| /dports/biology/gmap/gmap-2020-09-12/src/ |
| H A D | chimera.h | 35 Chimera_new (Stage3_T from, Stage3_T to, int chimerapos, int chimeraequivpos,
52 Chimera_bestpath (int *five_score, int *three_score, int *chimerapos, int *chimeraequivpos, int *be…
56 Chimera_find_breakpoint (int *chimeraequivpos, int *rangelow, int *rangehigh,
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| H A D | chimera.c | 178 Chimera_new (Stage3_T from, Stage3_T to, int chimerapos, int chimeraequivpos, in Chimera_new() argument
189 new->equivpos = chimeraequivpos; in Chimera_new()
567 *chimerapos = *chimeraequivpos = pos; in Chimera_bestpath()
572 *chimeraequivpos = pos; in Chimera_bestpath()
602 if (pos >= *chimerapos && pos <= *chimeraequivpos) { in Chimera_bestpath()
696 chimerapos = *chimeraequivpos = pos; in Chimera_find_breakpoint()
698 *chimeraequivpos = pos; in Chimera_find_breakpoint()
705 if (pos >= chimerapos && pos <= *chimeraequivpos) { in Chimera_find_breakpoint()
743 if (*rangehigh < *chimeraequivpos) { in Chimera_find_breakpoint()
744 *rangehigh = *chimeraequivpos; in Chimera_find_breakpoint()
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| H A D | output.c | 665 int chimerapos, chimeraequivpos, chimera_cdna_direction; in Output_filestring_fromresult() local
683 chimerapos = chimeraequivpos = -1; in Output_filestring_fromresult()
738 chimeraequivpos = Chimera_equivpos(chimera); in Output_filestring_fromresult()
863 checksump,chimerapos,chimeraequivpos, in Output_filestring_fromresult()
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| H A D | gmap.c | 2477 find_breakpoint (int *cdna_direction, int *chimerapos, int *chimeraequivpos, int *exonexonpos, in find_breakpoint() argument
2597 if ((*chimerapos = Chimera_find_breakpoint(&(*chimeraequivpos),&rangelow,&rangehigh, in find_breakpoint()
2608 debug2(printf("Chimera_find_breakpoint has chimerapos %d..%d\n",*chimerapos,*chimeraequivpos)); in find_breakpoint()
2634 *chimerapos,*chimeraequivpos,(*chimerapos)-1,*chimeraequivpos)); in find_breakpoint()
2636 breakpoint = ((*chimerapos) + (*chimeraequivpos))/2; in find_breakpoint()
2643 breakpoint = *chimerapos = *chimeraequivpos = *exonexonpos; in find_breakpoint()
2675 int breakpoint, chimerapos, chimeraequivpos, exonexonpos; in check_for_local() local
3011 if (Chimera_bestpath(&five_score,&three_score,&chimerapos,&chimeraequivpos,&bestfrom,&bestto, in check_for_local()
3025 …if ((breakpoint = find_breakpoint(&chimera_cdna_direction,&chimerapos,&chimeraequivpos,&exonexonpo… in check_for_local()
3119 int breakpoint, chimerapos, chimeraequivpos, exonexonpos; in check_for_chimera() local
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| H A D | pair.h | 267 int chimerapos, int chimeraequivpos, double donor_prob, double acceptor_prob,
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| H A D | stage3.h | 290 bool checksump, int chimerapos, int chimeraequivpos,
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| H A D | pair.c | 8697 int chimerapos, int chimeraequivpos, double donor_prob, double acceptor_prob,
8792 if (chimeraequivpos == chimerapos) {
8803 FPRINTF(fp," chimera:%d..%d",chimerapos + ONEBASEDP,chimeraequivpos + ONEBASEDP);
9002 int chimerapos, int chimeraequivpos, double donor_prob, double acceptor_prob,
9093 if (chimeraequivpos == chimerapos) {
9104 FPRINTF(fp," chimera:%d..%d",chimerapos + ONEBASEDP,chimeraequivpos + ONEBASEDP);
9190 int chimerapos, int chimeraequivpos, double donor_prob, double acceptor_prob, in Pair_print_compressed() argument
9277 if (chimeraequivpos == chimerapos) { in Pair_print_compressed()
9288 FPRINTF(fp," chimera:%d..%d",chimerapos + ONEBASEDP,chimeraequivpos + ONEBASEDP); in Pair_print_compressed()
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| H A D | stage3.c | 6989 bool checksump, int chimerapos, int chimeraequivpos, in Stage3_print_compressed() argument
7013 checksump,chimerapos,chimeraequivpos,donor_prob,acceptor_prob, in Stage3_print_compressed()
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| /dports/biology/gmap/gmap-2020-09-12/ |
| H A D | ChangeLog | 11016 breakpoint instead of chimerapos and chimeraequivpos, to avoid issues
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