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r525

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chhylp123
2023-02-21 20:22:56 -05:00
parent 8ea2d5a622
commit 2b4b4f29e0
3 changed files with 12 additions and 5 deletions
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CommandLines.h
+1 -1
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@@ -5,7 +5,7 @@
#include <pthread.h> #include <pthread.h>
#include <stdint.h> #include <stdint.h>
#define HA_VERSION "0.18.7-r523" #define HA_VERSION "0.18.8-r525"
#define VERBOSE 0 #define VERBOSE 0
gfa_ut.cpp
+1 -1
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@@ -16912,7 +16912,7 @@ ul_renew_t *ropt, const char *bin_file, uint64_t free_uld, uint64_t is_bridg, ui
// print_ul_alignment(init_ug, &UL_INF, 47072, "after-2"); // print_ul_alignment(init_ug, &UL_INF, 47072, "after-2");
// exit(1); // exit(1);
// if(free_uld) { // if(free_uld) {
print_raw_uls_seq(uidx, asm_opt.output_file_name); // print_raw_uls_seq(uidx, asm_opt.output_file_name);
// print_raw_uls_aln(uidx, asm_opt.output_file_name); // print_raw_uls_aln(uidx, asm_opt.output_file_name);
// } // }
horder.cpp
+10 -3
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@@ -4117,6 +4117,7 @@ void gen_mc_clus_backbone_layout(scg_t *sg, asg64_v *res, uint32_t *out, uint32_
uint64_t k, l, i, rn, n0, n1, v, z; int64_t m, s, e; osg_arc_t *t = NULL; uint64_t k, l, i, rn, n0, n1, v, z; int64_t m, s, e; osg_arc_t *t = NULL;
kv_resize(uint64_t, *res, sg->g->n_seq); res->n = sg->g->n_seq; kv_resize(uint64_t, *res, sg->g->n_seq); res->n = sg->g->n_seq;
memset(res->a, 0, sizeof((*(res->a)))*res->n); rn = res->n; memset(res->a, 0, sizeof((*(res->a)))*res->n); rn = res->n;
// fprintf(stderr, "[M::%s::]******Start******\n",__func__);
for (k = 0; k < sg->g->n_seq; k++) { for (k = 0; k < sg->g->n_seq; k++) {
///I guess this should be (!!(asg_arc_n(lg, k<<1)))^(!!(asg_arc_n(lg, (k<<1)+1)))? ///I guess this should be (!!(asg_arc_n(lg, k<<1)))^(!!(asg_arc_n(lg, (k<<1)+1)))?
@@ -4200,12 +4201,12 @@ void gen_mc_clus_backbone_layout(scg_t *sg, asg64_v *res, uint32_t *out, uint32_
} }
} }
uint32_t db_on = 0, db_z = 0; // uint32_t db_on = 0, db_z = 0;
assert((res->n-rn) == sg->g->n_seq); assert((res->n-rn) == sg->g->n_seq);
for (l = 0, k = 1, i = 0; k <= out_n; k++) { for (l = 0, k = 1, i = 0; k <= out_n; k++) {
if(k == out_n || out[k] == (uint32_t)-1) { if(k == out_n || out[k] == (uint32_t)-1) {
if(k > l) { if(k > l) {
res->a[i++] = ((l<<32)|(k)); db_on += k - l; res->a[i++] = ((l<<32)|(k)); ///db_on += k - l;
} else { } else {
assert(k == out_n); assert(k == out_n);
} }
@@ -4221,8 +4222,14 @@ void gen_mc_clus_backbone_layout(scg_t *sg, asg64_v *res, uint32_t *out, uint32_
} else { } else {
for (m = e-1; m >= s; m--) buf[z++] = out[m]; for (m = e-1; m >= s; m--) buf[z++] = out[m];
} }
// if(e > s) {
// fprintf(stderr, "[M::%s::]\t#chain::%ld\tutg%.6ul->utg%.6ul\n",
// __func__, (e-s), buf[z-(e-s)]+1, buf[z-1]+1);
// }
buf[z++] = (uint32_t)-1; buf[z++] = (uint32_t)-1;
db_z += e - s; // db_z += e - s;
} }
// if(!(z == out_n)) { // if(!(z == out_n)) {
// fprintf(stderr, "[M::%s] sg->g->n_arc::%u, sg->g->n_seq::%u, z::%lu, out_n::%u, db_z::%u, db_on::%u\n", __func__, // fprintf(stderr, "[M::%s] sg->g->n_arc::%u, sg->g->n_seq::%u, z::%lu, out_n::%u, db_z::%u, db_on::%u\n", __func__,