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Searched refs:queryjump (Results 1 – 10 of 10) sorted by relevance

/dports/biology/gmap/gmap-2020-09-12/src/
H A Dpairpool.c228 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
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H A Ddynprog_cdna.c842 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()
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H A Dstage3.c1285 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()
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H A Dpairdef.h17 int queryjump; /* Used only for gaps */ member
H A Dpairpool.h33 Pairpool_push_gapholder (List_T list, T this, int queryjump, int genomejump,
H A Dsmooth.c76 } 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()
H A Dstage2.c5292 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()
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H A Dgmap.c2492 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()
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H A Dpair.c1525 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()
/dports/biology/gmap/gmap-2020-09-12/
H A DChangeLog2393 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.
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