334 		      int *left_known, int *right_known, Univcoord_T leftoffset, Univcoord_T rightoffset,  in get_splicesite_probs()  argument
343     splicesitepos = chroffset + leftoffset + cL;  in get_splicesite_probs()
356     splicesitepos = chrhigh - leftoffset - cL + 1;  in get_splicesite_probs()
405 		       int leftoffset, int rightoffset, int cdna_direction, bool watsonp,  in get_known_splicesites()  argument
417 						  leftoffset+1,leftoffset+glengthL-2,donor_typeint,/*sign*/+1,/*sortp*/false);  in get_known_splicesites()
421 	  left_known[splicesitepos - leftoffset] = KNOWN_SPLICESITE_REWARD;  in get_known_splicesites()
438 						  leftoffset+1,leftoffset+glengthL-2,acceptor_typeint,/*sign*/-1,/*sortp*/false);  in get_known_splicesites()
442 	  left_known[splicesitepos - leftoffset] = KNOWN_SPLICESITE_REWARD;  in get_known_splicesites()
462 						  (chrhigh - chroffset) - leftoffset - glengthL + 4,  in get_known_splicesites()
463 						  (chrhigh - chroffset) - leftoffset + 1,  in get_known_splicesites()
468 	  left_known[(chrhigh - chroffset) - leftoffset - splicesitepos + 1] = KNOWN_SPLICESITE_REWARD;  in get_known_splicesites()
487 						  (chrhigh - chroffset) - leftoffset - glengthL + 4,  in get_known_splicesites()
488 						  (chrhigh - chroffset) - leftoffset + 1,  in get_known_splicesites()
493 	  left_known[(chrhigh - chroffset) - leftoffset - splicesitepos + 1] = KNOWN_SPLICESITE_REWARD;  in get_known_splicesites()
518 				      leftoffset,leftoffset+glengthL-2,/*sign*/+1);  in get_known_splicesites()
522 	  left_known[splicesitepos - leftoffset] = KNOWN_SPLICESITE_REWARD;  in get_known_splicesites()
539 				      leftoffset,leftoffset+glengthL-2,/*sign*/-1);  in get_known_splicesites()
543 	  left_known[splicesitepos - leftoffset] = KNOWN_SPLICESITE_REWARD;  in get_known_splicesites()
562 				       (chrhigh - chroffset) - leftoffset - glengthL + 4,  in get_known_splicesites()
563 				       (chrhigh - chroffset) - leftoffset + 2,/*sign*/-1);  in get_known_splicesites()
567 	  left_known[(chrhigh - chroffset) - leftoffset - splicesitepos + 2] = KNOWN_SPLICESITE_REWARD;  in get_known_splicesites()
585 				       (chrhigh - chroffset) - leftoffset - glengthL + 4,  in get_known_splicesites()
586 				       (chrhigh - chroffset) - leftoffset + 2,/*sign*/+1);  in get_known_splicesites()
590 	  left_known[(chrhigh - chroffset) - leftoffset - splicesitepos + 2] = KNOWN_SPLICESITE_REWARD;  in get_known_splicesites()
623 				  int leftoffset, int rightoffset,  in bridge_intron_gap_8_intron_level()  argument
665 	for (cR = cloR; cR < /* left of main diagonal*/rR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_8_intron_level()
679 		splicesitepos1 = leftoffset + cL;  in bridge_intron_gap_8_intron_level()
686 		splicesitepos1 = (chrhigh - chroffset) - leftoffset - cL + 1;  in bridge_intron_gap_8_intron_level()
709 	for (/* at main diagonal*/; cR < chighR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_8_intron_level()
723 		splicesitepos1 = leftoffset + cL;  in bridge_intron_gap_8_intron_level()
730 		splicesitepos1 = (chrhigh - chroffset) - leftoffset - cL + 1;  in bridge_intron_gap_8_intron_level()
768 	for (cR = cloR; cR < /* left of main diagonal*/rR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_8_intron_level()
782 		splicesitepos1 = leftoffset + cL;  in bridge_intron_gap_8_intron_level()
789 		splicesitepos1 = (chrhigh - chroffset) - leftoffset - cL + 1;  in bridge_intron_gap_8_intron_level()
