525 printf("*** Gap: queryjump = %d, genomejump = %d, type: ",this->queryjump,this->genomejump); in Pair_dump_one() 7801 } else if (this->genomejump - this->queryjump < 50) { in Pair_fracidentity() 7803 (*tindels) += this->genomejump - this->queryjump; in Pair_fracidentity() 7817 } else if (this->genomejump - this->queryjump < 50) { in Pair_fracidentity() 7819 (*tindels) += this->genomejump - this->queryjump; in Pair_fracidentity() 7896 } else if (this->genomejump - this->queryjump < 50) { in Pair_fracidentity_array() 7898 (*tindels) += this->genomejump - this->queryjump; in Pair_fracidentity_array() 7912 } else if (this->genomejump - this->queryjump < 50) { in Pair_fracidentity_array() 7914 (*tindels) += this->genomejump - this->queryjump; in Pair_fracidentity_array()
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/dports/biology/gmap/gmap-2020-09-12/ |
H A D | ChangeLog | 2393 original queryjump or genomejump is negative 2847 filling the gap with nucleotides if queryjump == genomejump 7112 (queryjump < 0 || genomejump < 0) to (queryjump <= 0 || genomejump <= 0) 8309 * stage3.c: When queryjump > nullgap and genomejump < 16 (not enough 8443 queryjump exceeds nullgap, traversing a dual break. 21523 * smooth.c: Distinguishing use of genomejump and queryjump lengths in 21811 * smooth.c: Using difference between genomejump and queryjump to define 21968 * dynprog.c: Returning null in genome gap if queryjump <= 1 22149 * pair.c: Showing queryjump and genomejump in debugging statements 26186 queryjump exceeds maxlookback. [all …]
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