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changed the output file names

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This commit is contained in:
Heng Li
2019-12-30 12:01:54 -05:00
parent 30eddefc57
commit 3a61b1b0b0
4 changed files with 102 additions and 78 deletions
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2
Assembly.cpp
View File

@@ -1717,7 +1717,7 @@ void Output_PAF()
fprintf(stderr, "Writing PAF to disk ...... \n");
char* paf_name = (char*)malloc(strlen(asm_opt.output_file_name)+5);
sprintf(paf_name, "%s.paf", asm_opt.output_file_name);
sprintf(paf_name, "%s.ovlp.paf", asm_opt.output_file_name);
FILE* output_file = fopen(paf_name, "w");
uint64_t i, j;
ma_hit_t_alloc* sources = R_INF.paf;

7
CommandLines.cpp
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@@ -21,8 +21,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
{
fprintf(stderr, "Usage: hifiasm [options] <in_1.fq> <in_2.fq> <...>\n");
fprintf(stderr, "Options:\n");
///fprintf(stderr, " -q FILE input in the fastq(.gz)/fasta(.gz) formats\n");
fprintf(stderr, " -o FILE output assembly (in gfa format) and corrected reads [%s]\n", asm_opt->output_file_name);
fprintf(stderr, " -o FILE prefix of output files [%s]\n", asm_opt->output_file_name);
fprintf(stderr, " -t INT number of threads [%d]\n", asm_opt->thread_num);
fprintf(stderr, " -r INT round of correction [%d]\n", asm_opt->number_of_round);
fprintf(stderr, " -a INT round of assembly cleaning [%d]\n", asm_opt->clean_round);
@@ -36,7 +35,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -y FLOAT min overlap drop ratio [%.2g]\n", asm_opt->min_drop_rate);
fprintf(stderr, " -v show version number\n");
fprintf(stderr, " -h show help information\n");
fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -k 40 -t 32 -r 2 NA12878.fq.gz\n");
fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n");
}
@@ -247,4 +246,4 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
get_queries(argc, argv, &opt, asm_opt);
return check_option(asm_opt);
}
}

94
Overlaps.cpp
View File

@@ -7041,29 +7041,34 @@ const long long n_read)
return 0;
}
void ma_ug_print(const ma_ug_t *ug, All_reads *RNF, const ma_sub_t *coverage_cut, FILE *fp)
void ma_ug_print2(const ma_ug_t *ug, All_reads *RNF, const ma_sub_t *coverage_cut, int print_seq, FILE *fp)
{
uint32_t i, j, l;
char name[32];
for (i = 0; i < ug->u.n; ++i) { // the Segment lines in GFA
ma_utg_t *p = &ug->u.a[i];
sprintf(name, "utg%.6d%c", i + 1, "lc"[p->circ]);
fprintf(fp, "S\t%s\t%s\tLN:i:%d\n", name, p->s? p->s : "*", p->len);
if (print_seq) fprintf(fp, "S\t%s\t%s\tLN:i:%d\n", name, p->s? p->s : "*", p->len);
else fprintf(fp, "S\t%s\t*\tLN:i:%d\n", name, p->len);
for (j = l = 0; j < p->n; l += (uint32_t)p->a[j++]) {
uint32_t x = p->a[j]>>33;
fprintf(fp, "a\t%s\t%d\t%.*s(%u):%d-%d\t%c\t%d\n", name, l,
(int)Get_NAME_LENGTH((*RNF), x), Get_NAME((*RNF), x), x,
coverage_cut[x].s + 1, coverage_cut[x].e, "+-"[p->a[j]>>32&1], (uint32_t)p->a[j]);
fprintf(fp, "A\t%s\t%d\t%c\t%.*s\t%d\t%d\tid:i:%d\n", name, l, "+-"[p->a[j]>>32&1], (int)Get_NAME_LENGTH((*RNF), x),
Get_NAME((*RNF), x), coverage_cut[x].s, coverage_cut[x].e, x);
}
}
for (i = 0; i < ug->g->n_arc; ++i) { // the Link lines in GFA
uint32_t u = ug->g->arc[i].ul>>32, v = ug->g->arc[i].v;
fprintf(fp, "L\tutg%.6d%c\t%c\tutg%.6d%c\t%c\t%dM\tSD:i:%d\n", (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
fprintf(fp, "L\tutg%.6d%c\t%c\tutg%.6d%c\t%c\t%dM\tL1:i:%d\n", (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
(v>>1)+1, "lc"[ug->u.a[v>>1].circ], "+-"[v&1], ug->g->arc[i].ol, asg_arc_len(ug->g->arc[i]));
}
}
void ma_ug_print(const ma_ug_t *ug, All_reads *RNF, const ma_sub_t *coverage_cut, FILE *fp)
{
ma_ug_print2(ug, RNF, coverage_cut, 1, fp);
}
int asg_cut_internal(asg_t *g, int max_ext)
{
asg64_v a = {0,0,0};
@@ -7310,18 +7315,7 @@ void ma_sg_print(const asg_t *g, const All_reads *RNF, const ma_sub_t *sub, FILE
void ma_ug_print_simple(const ma_ug_t *ug, All_reads *RNF, const ma_sub_t *coverage_cut, FILE *fp)
