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seperate phase dp to ont/hifi

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chhylp123
2026-04-15 11:59:09 -04:00
parent 6b026f0caa
commit f5078f7b23
3 changed files with 74 additions and 73 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 "0.25.1-r909" #define HA_VERSION "0.25.1-r910"
#define VERBOSE 0 #define VERBOSE 0
Correct.cpp
+8 -7
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@@ -10781,7 +10781,7 @@ inline int64_t comput_sc_rphase(SnpStats *ai, uint64_t id, SnpStats *aj, uint64_
return INT64_MIN; return INT64_MIN;
} }
inline void comput_sc_rphase_hybrid(SnpStats *ai, uint64_t id, SnpStats *aj, uint64_t jd, haplotype_evdience *za, uint64_t occ0_cut, uint8_t hf_only, int64_t *sca, int64_t *sch, uint32_t *oid, uint8_t *oph, uint8_t *ohf) inline void comput_sc_rphase_hybrid(SnpStats *ai, uint64_t id, SnpStats *aj, uint64_t jd, haplotype_evdience *za, uint64_t occ0_cut, uint8_t enable_hf, uint8_t enable_ont, int64_t *sca, int64_t *sch, uint32_t *oid, uint8_t *oph, uint8_t *ohf)
{ {
(*sca) = (*sch) = INT64_MIN; (*oid) = ((uint32_t)-1); (*oph) = ((uint8_t)-1); (*ohf) = 0; (*sca) = (*sch) = INT64_MIN; (*oid) = ((uint32_t)-1); (*oph) = ((uint8_t)-1); (*ohf) = 0;
if(ai->site == aj->site) return; if(ai->site == aj->site) return;
@@ -10791,7 +10791,8 @@ inline void comput_sc_rphase_hybrid(SnpStats *ai, uint64_t id, SnpStats *aj, uin
jz = za + aj->non_homopolymer_num; jn = aj->homopolymer_num - aj->non_homopolymer_num; jz = za + aj->non_homopolymer_num; jn = aj->homopolymer_num - aj->non_homopolymer_num;
na[0] = na[1] = nh[0] = nh[1] = 0; na[0] = na[1] = nh[0] = nh[1] = 0;
(*ohf) = 1; if(enable_hf) {
(*ohf) = 1; (*sch) = INT64_MIN;
for (ik = jk = 0; (ik < in) && (iz[ik].overlapID&HQ_MASK) && (jk < jn) && (jz[jk].overlapID&HQ_MASK); ik++) { for (ik = jk = 0; (ik < in) && (iz[ik].overlapID&HQ_MASK) && (jk < jn) && (jz[jk].overlapID&HQ_MASK); ik++) {
for (; (jk < jn) && (jz[jk].overlapID < iz[ik].overlapID) && (jz[jk].overlapID&HQ_MASK); jk++); for (; (jk < jn) && (jz[jk].overlapID < iz[ik].overlapID) && (jz[jk].overlapID&HQ_MASK); jk++);
if((jk < jn) && (jz[jk].overlapID == iz[ik].overlapID)) { if((jk < jn) && (jz[jk].overlapID == iz[ik].overlapID)) {
@@ -10827,11 +10828,11 @@ inline void comput_sc_rphase_hybrid(SnpStats *ai, uint64_t id, SnpStats *aj, uin
} }
} }
na[0] = nh[0]; na[1] = nh[1]; na[0] = nh[0]; na[1] = nh[1];
}
if((nh[0] > 0) && (nh[1] > 0)) (*sch) = 1; if((nh[0] > 0) && (nh[1] > 0)) (*sch) = 1;
if((na[0] > 0) && (na[1] > 0)) (*sca) = 1; if((na[0] > 0) && (na[1] > 0)) (*sca) = 1;
if(hf_only) return; if(enable_ont) {
(*ohf) = 0; (*sca) = INT64_MIN; (*ohf) = 0; (*sca) = INT64_MIN;
for (ik = in - 1, jk = jn - 1; (ik >= 0) && (!(iz[ik].overlapID&HQ_MASK)) && (jk >= 0) && (!(jz[jk].overlapID&HQ_MASK)); ik--) { for (ik = in - 1, jk = jn - 1; (ik >= 0) && (!(iz[ik].overlapID&HQ_MASK)) && (jk >= 0) && (!(jz[jk].overlapID&HQ_MASK)); ik--) {
