mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-02 04:08:12 +08:00
update for 0.2.0
This commit is contained in:
chhylp123
+3
-1
@@ -1716,7 +1716,7 @@ void Output_PAF()
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{
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fprintf(stderr, "Writing PAF to disk ...... \n");
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char* paf_name = (char*)malloc(strlen(asm_opt.output_file_name)+5);
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char* paf_name = (char*)malloc(strlen(asm_opt.output_file_name)+50);
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sprintf(paf_name, "%s.ovlp.paf", asm_opt.output_file_name);
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FILE* output_file = fopen(paf_name, "w");
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uint64_t i, j;
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@@ -1757,6 +1757,8 @@ void Output_PAF()
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free(paf_name);
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fclose(output_file);
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fprintf(stderr, "PAF has beem written.\n");
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}
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+1
-1
@@ -5,7 +5,7 @@
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#include "ketopt.h"
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#include <sys/time.h>
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#define VERSION "0.1.0"
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#define VERSION "0.2.0"
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#define DEFAULT_OUTPUT "hifiasm.asm"
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hifiasm_opt_t asm_opt;
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+8
-4
@@ -5024,7 +5024,8 @@ long long xBeg, long long xEnd, long long flag_offset)
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for (i = 0; i < operationLen; i++)
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{
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/// note we need to deal with flag_offset carefully
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if(flag[x_i - flag_offset] < 127 && x_i >= xBeg && x_i <= xEnd)
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///if(flag[x_i - flag_offset] < 127 && x_i >= xBeg && x_i <= xEnd)
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if(x_i >= xBeg && x_i <= xEnd && flag[x_i - flag_offset] < 127)
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{
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flag[x_i - flag_offset]++;
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}
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@@ -5275,7 +5276,8 @@ haplotype_evdience_alloc* hap, long long snp_threshold)
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{
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///should be at least 2 mismatches
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/// note we need to deal with flag_offset carefully
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if(flag[x_i - flag_offset] > snp_threshold && x_i >= xBeg && x_i <= xEnd)
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///if(flag[x_i - flag_offset] > snp_threshold && x_i >= xBeg && x_i <= xEnd)
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if(x_i >= xBeg && x_i <= xEnd && flag[x_i - flag_offset] > snp_threshold)
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{
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ev.misBase = y_string[y_i];
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ev.overlapID = overlapID;
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@@ -5296,7 +5298,8 @@ haplotype_evdience_alloc* hap, long long snp_threshold)
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/// should be at least 2 mismatches
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/// note we need to deal with flag_offset carefully
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if(flag[x_i - flag_offset] > snp_threshold && x_i >= xBeg && x_i <= xEnd)
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///if(flag[x_i - flag_offset] > snp_threshold && x_i >= xBeg && x_i <= xEnd)
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if(x_i >= xBeg && x_i <= xEnd && flag[x_i - flag_offset] > snp_threshold)
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{
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ev.misBase = y_string[y_i];
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ev.overlapID = overlapID;
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@@ -5323,7 +5326,8 @@ haplotype_evdience_alloc* hap, long long snp_threshold)
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///if(hap->flag[inner_offset] > snp_threshold)
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/// should be at least 2 mismatches
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/// note we need to deal with flag_offset carefully
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if(flag[x_i - flag_offset] > snp_threshold && x_i >= xBeg && x_i <= xEnd)
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///if(flag[x_i - flag_offset] > snp_threshold && x_i >= xBeg && x_i <= xEnd)
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if(x_i >= xBeg && x_i <= xEnd && flag[x_i - flag_offset] > snp_threshold)
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{
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ev.misBase = 'N';
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ev.overlapID = overlapID;
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@@ -1,11 +1,11 @@
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CXX= g++
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CXXFLAGS= -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Wall #-Winline
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CXXFLAGS= -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Wall #-fsanitize=address -fno-omit-frame-pointer#-Winline
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CPPFLAGS=
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INCLUDES=
