r213: renamed trio binning output files

CommandLines.cpp

@@ -50,8 +50,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
     fprintf(stderr, "    -h            show help information\n");
 
     fprintf(stderr, "  Trio-partition:\n");
-    fprintf(stderr, "    -P FILE       paternal trio index generated by \"yak count\" []\n");
+    fprintf(stderr, "    -1 FILE       hap1/paternal k-mer dump generated by \"yak count\" []\n");
-    fprintf(stderr, "    -M FILE       maternal trio index generated by \"yak count\" []\n");
+    fprintf(stderr, "    -2 FILE       hap2/maternal k-mer dump generated by \"yak count\" []\n");
     fprintf(stderr, "    -c INT        lower bound of the binned k-mer's frequency [%d]\n", asm_opt->min_cnt);
     fprintf(stderr, "    -d INT        upper bound of the binned k-mer's frequency [%d]\n", asm_opt->mid_cnt);
 
@@ -313,7 +313,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
 
     int c;
 
-    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) {
+    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) {
         if (c == 'h')
         {
             Print_H(asm_opt);
@@ -339,8 +339,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
         else if (c == 'b') asm_opt->required_read_name = opt.arg;
         else if (c == 'c') asm_opt->min_cnt = atoi(opt.arg);
         else if (c == 'd') asm_opt->mid_cnt = atoi(opt.arg);
-        else if (c == 'P') asm_opt->pat_index = opt.arg;
+        else if (c == '1' || c == 'P') asm_opt->pat_index = opt.arg; // -P/-M reserved for backward compatibility
-        else if (c == 'M') asm_opt->mat_index = opt.arg;
+        else if (c == '2' || c == 'M') asm_opt->mat_index = opt.arg;
         else if (c == 'x') asm_opt->max_drop_rate = atof(opt.arg);
         else if (c == 'y') asm_opt->min_drop_rate = atof(opt.arg);
         else if (c == 'p') asm_opt->small_pop_bubble_size = atoll(opt.arg);

CommandLines.h

@@ -3,7 +3,7 @@
 
 #include <pthread.h>
 
-#define HA_VERSION "0.3.0-dirty-r212"
+#define HA_VERSION "0.3.0-dirty-r213"
 
 #define VERBOSE 0
 

Overlaps.cpp

@@ -9664,13 +9664,13 @@ void ma_ug_print2(const ma_ug_t *ug, All_reads *RNF, const ma_sub_t *coverage_cu
 			uint32_t x = p->a[j]>>33;
 			if(x<RNF->total_reads)
             {
-                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], 
+                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],
                 (int)Get_NAME_LENGTH((*RNF), x), Get_NAME((*RNF), x), 
                 coverage_cut[x].s, coverage_cut[x].e, x, "apmaaa"[RNF->trio_flag[x]]);
             }
             else
             {
-                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], 
+                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],
 					"FAKE", coverage_cut[x].s, coverage_cut[x].e, x, '*');
             }
             
@@ -13527,7 +13527,7 @@ long long tipsLen, float tip_drop_ratio, long long stops_threshold, R_to_U* ruIn
 float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp)
 {
     char* gfa_name = (char*)malloc(strlen(output_file_name)+100);
-    sprintf(gfa_name, "%s.%s.r_utg.gfa", output_file_name, (flag==FATHER?"p":"m"));
+    sprintf(gfa_name, "%s.%s.p_ctg.gfa", output_file_name, (flag==FATHER?"hap1":"hap2"));
     fprintf(stderr, "Writing %s to disk... \n", gfa_name);
     FILE* output_file = fopen(gfa_name, "w");
 
@@ -13548,7 +13548,7 @@ float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp)
     ma_ug_print(ug, &R_INF, coverage_cut, output_file);
     fclose(output_file);
 
-    sprintf(gfa_name, "%s.%s.r_utg.noseq.gfa", output_file_name, (flag==FATHER?"p":"m"));
+    sprintf(gfa_name, "%s.%s.p_ctg.noseq.gfa", output_file_name, (flag==FATHER?"hap1":"hap2"));
     output_file = fopen(gfa_name, "w");
     ma_ug_print_simple(ug, &R_INF, coverage_cut, output_file);
     fclose(output_file);
@@ -26495,7 +26495,10 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
 
     if ((asm_opt.pat_index && asm_opt.mat_index))
     {
-        output_unitig_graph(sg, coverage_cut, output_file_name, sources, max_hang_length, mini_overlap_length);
+		char *buf = (char*)calloc(strlen(output_file_name) + 25, 1);
+		sprintf(buf, "%s.dip", output_file_name);
+        output_unitig_graph(sg, coverage_cut, buf, sources, max_hang_length, mini_overlap_length);
+		free(buf);
         
         output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, 
         reverse_sources, bubble_dist, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 