for (; (jk >= 0) && (jz[jk].overlapID < iz[ik].overlapID) && (!(jz[jk].overlapID&HQ_MASK)); jk--); for (; (jk >= 0) && (jz[jk].overlapID < iz[ik].overlapID) && (!(jz[jk].overlapID&HQ_MASK)); jk--);
@@ -10866,9 +10867,9 @@ inline void comput_sc_rphase_hybrid(SnpStats *ai, uint64_t id, SnpStats *aj, uin
na[fi]++; na[fi]++;
} }
} }
if((na[0] > 0) && (na[1] > 0)) (*sca) = 1; if((na[0] > 0) && (na[1] > 0)) (*sca) = 1;
} }
}
/** /**
inline void comput_sc_rphase_hybrid(SnpStats *ai, uint64_t id, SnpStats *aj, uint64_t jd, haplotype_evdience *za, uint64_t occ0_cut, overlap_region_alloc *ol, uint64_t tcut, int64_t *sca, int64_t *sch) inline void comput_sc_rphase_hybrid(SnpStats *ai, uint64_t id, SnpStats *aj, uint64_t jd, haplotype_evdience *za, uint64_t occ0_cut, overlap_region_alloc *ol, uint64_t tcut, int64_t *sca, int64_t *sch)
@@ -11814,7 +11815,7 @@ void gen_rphase_dp0_single_path_hybrid(SnpStats *a, int64_t an, haplotype_evdien
if(ch && ca) continue;; if(ch && ca) continue;;
comput_sc_rphase_hybrid(&a[i], i, &a[j], j, za, 0, ((ca)||(a[j].site < sa0))?1:0, &sc_a, &sc_h, &srid, &rh, &rhf); comput_sc_rphase_hybrid(&a[i], i, &a[j], j, za, 0, (a[j].site>=sh0)?1:0/**((ca)||(a[j].site < sa0))?1:0,**/, ((a[j].site>=sa0)&&(!ca))?1:0, &sc_a, &sc_h, &srid, &rh, &rhf);
if(srid != ((uint32_t)-1)) { if(srid != ((uint32_t)-1)) {
label_skip_mmb_fast(1 - rh, osi[srid], omm + oss[srid], oss[srid+1] - oss[srid], rhf?ii_h:ii_a, i, j); label_skip_mmb_fast(1 - rh, osi[srid], omm + oss[srid], oss[srid+1] - oss[srid], rhf?ii_h:ii_a, i, j);
} }
@@ -11824,7 +11825,7 @@ void gen_rphase_dp0_single_path_hybrid(SnpStats *a, int64_t an, haplotype_evdien
sth = (max_f_h>=1)?(max_f_h-1):(0);///f[max_f - 1] <= max_f -> f[st] <= max_f -> max(f[st]) = max_f sth = (max_f_h>=1)?(max_f_h-1):(0);///f[max_f - 1] <= max_f -> f[st] <= max_f -> max(f[st]) = max_f
} }
if ((sc_a != INT64_MIN) && (f_a[j] + 1 > max_f_a)) { if ((sc_a != INT64_MIN) && (f_a[j] + 1 > max_f_a)) {
if(!ca) { if(!ca) {///need check ca; in some case, comput_sc_rphase_hybrid only checked HF overlaps
max_f_a = f_a[j] + 1; max_j_a = j; max_f_a = f_a[j] + 1; max_j_a = j;
sta = (max_f_a>=1)?(max_f_a-1):(0);///f[max_f - 1] <= max_f -> f[st] <= max_f -> max(f[st]) = max_f sta = (max_f_a>=1)?(max_f_a-1):(0);///f[max_f - 1] <= max_f -> f[st] <= max_f -> max(f[st]) = max_f
} }
ecovlp.cpp
+1 -1
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@@ -5353,7 +5353,7 @@ static void worker_hap_ec_hybrid(void *data, long i, int tid)
} }
b->v8q.n = b->v8t.n = 0; set_ec_cov(asm_opt.het_cov, asm_opt.hom_cov, asm_opt.het_cov_set, asm_opt.polyploidy, het_a, hom_a); b->v8q.n = b->v8t.n = 0; set_ec_cov(asm_opt.het_cov, asm_opt.hom_cov, asm_opt.het_cov_set, asm_opt.polyploidy, het_a, hom_a);
// if(i != 937) return; // if((i%16) != 0) return;
// if(i != 5966) return; // if(i != 5966) return;
// fprintf(stderr, "-a-[M::%s] rid::%ld\n", __func__, i); // fprintf(stderr, "-a-[M::%s] rid::%ld\n", __func__, i);