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OBJS= Output.o CommandLines.o Process_Read.o Assembly.o kmer.o Hash_Table.o \
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POA.o Correct.o Levenshtein_distance.o Overlaps.o #ksw2_extz2_sse.o
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EXE= hifiasm
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LIBS= -lz -lpthread -lm
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LIBS= -lz -lpthread -lm #-fsanitize=address -fno-omit-frame-pointer
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ifneq ($(asan),)
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CXXFLAGS+=-fsanitize=address
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+6032
-670
File diff suppressed because it is too large
Load Diff
+77
-5
@@ -17,7 +17,12 @@
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///#define MAX_BUBBLE_DIST 10000000
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#define SMALL_BUBBLE_SIZE (uint32_t)-1
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//#define SMALL_BUBBLE_SIZE 1000
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#define PRIMARY_LABLE 0
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#define ALTER_LABLE 1
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#define HAP_LABLE 2
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// #define PRIMARY_LABLE 1
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// #define ALTER_LABLE 2
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// #define HAP_LABLE 4
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#define Get_qn(RECORD) ((uint32_t)((RECORD).qns>>32))
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#define Get_qs(RECORD) ((uint32_t)((RECORD).qns))
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@@ -36,6 +41,8 @@
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#define LOOP 7
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///query is the read itself
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typedef struct {
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uint64_t qns;
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@@ -46,7 +53,6 @@ typedef struct {
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uint8_t no_l_indel;
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} ma_hit_t;
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typedef struct {
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ma_hit_t* buffer;
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uint32_t size;
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@@ -241,7 +247,7 @@ static inline void asg_seq_del(asg_t *g, uint32_t s)
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static inline void asg_seq_drop(asg_t *g, uint32_t s)
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{
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///s is not at primary
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if(g->seq[s].c)
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if(g->seq[s].c == ALTER_LABLE)
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{
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uint32_t k;
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for (k = 0; k < 2; ++k)
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@@ -254,8 +260,10 @@ static inline void asg_seq_drop(asg_t *g, uint32_t s)
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{
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if(av[i].del) continue;
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///if output node is at primary
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if(g->seq[(av[i].v>>1)].c == 0)
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{
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/****************************may have hap bugs********************************/
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///if(g->seq[(av[i].v>>1)].c == PRIMARY_LABLE)
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if(g->seq[(av[i].v>>1)].c == PRIMARY_LABLE || g->seq[(av[i].v>>1)].c == HAP_LABLE)
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{/****************************may have hap bugs********************************/
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av[i].del = 1;
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asg_arc_del(g, av[i].v^1, v^1, 1);
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}
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@@ -313,6 +321,36 @@ typedef struct {
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uint32_t pre_n_seq, seqID;
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} C_graph;
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typedef struct {
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kvec_t(uint32_t) a;
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uint32_t i;
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} kvec_t_u32_warp;
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typedef struct {
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kvec_t(uint64_t) a;
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uint64_t i;
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} kvec_t_u64_warp;
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typedef struct {
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uint32_t q_pos;
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uint32_t t_pos;
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uint32_t t_id;
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uint32_t is_color;
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} Hap_Align;
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typedef struct {
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kvec_t(Hap_Align) x;
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uint64_t i;
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} Hap_Align_warp;
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typedef struct {
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buf_t* b_0;
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uint32_t untigI;
