update readme for ont

CommandLines.cpp

@@ -78,6 +78,7 @@ static ko_longopt_t long_options[] = {
     // { "sc-n",       ko_no_argument, 360},
     { "chem-c",     ko_required_argument, 361},
     { "chem-f",     ko_required_argument, 362},
+    { "ul-m",     ko_required_argument, 363},
     // { "path-round",     ko_required_argument, 348},
 	{ 0, 0, 0 }
 };
@@ -186,6 +187,11 @@ void Print_H(hifiasm_opt_t* asm_opt)
 
     fprintf(stderr, "  Ultra-Long-integration:\n");
     fprintf(stderr, "    --ul FILEs   file names of Ultra-Long reads [r1.fq,r2.fq,...]\n");
+    ///pending for integration
+    /**
+    fprintf(stderr, "    --ul-m       INT\n");
+    fprintf(stderr, "                 hybrid assembly mode. 0: fast and memory efficent; 1: may produce better assembly with ONT R10 [%d]\n", asm_opt->ul_mod);
+    **/
     fprintf(stderr, "    --ul-rate    FLOAT\n");
     fprintf(stderr, "                 error rate of Ultra-Long reads [%.3g]\n", asm_opt->ul_error_rate);
     fprintf(stderr, "    --ul-tip     INT\n");
@@ -357,6 +363,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
     asm_opt->is_sc = 0;
     asm_opt->chemical_cov = 1;
     asm_opt->chemical_flank = 256;
+    asm_opt->ul_mod = 0;
 }   
 
 void destory_enzyme(enzyme* f)
@@ -430,14 +437,43 @@ static int check_file(char* name, const char* opt)
 
 static int check_hic_reads(enzyme* f, const char* opt)
 {
-    int i;
-    for (i = 0; i < f->n; i++)
-    {
+    int32_t i;
+    for (i = 0; i < f->n; i++) {
         if(check_file(f->a[i], opt) == 0) return 0;
     }
     return 1;
 }
 
+static int check_fq_files(enzyme* f, const char* opt, int32_t is_fq)
+{
+    int32_t i, ret; gzFile dfp; kseq_t *ks = NULL;
+    for (i = 0; i < f->n; i++) {
+        if(!(f->a[i])) {
+            fprintf(stderr, "[ERROR] input file does not exist (%s)\n", opt);
+            return 0;
+        }
+
+        dfp = gzopen(f->a[i], "r");
+        if (dfp == 0) {
+            fprintf(stderr, "[ERROR] Cannot find the input file: %s (%s)\n", f->a[i], opt);
+            return 0;
+        } else if(is_fq){
+            ks = kseq_init(dfp);
+            while (((ret = kseq_read(ks)) >= 0)) {
+                if((ks->qual.l == 0) || (ks->qual.s == NULL)) {
+                    fprintf(stderr, "[ERROR] %s is in fasta format rather than fastq format (%s)\n", f->a[i], opt);
+                    fprintf(stderr, "[ERROR] set --ul-m 0 for fasta files\n");
+                    return 0;
+                }
+                break;
+            }
+            kseq_destroy(ks); ks = NULL;
+        }
+        gzclose(dfp);
+    }
+    return 1;
+}
+
 int check_option(hifiasm_opt_t* asm_opt)
 {
     if(asm_opt->read_file_names == NULL || asm_opt->num_reads == 0)
@@ -637,7 +673,7 @@ int check_option(hifiasm_opt_t* asm_opt)
         return 0;
     }
 
-    if(asm_opt->ar != NULL && check_hic_reads(asm_opt->ar, "UL") == 0) return 0;
+    if(asm_opt->ar != NULL && check_fq_files(asm_opt->ar, "--ul", asm_opt->ul_mod) == 0) return 0;
     if(asm_opt->ar != NULL && asm_opt->ar->n == 0)
     {
         fprintf(stderr, "[ERROR] wrong UL reads (--ul)\n");
@@ -686,6 +722,11 @@ int check_option(hifiasm_opt_t* asm_opt)
         return 0;
     }
 
+    if(asm_opt->ul_mod != 0 && asm_opt->ul_mod != 1) {
+        fprintf(stderr, "[ERROR] must be 0 or 1 (--ul-m)\n");
+        return 0;
+    }
+
     if(asm_opt->telo_motif) {
         uint64_t k, tlen = strlen((asm_opt->telo_motif)); char c;
         if(tlen > 32) {
@@ -944,6 +985,11 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
             asm_opt->chemical_cov = atol(opt.arg);
         } else if (c == 362) {
             asm_opt->chemical_flank = atol(opt.arg);
+        ///pending for integration
+        /**        
+        } else if (c == 363) {
+            asm_opt->ul_mod = atol(opt.arg); 
+        **/
         } else if (c == 'l') {   ///0: disable purge_dup; 1: purge containment; 2: purge overlap
             asm_opt->purge_level_primary = asm_opt->purge_level_trio = atoi(opt.arg);
         }

CommandLines.h

@@ -137,6 +137,7 @@ typedef struct {
     int64_t infor_cov, s_hap_cov, trio_cov_het_ovlp;
     double ul_error_rate, ul_error_rate_low, ul_error_rate_hpc;
     int32_t ul_ec_round;
+    int32_t ul_mod;
     uint8_t is_dbg_het_cnt;
     uint8_t is_low_het_ul;
     uint8_t is_base_trans;

README.md

@@ -15,6 +15,9 @@ hifiasm -o CHM13.asm -t32 -l0 CHM13-HiFi.fa.gz 2> CHM13.asm.log
 # Assemble heterozygous genomes with built-in duplication purging
 hifiasm -o HG002.asm -t32 HG002-file1.fq.gz HG002-file2.fq.gz
 
+# Assemble genomes with ONT R10 reads rather than PacBio HiFi reads using the latest release of hifiasm (>0.21.0-r686)
+hifiasm -o HG002.asm --ont -t32 HG002-ont.fq.gz
+
 # Hi-C phasing with paired-end short reads in two FASTQ files
 hifiasm -o HG002.asm --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz
 

htab.cpp

@@ -991,8 +991,18 @@ ha_ct_t *ha_count(const hifiasm_opt_t *asm_o, int flag, int HPC, int k, int w, h
 	opt.adaLen = (keep_adapter? asm_o->adapterLen : 0);
 	opt.min_rcnt = (low_freq?*low_freq:-1);
 	opt.uq = (unique_only?1:0);
+	
+	n_bs = 0;
+	///pending for integration
+	/**
+	if(rs && asm_o->ar && asm_o->ul_mod) {
+		for (i = 0; i < asm_o->ar->n; ++i){
+			h = yak_count(&opt, asm_o->ar->a[i], flag|HAF_CREATE_NEW, p0, h, flt_tab, rs, us, &n_seq);
+			if(h) n_bs += h->bs;
+		}
+	}**/
 	///asm_opt->num_reads is the number of fastq files
-	for (i = n_bs = 0; i < (us?1:asm_o->num_reads); ++i){
+	for (i = 0; i < (us?1:asm_o->num_reads); ++i){
 		h = yak_count(&opt, asm_o->read_file_names[i], flag|HAF_CREATE_NEW, p0, h, flt_tab, rs, us, &n_seq);
 		if(h) n_bs += h->bs;
 	}