812 	for (/* at main diagonal*/; cR < chighR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_8_intron_level()
826 		splicesitepos1 = leftoffset + cL;  in bridge_intron_gap_8_intron_level()
833 		splicesitepos1 = (chrhigh - chroffset) - leftoffset - cL + 1;  in bridge_intron_gap_8_intron_level()
877 				int leftoffset, int rightoffset, Univcoord_T chroffset, Univcoord_T chrhigh,  in bridge_intron_gap_8_site_level()  argument
976 	splicesitepos = chroffset + leftoffset + cL;  in bridge_intron_gap_8_site_level()
997 	splicesitepos = chroffset + leftoffset + cL;  in bridge_intron_gap_8_site_level()
1020 	splicesitepos = chrhigh - leftoffset - cL + 1;  in bridge_intron_gap_8_site_level()
1041 	splicesitepos = chrhigh - leftoffset - cL + 1;  in bridge_intron_gap_8_site_level()
1149     for (cR = cloR; cR < /*to main diagonal*/rR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_8_site_level()
1193     for (/*skip main diagonal*/cR++; cR < chighR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_8_site_level()
1249     for (cL = cloL; cL < /*to main diagonal*/rL && cL < rightoffset-leftoffset-cR; cL++) {  in bridge_intron_gap_8_site_level()
1293     for (/*Skip main diagonal*/cL++; cL < chighL && cL < rightoffset-leftoffset-cR; cL++) {  in bridge_intron_gap_8_site_level()
1396 			int leftoffset, int rightoffset,  in bridge_intron_gap_8_ud()  argument
1428 						  leftoffset,rightoffset,chrnum,chroffset,chrhigh,jump_late_p);  in bridge_intron_gap_8_ud()
1440 						leftoffset,rightoffset,chroffset,chrhigh,halfp,finalp);  in bridge_intron_gap_8_ud()
1468 			 left_known,right_known,leftoffset,rightoffset,chroffset,chrhigh,  in bridge_intron_gap_8_ud()
1496 				  int leftoffset, int rightoffset,  in bridge_intron_gap_16_intron_level()  argument
1538 	for (cR = cloR; cR < /* left of main diagonal*/rR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_16_intron_level()
1552 		splicesitepos1 = leftoffset + cL;  in bridge_intron_gap_16_intron_level()
1559 		splicesitepos1 = (chrhigh - chroffset) - leftoffset - cL + 1;  in bridge_intron_gap_16_intron_level()
1582 	for (/* at main diagonal*/; cR < chighR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_16_intron_level()
1596 		splicesitepos1 = leftoffset + cL;  in bridge_intron_gap_16_intron_level()
1603 		splicesitepos1 = (chrhigh - chroffset) - leftoffset - cL + 1;  in bridge_intron_gap_16_intron_level()
1641 	for (cR = cloR; cR < /* left of main diagonal*/rR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_16_intron_level()
1655 		splicesitepos1 = leftoffset + cL;  in bridge_intron_gap_16_intron_level()
1662 		splicesitepos1 = (chrhigh - chroffset) - leftoffset - cL + 1;  in bridge_intron_gap_16_intron_level()
1685 	for (/* at main diagonal*/; cR < chighR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_16_intron_level()
1699 		splicesitepos1 = leftoffset + cL;  in bridge_intron_gap_16_intron_level()
1706 		splicesitepos1 = (chrhigh - chroffset) - leftoffset - cL + 1;  in bridge_intron_gap_16_intron_level()
1750 				 int leftoffset, int rightoffset, Univcoord_T chroffset, Univcoord_T chrhigh,  in bridge_intron_gap_16_site_level()  argument
1850 	splicesitepos = chroffset + leftoffset + cL;  in bridge_intron_gap_16_site_level()
1871 	splicesitepos = chroffset + leftoffset + cL;  in bridge_intron_gap_16_site_level()
1894 	splicesitepos = chrhigh - leftoffset - cL + 1;  in bridge_intron_gap_16_site_level()
1915 	splicesitepos = chrhigh - leftoffset - cL + 1;  in bridge_intron_gap_16_site_level()
