mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-11 06:30:55 +08:00
r213: renamed trio binning output files
This commit is contained in:
Heng Li
+5
-5
@@ -50,8 +50,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
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fprintf(stderr, " -h show help information\n");
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fprintf(stderr, " Trio-partition:\n");
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fprintf(stderr, " -P FILE paternal trio index generated by \"yak count\" []\n");
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fprintf(stderr, " -M FILE maternal trio index generated by \"yak count\" []\n");
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fprintf(stderr, " -1 FILE hap1/paternal k-mer dump generated by \"yak count\" []\n");
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fprintf(stderr, " -2 FILE hap2/maternal k-mer dump generated by \"yak count\" []\n");
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fprintf(stderr, " -c INT lower bound of the binned k-mer's frequency [%d]\n", asm_opt->min_cnt);
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fprintf(stderr, " -d INT upper bound of the binned k-mer's frequency [%d]\n", asm_opt->mid_cnt);
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@@ -313,7 +313,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
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int c;
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while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:w:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:", long_options)) >= 0) {
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while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:w:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:1:2:", long_options)) >= 0) {
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if (c == 'h')
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{
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Print_H(asm_opt);
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@@ -339,8 +339,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
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else if (c == 'b') asm_opt->required_read_name = opt.arg;
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else if (c == 'c') asm_opt->min_cnt = atoi(opt.arg);
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else if (c == 'd') asm_opt->mid_cnt = atoi(opt.arg);
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else if (c == 'P') asm_opt->pat_index = opt.arg;
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else if (c == 'M') asm_opt->mat_index = opt.arg;
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else if (c == '1' || c == 'P') asm_opt->pat_index = opt.arg; // -P/-M reserved for backward compatibility
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else if (c == '2' || c == 'M') asm_opt->mat_index = opt.arg;
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else if (c == 'x') asm_opt->max_drop_rate = atof(opt.arg);
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else if (c == 'y') asm_opt->min_drop_rate = atof(opt.arg);
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else if (c == 'p') asm_opt->small_pop_bubble_size = atoll(opt.arg);
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+1
-1
@@ -3,7 +3,7 @@
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#include <pthread.h>
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#define HA_VERSION "0.3.0-dirty-r212"
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#define HA_VERSION "0.3.0-dirty-r213"
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#define VERBOSE 0
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+8
-5
@@ -9664,13 +9664,13 @@ void ma_ug_print2(const ma_ug_t *ug, All_reads *RNF, const ma_sub_t *coverage_cu
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uint32_t x = p->a[j]>>33;
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if(x<RNF->total_reads)
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{
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fprintf(fp, "A\t%s\t%d\t%c\t%.*s\t%d\t%d\tid:i:%d\t%c\n", name, l, "+-"[p->a[j]>>32&1],
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fprintf(fp, "A\t%s\t%d\t%c\t%.*s\t%d\t%d\tid:i:%d\tHG:A:%c\n", name, l, "+-"[p->a[j]>>32&1],
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(int)Get_NAME_LENGTH((*RNF), x), Get_NAME((*RNF), x),
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coverage_cut[x].s, coverage_cut[x].e, x, "apmaaa"[RNF->trio_flag[x]]);
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}
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else
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{
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fprintf(fp, "A\t%s\t%d\t%c\t%s\t%d\t%d\tid:i:%d\t%c\n", name, l, "+-"[p->a[j]>>32&1],
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fprintf(fp, "A\t%s\t%d\t%c\t%s\t%d\t%d\tid:i:%d\tHG:A:%c\n", name, l, "+-"[p->a[j]>>32&1],
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"FAKE", coverage_cut[x].s, coverage_cut[x].e, x, '*');
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}
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@@ -13527,7 +13527,7 @@ long long tipsLen, float tip_drop_ratio, long long stops_threshold, R_to_U* ruIn
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float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp)
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{
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char* gfa_name = (char*)malloc(strlen(output_file_name)+100);
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sprintf(gfa_name, "%s.%s.r_utg.gfa", output_file_name, (flag==FATHER?"p":"m"));
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sprintf(gfa_name, "%s.%s.p_ctg.gfa", output_file_name, (flag==FATHER?"hap1":"hap2"));
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fprintf(stderr, "Writing %s to disk... \n", gfa_name);
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FILE* output_file = fopen(gfa_name, "w");
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@@ -13548,7 +13548,7 @@ float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp)
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ma_ug_print(ug, &R_INF, coverage_cut, output_file);
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fclose(output_file);
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sprintf(gfa_name, "%s.%s.r_utg.noseq.gfa", output_file_name, (flag==FATHER?"p":"m"));
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sprintf(gfa_name, "%s.%s.p_ctg.noseq.gfa", output_file_name, (flag==FATHER?"hap1":"hap2"));
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output_file = fopen(gfa_name, "w");
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ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
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fclose(output_file);
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@@ -26495,7 +26495,10 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
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if ((asm_opt.pat_index && asm_opt.mat_index))
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{
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output_unitig_graph(sg, coverage_cut, output_file_name, sources, max_hang_length, mini_overlap_length);
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char *buf = (char*)calloc(strlen(output_file_name) + 25, 1);
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sprintf(buf, "%s.dip", output_file_name);
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output_unitig_graph(sg, coverage_cut, buf, sources, max_hang_length, mini_overlap_length);
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free(buf);
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output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources,
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reverse_sources, bubble_dist, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
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@@ -255,9 +255,6 @@ void trio_partition(void)
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return;
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}
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double start_time = Get_T();
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fprintf(stderr, "Start trio binning ...... \n");
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yak_ch_t *ch;
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int i /**, min_cnt = 2, mid_cnt = 5**/;
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tb_shared_t aux;
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@@ -286,6 +283,5 @@ void trio_partition(void)
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free(aux.bseq);
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yak_ch_destroy(ch);
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fprintf(stderr, "Trio binning has been done.\n");
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fprintf(stderr, "%-30s%18.2f\n\n", "Trio binning time:", Get_T() - start_time);
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fprintf(stderr, "[M::%s::%.3f*%.2f] ==> partitioned reads using yak dumps\n", __func__, yak_realtime(), yak_cpu_usage());
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}
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@@ -8,7 +8,7 @@ hifiasm - haplotype-resolved de novo assembler for PacBio Hifi reads.
