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ont simplex support

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chhylp123
2024-11-27 13:27:13 -05:00
parent 80fa5ed436
commit 676385cf8e
10 changed files with 896 additions and 88 deletions
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49
CommandLines.cpp
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@@ -7,6 +7,9 @@
#include <sys/time.h>
#include "CommandLines.h"
#include "ketopt.h"
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
#define DEFAULT_OUTPUT "hifiasm.asm"
@@ -72,7 +75,9 @@ static ko_longopt_t long_options[] = {
{ "telo-s", ko_required_argument, 357},
{ "ctg-n", ko_required_argument, 358},
{ "ont", ko_no_argument, 359},
{ "sc-n", ko_no_argument, 360},
// { "sc-n", ko_no_argument, 360},
{ "chem-c", ko_required_argument, 361},
{ "chem-f", ko_required_argument, 362},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -210,6 +215,14 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " --telo-s INT\n");
fprintf(stderr, " min score for telomere reads [%ld]\n", asm_opt->telo_mic_sc);
fprintf(stderr, " ONT simplex assembly (beta):\n");
fprintf(stderr, " --ont assemble ONT simplex reads in fastq format\n");
// fprintf(stderr, " --sc-n consider base qual value for assembly\n");
fprintf(stderr, " --chem-c INT\n");
fprintf(stderr, " detect chemical reads with <=INT other reads support [%lu]\n", asm_opt->chemical_cov);
fprintf(stderr, " --chem-f INT\n");
fprintf(stderr, " length of flanking regions for chemical read detection [%lu]\n", asm_opt->chemical_flank);
fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n");
fprintf(stderr, "See `https://hifiasm.readthedocs.io/en/latest/' or `man ./hifiasm.1' for complete documentation.\n");
@@ -342,6 +355,8 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->is_ont = 0;
asm_opt->is_sc = 0;
asm_opt->chemical_cov = 1;
asm_opt->chemical_flank = 256;
}
void destory_enzyme(enzyme* f)
@@ -692,25 +707,33 @@ int check_option(hifiasm_opt_t* asm_opt)
void get_queries(int argc, char *argv[], ketopt_t* opt, hifiasm_opt_t* asm_opt)
{
if(opt->ind == argc)
{
if(opt->ind == argc) {
return;
}
asm_opt->num_reads = argc - opt->ind;
asm_opt->read_file_names = (char**)malloc(sizeof(char*)*asm_opt->num_reads);
long long i;
gzFile dfp;
for (i = 0; i < asm_opt->num_reads; i++)
{
long long i; int ret;
gzFile dfp; kseq_t *ks = NULL;
for (i = 0; i < asm_opt->num_reads; i++) {
asm_opt->read_file_names[i] = argv[i + opt->ind];
dfp = gzopen(asm_opt->read_file_names[i], "r");
if (dfp == 0)
{
if (dfp == 0) {
fprintf(stderr, "[ERROR] Cannot find the input read file: %s\n",
asm_opt->read_file_names[i]);
exit(0);
} else if(asm_opt->is_sc){
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\n", asm_opt->read_file_names[i]);
asm_opt->is_sc = 0;
exit(0);
}
break;
}
kseq_destroy(ks); ks = NULL;
}
gzclose(dfp);
}
@@ -914,9 +937,13 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 357) asm_opt->telo_mic_sc = atol(opt.arg);
else if (c == 358) asm_opt->max_contig_tip = atol(opt.arg);
else if (c == 359) {
asm_opt->is_ont = 1; asm_opt->max_ov_diff_ec = 0.07; ///asm_opt->mz_win = 37; asm_opt->k_mer_length = 37;
} else if (c == 360) {
asm_opt->is_ont = 1; asm_opt->max_ov_diff_ec = 0.07; asm_opt->is_sc = 1; ///asm_opt->mz_win = 37; asm_opt->k_mer_length = 37;
} /**else if (c == 360) {
asm_opt->is_sc = 1;
}**/ else if (c == 361) {
asm_opt->chemical_cov = atol(opt.arg);
} else if (c == 362) {
asm_opt->chemical_flank = 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);
}