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keep l1 trans

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chhylp123
2021-04-04 14:00:28 -04:00
parent ebfc04d253
commit 8e75eb5a05
6 changed files with 356 additions and 72 deletions
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hic.cpp
+15 -10
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@@ -13364,6 +13364,11 @@ const char* aln)
}
**/
void reduce_trans_chain(hc_links *link)
{
;
}
int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
{
double index_time = yak_realtime();
@@ -13416,28 +13421,28 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
bub.round_id = 0; bub.n_round = 2;
for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
{
fprintf(stderr, "0********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///fprintf(stderr, "0********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
identify_bubbles(idx->ug, &bub, idx->cov->t_ch->is_r_het);
fprintf(stderr, "1********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///fprintf(stderr, "1********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
if(bub.round_id == 0)
{
fprintf(stderr, "2********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///fprintf(stderr, "2********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
collect_hc_links(sl.idx, &sl.hits, &link, &bub, &M);
fprintf(stderr, "3********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///fprintf(stderr, "3********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
collect_hc_reverse_links(&link, idx->ug, &bub);
fprintf(stderr, "4********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///fprintf(stderr, "4********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
}
init_hic_p((ha_ug_index*)sl.idx, &sl.hits, &link, &bub, &back_hc_edge, &M, &hap, 0);
fprintf(stderr, "5********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///fprintf(stderr, "5********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///init_hic_p_new((ha_ug_index*)sl.idx, &sl.hits, idx->link, &bub, &back_hc_edge, &M);
reset_H_partition(&hap, (bub.round_id == 0? 1 : 0));
fprintf(stderr, "6********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///fprintf(stderr, "6********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
init_contig_partition(&hap, idx, &bub, &link);
fprintf(stderr, "7********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///fprintf(stderr, "7********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
phasing_improvement(&hap, &(hap.g_p), idx, &bub, &link);
fprintf(stderr, "8********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///fprintf(stderr, "8********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
label_unitigs(&(hap.g_p), idx->ug);
fprintf(stderr, "9********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///fprintf(stderr, "9********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///print_hc_links(idx->link, 0, &hap);
}