diff --git a/CommandLines.h b/CommandLines.h index 3107983..0e9152c 100644 --- a/CommandLines.h +++ b/CommandLines.h @@ -5,7 +5,7 @@ #include #include -#define HA_VERSION "0.19.4-r583" +#define HA_VERSION "0.19.4-r584" #define VERBOSE 0 diff --git a/gfa_ut.cpp b/gfa_ut.cpp index cf0ed28..dbc04a2 100644 --- a/gfa_ut.cpp +++ b/gfa_ut.cpp @@ -7365,7 +7365,7 @@ void rebuid_idx(ul_resolve_t *uidx) init_ul_str_idx_t(uidx); } -void shrink_1b(ma_ug_t *ug, uc_block_t *z, uint32_t is_forward) +void shrink_1b(ma_ug_t *ug, uc_block_t *z, uc_block_t *lim, uint32_t is_forward) { if(z->ts != 0 || z->te != ug->g->seq[z->hid].len) return; uc_block_t bc = *z; @@ -7377,12 +7377,14 @@ void shrink_1b(ma_ug_t *ug, uc_block_t *z, uint32_t is_forward) } else { z->te -= 1; z->qs += off; } + if((lim) && (!((z->qs <= lim->qs) && (z->qe <= lim->qe)))) *z = bc; } else { if((!z->rev)) { z->te -= 1; z->qe -= off; } else { z->ts += 1; z->qe -= off; } + if((lim) && (!((z->qs >= lim->qs) && (z->qe >= lim->qe)))) *z = bc; } if((ugl_cover_check(bc.ts, bc.te, &(ug->u.a[bc.hid]))) && (!ugl_cover_check(z->ts, z->te, &(ug->u.a[z->hid])))) { @@ -7436,7 +7438,7 @@ void renew_ul_vec_t(ul_vec_t *x, ma_ug_t *ug) void shrink_ul0(all_ul_t *uls, ul_str_t *str, uint64_t id, integer_t *buf, ma_ug_t *ug) { - uint32_t k, c_k, p_k, cv, pv, bl, i; uc_block_t *xi; buf->u.n = 0; nid_t *np = NULL; + uint32_t k, c_k, p_k, cv, pv, bl, i; uc_block_t *xi, *yi; buf->u.n = 0; nid_t *np = NULL; asg_arc_t *av; uint32_t nv, s, e, m, d, mm, is_conn; uint64_t *z; ul_vec_t *x; if(str->cn < 2) return; for (k = 0, bl = 0, c_k = p_k = pv = (uint32_t)-1; k < str->cn; k++) { @@ -7464,6 +7466,11 @@ void shrink_ul0(all_ul_t *uls, ul_str_t *str, uint64_t id, integer_t *buf, ma_ug is_conn = 1; } } + if(is_conn) { + is_conn = 0; assert(k); + yi = &(uls->a[id].bb.a[str->a[k-1]>>32]); + if((xi->qs >= yi->qs) && (xi->qe >= yi->qe)) is_conn = 1; + } if(is_conn) { bl++; } else { @@ -7514,10 +7521,9 @@ void shrink_ul0(all_ul_t *uls, ul_str_t *str, uint64_t id, integer_t *buf, ma_ug x->bb.n = m; assert(x->bb.n > 1); - - - shrink_1b(ug, &(x->bb.a[0]), 1); - shrink_1b(ug, &(x->bb.a[x->bb.n-1]), 0); + shrink_1b(ug, &(x->bb.a[0]), ((x->bb.n>=2)?&(x->bb.a[1]):(NULL)), 1); + shrink_1b(ug, &(x->bb.a[x->bb.n-1]), ((x->bb.n>=2)?&(x->bb.a[x->bb.n-2]):(NULL)), 0); + d = x->bb.a[0].qs; for (k = 0; k < x->bb.n; k++) { x->bb.a[k].qs -= d; x->bb.a[k].qe -= d; @@ -7546,8 +7552,8 @@ void shrink_ul0(all_ul_t *uls, ul_str_t *str, uint64_t id, integer_t *buf, ma_ug } x->bb.n = m; assert(x->bb.n > 1); - shrink_1b(ug, &(x->bb.a[0]), 1); - shrink_1b(ug, &(x->bb.a[x->bb.n-1]), 0); + shrink_1b(ug, &(x->bb.a[0]), ((x->bb.n>=2)?&(x->bb.a[1]):(NULL)), 1); + shrink_1b(ug, &(x->bb.a[x->bb.n-1]), ((x->bb.n>=2)?&(x->bb.a[x->bb.n-2]):(NULL)), 0); d = x->bb.a[0].qs; for (k = 0; k < x->bb.n; k++) { x->bb.a[k].qs -= d; x->bb.a[k].qe -= d;