2023     for (cR = cloR; cR < /*to main diagonal*/rR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_16_site_level()
2066     for (/*Skip main diagonal*/cR++; cR < chighR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_16_site_level()
2122     for (cL = cloL; cL < /*to main diagonal*/rL && cL < rightoffset-leftoffset-cR; cL++) {  in bridge_intron_gap_16_site_level()
2165     for (/*Skip main diagonal*/cL++; cL < chighL && cL < rightoffset-leftoffset-cR; cL++) {  in bridge_intron_gap_16_site_level()
2269 			 int leftoffset, int rightoffset,  in bridge_intron_gap_16_ud()  argument
2301 						   leftoffset,rightoffset,chrnum,chroffset,chrhigh,jump_late_p);  in bridge_intron_gap_16_ud()
2314 						 leftoffset,rightoffset,chroffset,chrhigh,halfp,finalp);  in bridge_intron_gap_16_ud()
2342 			 left_known,right_known,leftoffset,rightoffset,chroffset,chrhigh,  in bridge_intron_gap_16_ud()
2368 				int leftoffset, int rightoffset,  in bridge_intron_gap_intron_level()  argument
2410 	for (cR = cloR; cR < chighR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_intron_level()
2424 		splicesitepos1 = leftoffset + cL;  in bridge_intron_gap_intron_level()
2431 		splicesitepos1 = (chrhigh - chroffset) - leftoffset - cL + 1;  in bridge_intron_gap_intron_level()
2471 			      int leftoffset, int rightoffset, Univcoord_T chroffset, Univcoord_T chrhigh,  in bridge_intron_gap_site_level()  argument
2571 	splicesitepos = chroffset + leftoffset + cL;  in bridge_intron_gap_site_level()
2592 	splicesitepos = chroffset + leftoffset + cL;  in bridge_intron_gap_site_level()
2615 	splicesitepos = chrhigh - leftoffset - cL + 1;  in bridge_intron_gap_site_level()
2636 	splicesitepos = chrhigh - leftoffset - cL + 1;  in bridge_intron_gap_site_level()
2744     for (cR = cloR; cR < chighR && cR < rightoffset-leftoffset-cL; cR++) {  in bridge_intron_gap_site_level()
2799     for (cL = cloL; cL < chighL && cL < rightoffset-leftoffset-cR; cL++) {  in bridge_intron_gap_site_level()
2899 		   int leftoffset, int rightoffset, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh,  in bridge_intron_gap()  argument
2944 						leftoffset,rightoffset,chrnum,chroffset,chrhigh,jump_late_p);  in bridge_intron_gap()
2952 					      leftoffset,rightoffset,chroffset,chrhigh,halfp,finalp);  in bridge_intron_gap()
2980 			 left_known,right_known,leftoffset,rightoffset,chroffset,chrhigh,  in bridge_intron_gap()
3002 		   int roffset, int rev_roffset, int leftoffset, int rightoffset,  in genome_gap_simple()  argument
3036 			leftoffset,rightoffset,  in genome_gap_simple()
3160 			 left_known,right_known,leftoffset,rightoffset,  in genome_gap_simple()
3183 		     leftoffset,genomecoord,chroffset,chrhigh,watsonp));  in genome_gap_simple()
3187 		     r,/*c*/r,roffset+querycoord,leftoffset+genomecoord,c1_uc,c2));  in genome_gap_simple()
3189 	pairs = Pairpool_push(pairs,pairpool,roffset+querycoord,leftoffset+genomecoord,  in genome_gap_simple()
3194 		     r,/*c*/r,roffset+querycoord,leftoffset+genomecoord,c1_uc,c2));  in genome_gap_simple()
3196 	pairs = Pairpool_push(pairs,pairpool,roffset+querycoord,leftoffset+genomecoord,  in genome_gap_simple()
3201 		     r,/*c*/r,roffset+querycoord,leftoffset+genomecoord,c1_uc,c2));  in genome_gap_simple()
3203 	pairs = Pairpool_push(pairs,pairpool,roffset+querycoord,leftoffset+genomecoord,  in genome_gap_simple()
3209     *new_leftgenomepos = leftoffset+(bestrL-1);  in genome_gap_simple()