Trio.cpp

@@ -255,9 +255,6 @@ void trio_partition(void)
 		return;
 	}
 
-	double start_time = Get_T();
-	fprintf(stderr, "Start trio binning ...... \n");
-
     yak_ch_t *ch;
     int i /**, min_cnt = 2, mid_cnt = 5**/;
     tb_shared_t aux;
@@ -286,6 +283,5 @@ void trio_partition(void)
 	free(aux.bseq);
     yak_ch_destroy(ch);
 
-	fprintf(stderr, "Trio binning has been done.\n");
+	fprintf(stderr, "[M::%s::%.3f*%.2f] ==> partitioned reads using yak dumps\n", __func__, yak_realtime(), yak_cpu_usage());
-	fprintf(stderr, "%-30s%18.2f\n\n", "Trio binning time:", Get_T() - start_time); 
 }

hifiasm.1

@@ -8,7 +8,7 @@ hifiasm - haplotype-resolved de novo assembler for PacBio Hifi reads.
 .PP
 hifiasm
 .RB [ -o
-.IR outPrefix ]
+.IR prefix ]
 .RB [ -t
 .IR numThres ]
 .RB [ -r
@@ -51,8 +51,8 @@ outputs consist of multiple types of assembly graph in GFA format.
 .BI -o \ FILE
 Prefix of output files [hifiasm.asm]. The outputs of hifiasm include error corrected
 reads in fasta format, all-to-all overlaps in paf format, and four types of assembly
-graph in GFA format. For detailed description of all assembly graphs, please see
+graph in GFA format. For detailed description of all assembly graphs, please see the
-.I 'Outputs'
+.B OUTPUTS
 section of this man-page. 
 
 .TP 10
@@ -83,11 +83,11 @@ Rounds of haplotype-aware error corrections [2]. This option affects all outputs
 .TP 10
 .BI -a \ INT
 Rounds of assembly graph cleaning [4]. This option is used with
-.I [-x maxDropRatio]
+.B -x
 and
-.I [-y minDropRatio].
+.BR -y .
 Note that unlike
-.I [-r],
+.BR -r ,
 this option does not affect error corrected reads and all-to-all overlaps.
 
 
@@ -103,11 +103,11 @@ significantly improve the assembly quality.
 
 .TP 10
 .BI -m \ INT
-Maximal probing distance for bubble popping when generating primary/alternate assembly
+Maximal probing distance for bubble popping when generating primary/alternate
 contig graphs [10000000]. Bubbles longer than
 .I INT
-bases will not be popped. For detailed description of these graphs, please see
+bases will not be popped. For detailed description of these graphs, please see the
-.I 'Outputs'
+.B OUTPUTS
 section of this man-page. 
 
 
@@ -117,8 +117,8 @@ Maximal probing distance for bubble popping when generating haplotype-resolved p
 without small bubbles [100000]. Bubbles longer than
 .I INT
 bases will not be popped. Small bubbles might be caused by somatic mutations or noise in data, which
-are not the real haplotype information. For detailed description of this graph, please see
+are not the real haplotype information. For detailed description of this graph, please see the
-.I 'Outputs'
+.B OUTPUTS
 section of this man-page. 
 
 
@@ -133,7 +133,7 @@ reads [3]. Hifiasm may try to remove small unitigs at various steps.
 .TP 10
 .BI -x \ FLOAT, -y \ FLOAT
 Max and min overlap drop ratio [0.8, 0.2]. This option is used with
-.I [-r roundCorrection].
+.BR -r .
 Given a node
 .I N
 in the assembly graph, let max(N)
@@ -143,15 +143,15 @@ Hifiasm iteratively drops overlaps of
 .I N
 if their length / max(N)
 are below a threshold controlled by
-.I [-x maxDropRatio]
+.B -x
 and
-.I [-y minDropRatio].
+.BR -y .
 Hifiasm applies
-.I [-r roundCorrection]
+.B -r
 rounds of short overlap removal with an increasing threshold between
-.I [-x maxDropRatio]
+.B -x
 and
-.I [-y minDropRatio].
+.BR -y .
 
 .TP 10
 .BI -i
@@ -167,38 +167,37 @@ with different parameters.
 .SS Trio-partition options
 
 .TP 10
-.BI -P \ FILE
+.BI -1 \ FILE
-Paternal trio index. This index should be generated by
+Paternal/haplotype1 k-mer dump generated by
-.I [yak count]
+.B yak count
-with the paternal short reads. For details of yak, please see
+from the paternal/haplotype1 reads. For details of yak, please see
 .I [https://github.com/lh3/yak]
 
-
 .TP 10
-.BI -M \ FILE
+.BI -2 \ FILE
-Maternal trio index. This index should be generated by
+Maternal/haplotype2 k-mer dump generated by
-.I [yak count]
+.B yak count
-with the maternal short reads. For details of yak, please see
+from the maternal/haplotype2 reads. For details of yak, please see
 .I [https://github.com/lh3/yak]
 
 .TP 10
 .BI -c \ INT
 Lower bound of the binned k-mer's frequency [2]. When doing trio binning, 
 a k-mer is said to be differentiating if it occurs >=
-.I [-d upper_bound] 
+.B -d
 times in one sample 
 but occurs <
-.I [-c lower_bound]  
+.B -c
 times in the other sample.
 
