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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 DVCFRecord.java533 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()
H A DCDSFeature.java13 protected int intronlength = 0; field in CDSFeature
/dports/biology/gmap/gmap-2020-09-12/src/
H A Dget-genome.c688 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()
H A Dstage3.c1846 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()
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H A Dstage1.c2930 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()
/dports/biology/minimap2/minimap2-2.24/tex/
H A Dminimap2.tex580 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
/dports/biology/gmap/gmap-2020-09-12/
H A DChangeLog127 * 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.