{
uint32_t i;
char name[32];
for (i = 0; i < ug->u.n; ++i) { // the Segment lines in GFA
ma_utg_t *p = &ug->u.a[i];
sprintf(name, "utg%.6d%c", i + 1, "lc"[p->circ]);
fprintf(fp, "S\t%s\t%s\tLN:i:%d\n", name, "*", p->len);
}
for (i = 0; i < ug->g->n_arc; ++i) { // the Link lines in GFA
uint32_t u = ug->g->arc[i].ul>>32, v = ug->g->arc[i].v;
fprintf(fp, "L\tutg%.6d%c\t%c\tutg%.6d%c\t%c\t%dM\tSD:i:%d\n", (u>>1)+1, "lc"[ug->u.a[u>>1].circ], "+-"[u&1],
(v>>1)+1, "lc"[ug->u.a[v>>1].circ], "+-"[v&1], ug->g->arc[i].ol, asg_arc_len(ug->g->arc[i]));
}
ma_ug_print2(ug, RNF, coverage_cut, 0, fp);
}
@@ -7737,16 +7731,16 @@ void output_unitig_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_na
ug = ma_ug_gen(sg);
ma_ug_seq(ug, &R_INF, coverage_cut, n_read);
fprintf(stderr, "Writing unitig GFA to disk... \n");
fprintf(stderr, "Writing raw unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.utg.gfa", output_file_name);
sprintf(gfa_name, "%s.r_utg.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
// sprintf(gfa_name, "%s.simple.gfa", output_file_name);
// output_file = fopen(gfa_name, "w");
// ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
// fclose(output_file);
sprintf(gfa_name, "%s.r_utg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
free(gfa_name);
ma_ug_destroy(ug);
@@ -7887,13 +7881,13 @@ void write_all_data_to_disk(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sou
All_reads *RNF, char* output_file_name)
{
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.gfa.aux", output_file_name);
sprintf(gfa_name, "%s.ovlp", output_file_name);
write_All_reads(RNF, gfa_name);
sprintf(gfa_name, "%s.gfa.aux.source", output_file_name);
sprintf(gfa_name, "%s.ovlp.source", output_file_name);
write_ma_hit_ts(sources, RNF->total_reads, gfa_name);
sprintf(gfa_name, "%s.gfa.aux.reverse", output_file_name);
sprintf(gfa_name, "%s.ovlp.reverse", output_file_name);
write_ma_hit_ts(reverse_sources, RNF->total_reads, gfa_name);
free(gfa_name);
@@ -7903,20 +7897,20 @@ int load_all_data_from_disk(ma_hit_t_alloc **sources, ma_hit_t_alloc **reverse_s
char* output_file_name)
{
char* gfa_name = (char*)malloc(strlen(output_file_name)+25);
sprintf(gfa_name, "%s.gfa.aux", output_file_name);
sprintf(gfa_name, "%s.ovlp.aux", output_file_name);
if(!load_All_reads(&R_INF, gfa_name))
{
return 0;
}
sprintf(gfa_name, "%s.gfa.aux.source", output_file_name);
sprintf(gfa_name, "%s.ovlp.source", output_file_name);
if(!load_ma_hit_ts(sources, gfa_name))
{
return 0;
}
sprintf(gfa_name, "%s.gfa.aux.reverse", output_file_name);
sprintf(gfa_name, "%s.ovlp.reverse", output_file_name);
if(!load_ma_hit_ts(reverse_sources, gfa_name))
{
return 0;
@@ -8770,17 +8764,17 @@ char* output_file_name, long long n_read, long long bubble_dist, long long tipsL
ug = ma_ug_gen_primary(sg, 0);
ma_ug_seq(ug, &R_INF, coverage_cut, n_read);
fprintf(stderr, "Writing unitig GFA to disk... \n");
fprintf(stderr, "Writing processed unitig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
sprintf(gfa_name, "%s.wsb.utg.gfa", output_file_name);
sprintf(gfa_name, "%s.p_utg.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
// sprintf(gfa_name, "%s.simple.no_s_bub.gfa", output_file_name);
// output_file = fopen(gfa_name, "w");
// ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
// fclose(output_file);
sprintf(gfa_name, "%s.p_utg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
free(gfa_name);
ma_ug_destroy(ug);
@@ -8883,21 +8877,17 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
ug = ma_ug_gen_primary(sg, 0);
ma_ug_seq(ug, &R_INF, coverage_cut, n_read);
fprintf(stderr, "Writing unitig GFA to disk... \n");
fprintf(stderr, "Writing primary contig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
sprintf(gfa_name, "%s.ctg.gfa", output_file_name);
sprintf(gfa_name, "%s.p_ctg.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
// sprintf(gfa_name, "%s.simple.contig.gfa", output_file_name);
// output_file = fopen(gfa_name, "w");
// ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
// fclose(output_file);
sprintf(gfa_name, "%s.p_ctg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
free(gfa_name);
ma_ug_destroy(ug);
@@ -8910,17 +8900,17 @@ void output_contig_graph_alternative(asg_t *sg, ma_sub_t* coverage_cut, char* ou
ug = ma_ug_gen_primary(sg, 1);
ma_ug_seq(ug, &R_INF, coverage_cut, n_read);
fprintf(stderr, "Writing unitig GFA to disk... \n");
fprintf(stderr, "Writing alternate contig GFA to disk... \n");
char* gfa_name = (char*)malloc(strlen(output_file_name)+35);
sprintf(gfa_name, "%s.alter.ctg.gfa", output_file_name);
sprintf(gfa_name, "%s.a_ctg.gfa", output_file_name);
FILE* output_file = fopen(gfa_name, "w");
ma_ug_print(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
// sprintf(gfa_name, "%s.simple.alter.ctg.gfa", output_file_name);
// output_file = fopen(gfa_name, "w");
// ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
// fclose(output_file);
sprintf(gfa_name, "%s.a_ctg.noseq.gfa", output_file_name);
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
fclose(output_file);
free(gfa_name);
ma_ug_destroy(ug);

77
README.md
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@@ -2,24 +2,46 @@
```sh
# Install hifiasm (requiring g++ and zlib)
git clone https://github.com/chhylp123/hifiasm.git
git clone https://github.com/chhylp123/hifiasm
cd hifiasm && make
# Assembly
./hifiasm -t 32 NA12878.fq.gz
./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz
```
## Introduction
Hifiasm is an ultrafast haplotype-resolved de novo assembler based on PacBio Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed genome. Thus, it is able to keep the haplotype information as much as possible. The input of hifiasm is the PacBio Hifi reads in fasta/fastq format, and its outputs consist of:
1. Haplotype-resolved assembly [unitig][unitig] graph in [GFA][gfa] format (hifiasm.asm.utg.gfa in dafault).
2. Haplotype-resolved assembly [unitig][unitig] graph in [GFA][gfa] format without small bubbles (hifiasm.asm.wsb.utg.gfa in dafault). Small bubbles might be caused by somatic mutations, which are useless for some applications.
3. Primary assembly [contig][unitig] graph in [GFA][gfa] format (hifiasm.asm.ctg.gfa in dafault).
4. Alternate assembly [contig][unitig] graph in [GFA][gfa] format (hifiasm.asm.alter.ctg.gfa in dafault).
5. Haplotype-aware error corrected reads in fasta format (hifiasm.asm.ec.fa in dafault).
Hifiasm is an ultrafast haplotype-resolved de novo assembler based on PacBio
Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed
genome. Thus, it is able to keep the haplotype information as much as possible.
The input of hifiasm is the PacBio Hifi reads in fasta/fastq format, and its
outputs consist of:
1. Haplotype-resolved raw [unitig][unitig] graph in [GFA][gfa] format
(hifiasm.asm.r\_utg.gfa by default).
2. Haplotype-resolved processed [unitig][unitig] graph in [GFA][gfa] format
without small bubbles (hifiasm.asm.p\_utg.gfa by default). Small bubbles
might be caused by somatic mutations, which are useless for some
applications.
3. Primary assembly [contig][unitig] graph in [GFA][gfa] format
(hifiasm.asm.p\_ctg.gfa by default).
4. Alternate assembly [contig][unitig] graph in [GFA][gfa] format
(hifiasm.asm.a\_ctg.gfa by default).
5. Haplotype-aware error corrected reads in fasta format (hifiasm.asm.ec.fa by
default).
6. All-to-all overlaps in [paf][paf] format (hifiasm.asm.paf).
So far hifiasm is still in early development stage, it will output phased chromosome-level high-quality assembly in the near future. In addition, hifiasm also outputs three binary files that save all overlap inforamtion (hifiasm.asm.gfa.aux.bin, hifiasm.asm.gfa.aux.reverse.bin, hifiasm.asm.gfa.aux.source.bin in default). With these files, hifiasm can avoid the time-consuming all-to-all overlap calculation step, and do the assembly directly and quickly. This might be helpful when you want to get an optimized assembly by multiple round of experiments with different parameters.