 .TP 10
 .BI -d \ INT
 Upper bound of the binned k-mer's frequency [5]. When doing trio binning, 
 a k-mer is said to be differentiating if it occurs >=
-.I [-d upper_bound] 
+.B -d
 times in one sample 
 but occurs <
-.I [-c lower_bound]  
+.B -c
 times in the other sample.
 
 
@@ -235,60 +234,69 @@ Build maternal trio index from mat.fq.gz.
 Build paternal trio index from pat.fq.gz.
 
 .TP
-.BR ./hifiasm " " \-o " " NA12878.asm " " \-t " " 32 " " \-P " " pat.yak " " \-M " " mat.yak " " NA12878_1.fq.gz " " NA12878_2.fq.gz
+.BR ./hifiasm " " \-o " " NA12878.asm " " \-t " " 32 " " \-1 " " pat.yak " " \-2 " " mat.yak " " NA12878_1.fq.gz " " NA12878_2.fq.gz
-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],
+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],
-and the maternal assembly can be found at [NA12878.asm.m.r_utg.gfa].
+and the maternal assembly can be found at [NA12878.asm.hap2.p_ctg.gfa].
 
 
 
 .SH OUTPUTS
 
+.PP
+Without trio partition options
+.B -1
+and
+.BR -2 ,
+hifiasm generates the following assembly graphs in the GFA format:
+
+.RS 2
+.TP 2
+*
+.IR prefix .r_utg.gfa:
+haplotype-resolved raw unitig graph. This graph keeps all haplotype information.
+
+.TP
+*
+.IR prefix .p_utg.gfa:
+haplotype-resolved processed unitig graph without small bubbles.  Small bubbles
+might be caused by somatic mutations or noise in data, which are not the real
+haplotype information.  The size of popped small bubbles should be specified by
+.BR -p .
+
+.TP
+*
+.IR prefix .p_ctg.gfa:
+assembly graph of primary contigs. This graph collapses different haplotypes.
+
+.TP
+*
+.IR prefix .a_ctg.gfa:
+assembly graph of alternate contigs. This graph consists of all assemblies that
+are discarded in primary contig graph.
+
+.RE
 
 .PP
-Consider the prefix of output files has been specified by
+With trio partition, hifiasm outputs the following assembly graphs:
-.I [-o outPrefix].
-During the error correction step, hifiasm outputs the following two files:
 
-.IP
+.RS 2
-1. Haplotype-aware error corrected reads in fasta format [outPrefix.ec.fa].
+.TP 2
+*
+.IR prefix .dip.r_utg.gfa:
+haplotype-resolved raw unitig graph. This graph keeps all haplotype information.
 
-2. All-to-all overlaps in paf format [outPrefix.ovlp.paf].
+.TP
-
+*
-.PP
+.IR prefix .hap1.p_ctg.gfa:
-During the non-trio assembly step, hifiasm outputs the following four assembly graphs in GFA format:
+phased paternal/haplotype1 contig graph. This graph keeps the phased
-
+paternal/haplotype1 assembly.
-
-.IP
-1. Haplotype-resolved raw unitig graph [outPrefix.r_utg.gfa].
-This graph keeps all haplotype information.
-
-
-2. Haplotype-resolved processed unitig graph without small bubbles [outPrefix.p_utg.gfa].
-Small bubbles might be caused by somatic mutations or noise in data, which are not the real haplotype information.
-The size of popped small bubbles should be specified by
-.I [-p maxSmallBubbles].
-
-
-3. Primary assembly contig graph [outPrefix.p_ctg.gfa].
-This graph collapses different haplotypes.
-
-4. Alternate assembly contig graph [outPrefix.a_ctg.gfa].
-This graph consists of all assemblies that are discarded in primary assembly contig graph.
-
-
-.PP
-If you have trio information, hifiasm outputs the following three assembly graphs in GFA format:
-
-.IP
-1. Phased maternal unitig graph [outPrefix.m.r_utg.gfa].
-This graph keeps the phased maternal assembly.
-
-2. Phased paternal unitig graph [outPrefix.p.r_utg.gfa].
-This graph keeps the phased paternal assembly.
-
-3. Haplotype-resolved raw unitig graph [outPrefix.r_utg.gfa].
-This graph keeps all haplotype information.
 
+.TP
+*
+.IR prefix .hap2.p_ctg.gfa:
+phased maternal/haplotype2 contig graph. This graph keeps the phased
+maternal/haplotype2 assembly.
+.RE
 
 .PP
 For each graph, hifiasm also outputs a simplified version without sequences. These simplified