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.PP
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hifiasm
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.RB [ -o
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.IR outPrefix ]
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.IR prefix ]
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.RB [ -t
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.IR numThres ]
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.RB [ -r
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@@ -51,8 +51,8 @@ outputs consist of multiple types of assembly graph in GFA format.
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.BI -o \ FILE
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Prefix of output files [hifiasm.asm]. The outputs of hifiasm include error corrected
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reads in fasta format, all-to-all overlaps in paf format, and four types of assembly
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graph in GFA format. For detailed description of all assembly graphs, please see
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.I 'Outputs'
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graph in GFA format. For detailed description of all assembly graphs, please see the
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.B OUTPUTS
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section of this man-page.
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.TP 10
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@@ -83,11 +83,11 @@ Rounds of haplotype-aware error corrections [2]. This option affects all outputs
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.TP 10
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.BI -a \ INT
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Rounds of assembly graph cleaning [4]. This option is used with
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.I [-x maxDropRatio]
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.B -x
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and
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.I [-y minDropRatio].
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.BR -y .
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Note that unlike
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.I [-r],
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.BR -r ,
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this option does not affect error corrected reads and all-to-all overlaps.
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@@ -103,11 +103,11 @@ significantly improve the assembly quality.
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.TP 10
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.BI -m \ INT
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Maximal probing distance for bubble popping when generating primary/alternate assembly
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Maximal probing distance for bubble popping when generating primary/alternate
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contig graphs [10000000]. Bubbles longer than
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.I INT
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bases will not be popped. For detailed description of these graphs, please see
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.I 'Outputs'
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bases will not be popped. For detailed description of these graphs, please see the
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.B OUTPUTS
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section of this man-page.
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@@ -117,8 +117,8 @@ Maximal probing distance for bubble popping when generating haplotype-resolved p
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without small bubbles [100000]. Bubbles longer than
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.I INT
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bases will not be popped. Small bubbles might be caused by somatic mutations or noise in data, which
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are not the real haplotype information. For detailed description of this graph, please see
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.I 'Outputs'
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are not the real haplotype information. For detailed description of this graph, please see the
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.B OUTPUTS
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section of this man-page.
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@@ -133,7 +133,7 @@ reads [3]. Hifiasm may try to remove small unitigs at various steps.
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.TP 10
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.BI -x \ FLOAT, -y \ FLOAT
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Max and min overlap drop ratio [0.8, 0.2]. This option is used with
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.I [-r roundCorrection].
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.BR -r .
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Given a node
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.I N
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in the assembly graph, let max(N)
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@@ -143,15 +143,15 @@ Hifiasm iteratively drops overlaps of
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.I N
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if their length / max(N)
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are below a threshold controlled by
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.I [-x maxDropRatio]
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.B -x
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and
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.I [-y minDropRatio].
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.BR -y .
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Hifiasm applies
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.I [-r roundCorrection]
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.B -r
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rounds of short overlap removal with an increasing threshold between
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.I [-x maxDropRatio]
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.B -x
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and
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.I [-y minDropRatio].
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.BR -y .
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.TP 10
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.BI -i
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@@ -167,38 +167,37 @@ with different parameters.
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.SS Trio-partition options
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.TP 10
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.BI -P \ FILE
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Paternal trio index. This index should be generated by
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.I [yak count]
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with the paternal short reads. For details of yak, please see
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.BI -1 \ FILE
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Paternal/haplotype1 k-mer dump generated by
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.B yak count
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from the paternal/haplotype1 reads. For details of yak, please see
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.I [https://github.com/lh3/yak]
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.TP 10
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.BI -M \ FILE
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Maternal trio index. This index should be generated by
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.I [yak count]
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with the maternal short reads. For details of yak, please see
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.BI -2 \ FILE
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Maternal/haplotype2 k-mer dump generated by
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.B yak count
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from the maternal/haplotype2 reads. For details of yak, please see
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.I [https://github.com/lh3/yak]
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.TP 10
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.BI -c \ INT
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Lower bound of the binned k-mer's frequency [2]. When doing trio binning,
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a k-mer is said to be differentiating if it occurs >=
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.I [-d upper_bound]
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.B -d
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times in one sample
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but occurs <
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.I [-c lower_bound]
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.B -c
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times in the other sample.