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uint32_t readI;
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uint32_t offset;
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} rIdContig;
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// count the number of outgoing arcs, including reduced arcs
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static inline int count_out_with_del(const asg_t *g, uint32_t v)
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{
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@@ -350,4 +388,38 @@ void remove_overlaps(ma_hit_t_alloc* source_paf, uint64_t* source_index, long lo
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void add_overlaps_from_different_sources(ma_hit_t_alloc* source_paf_list, ma_hit_t_alloc* dest_paf,
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uint64_t* source_index, long long listLen);
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void print_revise_edges(ma_hit_t_alloc* source_paf, uint64_t* source_index, long long listLen);
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#define EvaluateLen(U, id) ((U).a[(id)].start)
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#define IsMerge(U, id) ((U).a[(id)].end)
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#define kv_reuse(v, rn, rm, r) ((v).n = (rn), (v).m = (rm), (v).a = (r))
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#define long_tip(U, id, threshold) ((EvaluateLen((U), (id))>=(threshold))&&(!((U).a[(id)].circ)))
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///there are threee cases:
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///1. if this untig is too long (>maxShortUntig), it must be not short untig/must be a long untig
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///2. if this untig is long (>minLongUntig && EvaluateLen(ug->u, av[i].v>>1) > (EvaluateLen(ug->u, v>>1)*l_untig_rate)), it might be a long tip
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#define check_long_tip(U, id, minLongUntig, maxShortUntig, ShortUntigRate, mainLen) \
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((!((U).a[(id)].circ)) \
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&& \
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((EvaluateLen((U), (id)) > (maxShortUntig))\
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||\
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((long_tip((U), (id), (minLongUntig)))\
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&&\
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(EvaluateLen((U), (id)) > (ShortUntigRate)*(mainLen)))))
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#define Get_vis(visit, v, d) (((visit)[(v)>>1])&(((((v)<<(d))&1)+1)))
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#define Set_vis(visit, v, d) (((visit)[(v)>>1])|=(((((v)<<(d))&1)+1)))
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typedef struct {
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uint64_t len;
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uint32_t* index;
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} R_to_U;
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void init_R_to_U(R_to_U* x, uint64_t len);
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void destory_R_to_U(R_to_U* x);
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void set_R_to_U(R_to_U* x, uint32_t rID, uint32_t uID, uint32_t is_Unitig);
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void get_R_to_U(R_to_U* x, uint32_t rID, uint32_t* uID, uint32_t* is_Unitig);
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void transfor_R_to_U(R_to_U* x);
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#endif
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@@ -43,9 +43,9 @@ assembly in a few hours. Hifiasm has been tested on the following datasets:
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|<sub>Dataset<sub>|<sub>GSize<sub>|<sub>Cov<sub>|<sub>Asm options<sub>|<sub>CPU time<sub>|<sub>Wall time<sub>|<sub>RAM<sub>|<sub>[unitig][unitig]/[contig][unitig] N50<sup>[1]</sup><sub>|
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|:---------------|-----:|-----:|:---------------------|-------:|--------:|----:|----------------:|
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|<sub>[Human NA12878]<sub>|<sub>3Gb<sub>|<sub>x28<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>200h<sub>| <sub>5h32m<sub>|<sub>114G<sub>|<sub>93.5Kb/21.5Mb<sub>|
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|<sub>[Human HG002]<sub>|<sub>3Gb<sub>|<sub>x43<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>405h10m<sub>|<sub>12h7m<sub>|<sub>146G<sub>|<sub>320kb/31.9Mb<sub>|
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|<sub>[Human CHM13]<sub>|<sub>3Gb<sub>|<sub>x27<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>157h28m<sub>|<sub>5h10m<sub>|<sub>85.8G<sub>|<sub>NA<sup>[2]</sup>/39.8Mb<sub>|
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|<sub>[Human NA12878]<sub>|<sub>3Gb<sub>|<sub>x28<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>200h<sub>| <sub>5h32m<sub>|<sub>114G<sub>|<sub>93.5Kb/28.2Mb<sub>|
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|<sub>[Human HG002]<sub>|<sub>3Gb<sub>|<sub>x43<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>405h10m<sub>|<sub>12h7m<sub>|<sub>146G<sub>|<sub>320kb/35.3Mb<sub>|
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|<sub>[Human CHM13]<sub>|<sub>3Gb<sub>|<sub>x27<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>157h28m<sub>|<sub>5h10m<sub>|<sub>85.8G<sub>|<sub>NA<sup>[2]</sup>/41.4Mb<sub>|
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|<sub>[Butterfly]<sub>|<sub>358Mb<sub>|<sub>x35<sub>|<sub>-k 40 -t 42 -r 2 -z 20<sub>|<sub>17h6m<sub>|<sub>36m<sub>|<sub>16G<sub>|<sub>7.5Mb/NA<sup>[3]</sup><sub>|
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<sub>[1] unitig N50 is the N50 of assembly graph with haplotype information (i.e., bubbles), while the contig N50 is the N50 of haplotype collapsed assembly (i.e., without bubbles).
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