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Searched refs:extraband_paired (Results 1 – 8 of 8) sorted by relevance

/dports/biology/gmap/gmap-2020-09-12/src/
H A Ddynprog_cdna.c153 lbandL = rlengthL - glength + extraband_paired; in bridge_cdna_gap_8_ud()
154 ubandL = extraband_paired; in bridge_cdna_gap_8_ud()
156 lbandR = rlengthR - glength + extraband_paired; in bridge_cdna_gap_8_ud()
157 ubandR = extraband_paired; in bridge_cdna_gap_8_ud()
417 lbandL = rlengthL - glength + extraband_paired; in bridge_cdna_gap_16_ud()
418 ubandL = extraband_paired; in bridge_cdna_gap_16_ud()
421 ubandR = extraband_paired; in bridge_cdna_gap_16_ud()
685 ubandL = extraband_paired; in bridge_cdna_gap()
688 ubandR = extraband_paired; in bridge_cdna_gap()
816 int extraband_paired, double defect_rate) { in Dynprog_cdna_gap() argument
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H A Ddynprog_cdna.h28 int extraband_paired, double defect_rate);
H A Ddynprog_genome.h31 bool jump_late_p, Pairpool_T pairpool, int extraband_paired,
H A Ddynprog_genome.c2898 int cdna_direction, bool watsonp, int extraband_paired, in bridge_intron_gap() argument
2918 ubandL = glengthL - rlength + extraband_paired; in bridge_intron_gap()
2919 lbandL = extraband_paired; in bridge_intron_gap()
2921 ubandR = glengthR - rlength + extraband_paired; in bridge_intron_gap()
2922 lbandR = extraband_paired; in bridge_intron_gap()
3278 bool jump_late_p, Pairpool_T pairpool, int extraband_paired, in Dynprog_genome_gap() argument
3506 Dynprog_compute_bands(&lbandL,&ubandL,rlength,glengthL,extraband_paired,/*widebandp*/true); in Dynprog_genome_gap()
3524 Dynprog_compute_bands(&lbandR,&ubandR,rlength,glengthR,extraband_paired,/*widebandp*/true); in Dynprog_genome_gap()
3780 Dynprog_compute_bands(&lbandL,&ubandL,rlength,glengthL,extraband_paired,/*widebandp*/true); in Dynprog_genome_gap()
3789 Dynprog_compute_bands(&lbandR,&ubandR,rlength,glengthR,extraband_paired,/*widebandp*/true); in Dynprog_genome_gap()
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H A Dstage3.c343 static int extraband_paired; variable
404 extraband_paired = extraband_paired_in; in Stage3_setup()
9316 extraband_paired,defect_rate); in traverse_cdna_gap()
9530 extraband_paired + n_peeled_indels_leftward + n_peeled_indels_rightward, in traverse_genome_gap()
9573 extraband_paired + n_peeled_indels_leftward + n_peeled_indels_rightward, in traverse_genome_gap()
9854 cdna_direction,watsonp,genestrand,jump_late_p,pairpool,extraband_paired, in traverse_dual_genome_gap()
9910 cdna_direction,watsonp,genestrand,jump_late_p,pairpool,extraband_paired, in traverse_dual_genome_gap()
9939 cdna_direction,watsonp,genestrand,jump_late_p,pairpool,extraband_paired, in traverse_dual_genome_gap()
10073 cdna_direction,watsonp,genestrand,jump_late_p,pairpool,extraband_paired, in traverse_dual_genome_gap()
10112 cdna_direction,watsonp,genestrand,jump_late_p,pairpool,extraband_paired, in traverse_dual_genome_gap()
H A Dgsnap.c178 static int extraband_paired = 7;
H A Dgmap.c291 static int extraband_paired = 14; /* This is in addition to length2 - length1 */ variable
7030 extraband_single,extraband_end,extraband_paired, in main()
/dports/biology/gmap/gmap-2020-09-12/
H A DChangeLog25359 extraband_single and extraband_paired.
25673 extraband_paired. Renamed maxlookback to nullgap. Created nsufflookback
25677 extraband_end and extraband_paired. Renamed maxlookback to nullgap.
25681 extraband_paired.
25684 extraband_paired. Extending last nucleotide at ends if possible. Removing