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.TP 10
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.BI -d \ INT
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Upper bound of the binned k-mer's frequency [5]. When doing trio binning,
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a k-mer is said to be differentiating if it occurs >=
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.I [-d upper_bound]
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.B -d
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times in one sample
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but occurs <
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.I [-c lower_bound]
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.B -c
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times in the other sample.
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@@ -235,60 +234,69 @@ Build maternal trio index from mat.fq.gz.
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Build paternal trio index from pat.fq.gz.
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.TP
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.BR ./hifiasm " " \-o " " NA12878.asm " " \-t " " 32 " " \-P " " pat.yak " " \-M " " mat.yak " " NA12878_1.fq.gz " " NA12878_2.fq.gz
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In this example, hifiasm will do trio assembly with 32 CPU threads. The paternal assembly can be found at [NA12878.asm.p.r_utg.gfa],
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and the maternal assembly can be found at [NA12878.asm.m.r_utg.gfa].
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.BR ./hifiasm " " \-o " " NA12878.asm " " \-t " " 32 " " \-1 " " pat.yak " " \-2 " " mat.yak " " NA12878_1.fq.gz " " NA12878_2.fq.gz
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In this example, hifiasm will do trio assembly with 32 CPU threads. The paternal assembly can be found at [NA12878.asm.hap1.p_ctg.gfa],
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and the maternal assembly can be found at [NA12878.asm.hap2.p_ctg.gfa].
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.SH OUTPUTS
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.PP
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Without trio partition options
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.B -1
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and
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.BR -2 ,
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hifiasm generates the following assembly graphs in the GFA format:
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.RS 2
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.TP 2
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*
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.IR prefix .r_utg.gfa:
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haplotype-resolved raw unitig graph. This graph keeps all haplotype information.
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.TP
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*
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.IR prefix .p_utg.gfa:
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haplotype-resolved processed unitig graph without small bubbles. Small bubbles
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might be caused by somatic mutations or noise in data, which are not the real
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haplotype information. The size of popped small bubbles should be specified by
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.BR -p .
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.TP
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*
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.IR prefix .p_ctg.gfa:
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assembly graph of primary contigs. This graph collapses different haplotypes.
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.TP
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*
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.IR prefix .a_ctg.gfa:
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assembly graph of alternate contigs. This graph consists of all assemblies that
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are discarded in primary contig graph.
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.RE
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.PP
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Consider the prefix of output files has been specified by
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.I [-o outPrefix].
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During the error correction step, hifiasm outputs the following two files:
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With trio partition, hifiasm outputs the following assembly graphs:
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.IP
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1. Haplotype-aware error corrected reads in fasta format [outPrefix.ec.fa].
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.RS 2
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.TP 2
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*
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.IR prefix .dip.r_utg.gfa:
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haplotype-resolved raw unitig graph. This graph keeps all haplotype information.
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2. All-to-all overlaps in paf format [outPrefix.ovlp.paf].
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.PP
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During the non-trio assembly step, hifiasm outputs the following four assembly graphs in GFA format:
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.IP
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1. Haplotype-resolved raw unitig graph [outPrefix.r_utg.gfa].
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This graph keeps all haplotype information.
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2. Haplotype-resolved processed unitig graph without small bubbles [outPrefix.p_utg.gfa].
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Small bubbles might be caused by somatic mutations or noise in data, which are not the real haplotype information.
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The size of popped small bubbles should be specified by
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.I [-p maxSmallBubbles].
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3. Primary assembly contig graph [outPrefix.p_ctg.gfa].
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This graph collapses different haplotypes.
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4. Alternate assembly contig graph [outPrefix.a_ctg.gfa].
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This graph consists of all assemblies that are discarded in primary assembly contig graph.
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.PP
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If you have trio information, hifiasm outputs the following three assembly graphs in GFA format:
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.IP
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1. Phased maternal unitig graph [outPrefix.m.r_utg.gfa].
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This graph keeps the phased maternal assembly.
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2. Phased paternal unitig graph [outPrefix.p.r_utg.gfa].
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This graph keeps the phased paternal assembly.
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3. Haplotype-resolved raw unitig graph [outPrefix.r_utg.gfa].
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This graph keeps all haplotype information.
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.TP
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*
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.IR prefix .hap1.p_ctg.gfa:
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phased paternal/haplotype1 contig graph. This graph keeps the phased
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paternal/haplotype1 assembly.
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.TP
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*
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.IR prefix .hap2.p_ctg.gfa:
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phased maternal/haplotype2 contig graph. This graph keeps the phased
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maternal/haplotype2 assembly.
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.RE
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.PP
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For each graph, hifiasm also outputs a simplified version without sequences. These simplified
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