So far hifiasm is still in early development stage, it will output phased
chromosome-level high-quality assembly in the near future. In addition, hifiasm
also outputs three binary files that save all overlap inforamtion
(hifiasm.asm.gfa.aux.bin, hifiasm.asm.gfa.aux.reverse.bin,
hifiasm.asm.gfa.aux.source.bin in default). With these files, hifiasm can avoid
the time-consuming all-to-all overlap calculation step, and do the assembly
directly and quickly. This might be helpful when you want to get an optimized
assembly by multiple round of experiments with different parameters.
Hifiasm is a standalone and lightweight assembler, which does not need external libraries (except zlib). For large genomes, it can generate high-quality assembly in a few hours. Hifiasm has been tested on the following datasets:
Hifiasm is a standalone and lightweight assembler, which does not need external
libraries (except zlib). For large genomes, it can generate high-quality
assembly in a few hours. Hifiasm has been tested on the following datasets:
|<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>|
|:---------------|-----:|-----:|:---------------------|-------:|--------:|----:|----------------:|
@@ -33,35 +55,48 @@ Hifiasm is a standalone and lightweight assembler, which does not need external
[3] Butterfly has high heterozygous rate, so that most chromosomes have been fully separated into two haplotypes. In this case, contig N50 makes no sense.<sub>
## Usage
For Hifi reads assembly, a typical command line looks like:
```sh
./hifiasm -o NA12878.asm -k 40 -t 32 -r 2 NA12878.fq.gz
./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz
```
where `NA12878.fq.gz` is the input reads and `-o` specifies the output files. In this example, all output files can be found at `NA12878.asm.*`. `-k`, `-t` and `-r` specify the length of k-mer, the number of CPU threads, and the number of correction rounds, respectively. Note that at first run, hifiasm will save all overlaps to disk, which can avoid the time-consuming all-to-all overlap calculation next time. For hifiasm, once the overlap information has been obtained during the previous run in advance, it is able to load all overlaps from disk and then directly do assembly. If you want to ignore the pre-computed overlap information, please specify `-i` or simply delete `*gfa.aux.bin`, `*gfa.aux.reverse.bin` and `*gfa.aux.source.bin`.
where `NA12878.fq.gz` is the input reads and `-o` specifies the output files.
In this example, all output files can be found at `NA12878.asm.*`. `-k`, `-t`
and `-r` specify the length of k-mer, the number of CPU threads, and the number
of correction rounds, respectively. Note that at first run, hifiasm will save
all overlaps to disk, which can avoid the time-consuming all-to-all overlap
calculation next time. For hifiasm, once the overlap information has been
obtained during the previous run in advance, it is able to load all overlaps
from disk and then directly do assembly. If you want to ignore the pre-computed
overlap information, please specify `-i` or simply delete `*gfa.aux.bin`,
`*gfa.aux.reverse.bin` and `*gfa.aux.source.bin`.
Please note that some old Hifi reads may consist of short adapters. To improve the assembly quality, adapters should be removed by `-z` as follow:
Please note that some old Hifi reads may consist of short adapters. To improve
the assembly quality, adapters should be removed by `-z` as follow:
```sh
./hifiasm -k 40 -t 42 -r 2 -z 20 butterfly.fq.gz
./hifiasm -o butterfly.asm -t 42 -z 20 butterfly.fq.gz
```
In this example, hifiasm will remove 20 bases from both ends of each read.
[unitig]: http://wgs-assembler.sourceforge.net/wiki/index.php/Celera_Assembler_Terminology
[gfa]: https://github.com/pmelsted/GFA-spec/blob/master/GFA-spec.md
[paf]: https://github.com/lh3/miniasm/blob/master/PAF.md
## Getting Help
The `-h` option of hifiasm provides detailed description of options. If you have further questions,
please raise an issue at the issue page.
## Limitations and future works
1. For genome with low heterozygous rate, hifiasm only outputs haplotype-resolved assembly graph, instead of the phased chromosome-level assembly (will support such output in the near future).
The `-h` option of hifiasm provides detailed description of options. If you
have further questions, please raise an issue at the issue page.
## Limitations and future works
1. For genome with low heterozygous rate, hifiasm only outputs
haplotype-resolved assembly graph, instead of the phased chromosome-level
assembly (will support such output in the near future).
2. The running time and memory usage should be further reduced.
3. The N50 should be further improved.
3. The N50 should be further improved.