update man

CommandLines.cpp

@@ -44,8 +44,8 @@ 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 [NULL]\n");
+    fprintf(stderr, "    -P FILE       paternal trio index generated by \"yak count\" [NULL]\n");
-    fprintf(stderr, "    -M FILE       Maternal trio index [NULL]\n");
+    fprintf(stderr, "    -M FILE       Maternal trio index generated by \"yak count\" [NULL]\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);
 

hifiasm.1

@@ -1,4 +1,4 @@
-.TH hifiasm 1 "3 Jan 2020" "hifiasm-0.1.0" "Bioinformatics tools"
+.TH hifiasm 1 "3 Jan 2020" "hifiasm-0.3.0" "Bioinformatics tools"
 
 .SH NAME
 .PP
@@ -181,6 +181,25 @@ Maternal trio index. This index should be generated by
 with the maternal short 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] 
+times in one sample 
+but occurs <
+.I [-c lower_bound]  
+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] 
+times in one sample 
+but occurs <
+.I [-c lower_bound]  
+times in the other sample.
 
 
 
@@ -202,6 +221,22 @@ With
 .I [-z 20],
 hifiasm will remove 20 bases from both ends of each read.
 
+.SH EXAMPLES FRO TRIO
+.TP
+.BR ./yak " " count " " \-k31 " " \-b37 " " \-t16 " " \-o " " mat.yak " " mat.fq.gz
+Build maternal trio index from mat.fq.gz.
+
+.TP
+.BR ./yak " " count " " \-k31 " " \-b37 " " \-t16 " " \-o " " pat.yak " " pat.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
+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],
+and the maternal assembly can be found at [NA12878.asm.m.r_utg.gfa].
+
+
+
 .SH OUTPUTS
 
 
@@ -216,7 +251,7 @@ During the error correction step, hifiasm outputs the following two files:
 2. All-to-all overlaps in paf format [outPrefix.ovlp.paf].
 
 .PP
-During the assembly step, hifiasm outputs the following four assembly graphs in GFA format:
+During the non-trio assembly step, hifiasm outputs the following four assembly graphs in GFA format:
 
 
 .IP
@@ -236,6 +271,21 @@ 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.
+
+
 .PP
 For each graph, hifiasm also outputs a simplified version without sequences. These simplified
 graphs can be easily visualized.