Searched refs:intronlength (Results 1 – 7 of 7) sorted by relevance
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/variant/ |
H A D | VCFRecord.java | 533 gfeat.intronlength+=range.getStart()-gfeat.lastRange.getEnd()-1; in checkSyn() 535 gfeat.intronlength+=gfeat.lastRange.getStart()-range.getEnd()-1; in checkSyn() 537 if(gfeat.intronlength < 0) in checkSyn() 538 gfeat.intronlength = 0; in checkSyn() 548 mod = (basePosition-gfeat.firstBase-gfeat.intronlength)%3; in checkSyn() 549 codonStart = basePosition-gfeat.firstBase-gfeat.intronlength-mod; in checkSyn() 553 mod = (gfeat.lastBase-basePosition-gfeat.intronlength)%3; in checkSyn() 554 codonStart = gfeat.lastBase-basePosition-gfeat.intronlength-mod; in checkSyn() 586 …System.out.println(gfeat.feature.getIDString()+" "+codonStart+" "+gfeat.intronlength+" basePositi… in checkSyn()
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H A D | CDSFeature.java | 13 protected int intronlength = 0; field in CDSFeature
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/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | get-genome.c | 688 Chrpos_T exonstart, exonend, exonlow, exonhigh, exonlength, intronlength, in genemap_print_gsequence() local 710 intronlength = exonlow - prev_exonhigh - 1; in genemap_print_gsequence() 711 gbuffer = (char *) CALLOC(intronlength+1,sizeof(char)); in genemap_print_gsequence() 713 intronlength,gbuffer); in genemap_print_gsequence() 727 intronlength = prev_exonlow - 1 - exonhigh; in genemap_print_gsequence() 728 gbuffer = (char *) CALLOC(intronlength+1,sizeof(char)); in genemap_print_gsequence() 730 intronlength,gbuffer); in genemap_print_gsequence() 731 make_complement_inplace(gbuffer,intronlength); in genemap_print_gsequence()
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H A D | stage3.c | 1846 if (intronlength < min_intronlength) { in assign_gap_types() 2112 if (intronlength < min_intronlength) { in assign_intron_probs() 2301 int intronlength; in remove_indel_gaps() local 2362 if (intronlength < min_intronlength) { in remove_indel_gaps() 2566 int intronlength; in add_intron() local 2603 if (intronlength < min_intronlength) { in add_intron() 2633 if (intronlength < min_intronlength) { in add_intron() 2643 if (intronlength < ngap + ngap + 3) { in add_intron() 4999 int intronlength; in fill_in_gaps() local 5089 intronlength,min_intronlength)); in fill_in_gaps() [all …]
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H A D | stage1.c | 2930 Univcoord_T diagonalj, intronlength; in compute_paths() local 2962 intronlength = diagonalj - segments[i].diagonal; in compute_paths() 2963 intronadj = intronlength/INTRONLEN_PENALTY; in compute_paths() 3020 intronlength = diagonalj - segments[i].diagonal; in compute_paths() 3021 intronadj = intronlength/INTRONLEN_PENALTY; in compute_paths()
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/dports/biology/minimap2/minimap2-2.24/tex/ |
H A D | minimap2.tex | 580 splice'); GMAP (`-n 0 --min-intronlength 30 --cross-species'); SpAln (`-Q7 -LS 602 GMAP under option `-k 14 -n 0 --min-intronlength 30 --cross-species' is 160
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/dports/biology/gmap/gmap-2020-09-12/ |
H A D | ChangeLog | 127 * stage3.c: Changed type of intronlength from Chrpos_T to int. Changed 2744 * gmap.c: Restored --intronlength option 3945 * gmap.c: Changed flag names to --max-intronlength-middle, 3946 --max-intronlength-ends, and --trim-end-exons 7460 * stage3.c: In Stage3_merge_local, traversing cDNA gap any time intronlength 9795 * stage3.c: In Stage3_merge_local_splice, if intronlength is small or 10176 intronlength.
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