forked from HongzheGuo/deBGA-VARA
/
load_input.c
1608 lines (1365 loc) · 44.6 KB
/
load_input.c
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#include <unistd.h>
#include <malloc.h>
#include <string.h>
#include <dirent.h>
#include <inttypes.h>
#include <inttypes.h>
#include "load_input.h"
//debug
#include "bit_operation.h"
//KSEQ_INIT(gzFile, gzread)
kseq_t *seq1 = NULL;
kseq_t *seq2 = NULL;
uint64_t* buffer_ref_seq = NULL;
#ifdef UNI_SEQ64
uint64_t* buffer_seq = NULL;
#else
uint8_t* buffer_seq = NULL;
#endif
#ifdef UNPIPATH_OFF_K20
uint64_t* buffer_seqf = NULL;
uint64_t* buffer_off_g = NULL;
uint64_t* buffer_p = NULL;
uint64_t* buffer_pp = NULL;
uint64_t* buffer_hash_g = NULL;
uint64_t* chr_end_n = NULL;
uint64_t* chr_end_n_rec = NULL;
uint64_t first_cnt_cl = 0;
#else
uint32_t* buffer_seqf = NULL;
uint32_t* buffer_off_g = NULL;
uint32_t* buffer_p = NULL;
uint32_t* buffer_pp = NULL;
uint32_t* buffer_hash_g = NULL;
uint32_t* chr_end_n = NULL;
uint32_t* chr_end_n_rec = NULL;
uint32_t first_cnt_cl = 0;
#endif
//uint8_t* buffer_edge = NULL;
uint32_t tol_s_n = 0;
uint32_t tol_u = 0;
uint32_t* buffer_pupos = NULL;
uint32_t* buffer_puid = NULL;
uint32_t* buffer_kmer_g = NULL;
uint64_t result_ref_seq = 0;
uint64_t result_seq = 0;
uint64_t result_seqf = 0;
uint64_t result_edge = 0;
uint64_t result_p = 0;
uint64_t result_pp = 0;
uint64_t result_pu = 0;
uint64_t result_hash_g = 0;
uint64_t result_kmer_g = 0;
uint64_t result_off_g = 0;
uint64_t result_ref_g = 0;
uint64_t ref_length_p = 0;
uint8_t* aseq_array = NULL;
uint8_t* type_array = NULL;
uint32_t* rpos_array = NULL;
uint32_t* aindex_array = NULL;
uint32_t* apos_array = NULL;
uint32_t* rpos_end_array = NULL;
uint64_t* ref_seqv_array = NULL;
uint32_t* chr_rpos_a = NULL;
uint8_t* aseq_array_rec = NULL;
uint8_t* type_array_rec = NULL;
uint32_t* rpos_array_rec = NULL;
uint32_t* aindex_array_rec = NULL;
uint32_t* apos_array_rec = NULL;
uint32_t* rpos_end_array_rec = NULL;
uint64_t* ref_seqv_array_rec = NULL;
uint32_t* chr_rpos_a_rec = NULL;
const char* refseqs = "ref.seq";
const char* uniseqs = "unipath.seq";
const char* uniseq_bs = "unipath.seqb";
const char* uniseqf_bs = "unipath.seqfb";
const char* uniedges = "unipath.edge";
const char* unipus = "unipath.pu";
const char* uniposs = "unipath.pos";
const char* uniposps = "unipath.posp";
//const char* unistas = "unipath.sta";
const char* unihash_gs = "unipath_g.hash";
const char* unikmer_gs = "unipath_g.kmer";
const char* unioff_gs = "unipath_g.offset";
const char* unichrs = "unipath.chr";
const char* f_n = "N.sta";
const char* graph = "graph.sta";
const char* divs = "div/";
const char* f_size = "unipath.size";
const char* sys_c_mkdir = "mkdir ";
const char* sys_c_rm = "rm -rf ";
const char* sys_rm = "rm ";
const char* vcf_rposs = "vcf_rpos";
const char* vcf_aindexs = "vcf_aindex";
const char* vcf_aposs = "vcf_apos";
const char* vcf_aseqs = "vcf_aseq";
const char* vcf_rpos_ends = "vcf_rpos_end";
const char* ref_vcfs = "ref_vcf.seq";
const char* vcf_sizes = "vcf_size";
const char* vcf_types = "vcf_type";
const char* vcf_chr_rposs = "vcf_chr_rpos";
const char* vcf_rposs_rev = "vcf_rpos_rev";
const char* vcf_aindexs_rev = "vcf_aindex_rev";
const char* vcf_aposs_rev = "vcf_apos_rev";
const char* vcf_aseqs_rev = "vcf_aseq_rev";
const char* vcf_rpos_ends_rev = "vcf_rpos_end_rev";
const char* ref_vcfs_rev = "ref_vcf_rev.seq";
const char* vcf_sizes_rev = "vcf_size_rev";
const char* vcf_types_rev = "vcf_type_rev";
char vcf_rpos[ROUTE_LENGTH_MAX];
char vcf_aindex[ROUTE_LENGTH_MAX];
char vcf_apos[ROUTE_LENGTH_MAX];
char vcf_aseq[ROUTE_LENGTH_MAX];
char vcf_rpos_end[ROUTE_LENGTH_MAX];
char ref_vcf[ROUTE_LENGTH_MAX];
char vcf_size[ROUTE_LENGTH_MAX];
char vcf_type[ROUTE_LENGTH_MAX];
char vcf_chr_rpos[ROUTE_LENGTH_MAX];
char vcf_rpos_rev[ROUTE_LENGTH_MAX];
char vcf_aindex_rev[ROUTE_LENGTH_MAX];
char vcf_apos_rev[ROUTE_LENGTH_MAX];
char vcf_aseq_rev[ROUTE_LENGTH_MAX];
char vcf_rpos_end_rev[ROUTE_LENGTH_MAX];
char ref_vcf_rev[ROUTE_LENGTH_MAX];
char vcf_size_rev[ROUTE_LENGTH_MAX];
char vcf_type_rev[ROUTE_LENGTH_MAX];
char sam_result[ROUTE_LENGTH_MAX];
char read_fastq1[ROUTE_LENGTH_MAX];
char read_fastq2[ROUTE_LENGTH_MAX];
char index_route[ROUTE_LENGTH_MAX];
char filename_ref[ROUTE_LENGTH_MAX];
char filename_div[ROUTE_LENGTH_MAX];
char filename_sta[ROUTE_LENGTH_MAX];
char ref_seq[ROUTE_LENGTH_MAX];
char uniseq[ROUTE_LENGTH_MAX];
char uniseq_b[ROUTE_LENGTH_MAX];
char uniseqf_b[ROUTE_LENGTH_MAX];
char uniedge[ROUTE_LENGTH_MAX];
char unipu[ROUTE_LENGTH_MAX];
char unipos[ROUTE_LENGTH_MAX];
char uniposp[ROUTE_LENGTH_MAX];
//char unista[ROUTE_LENGTH_MAX];
char unihash_g[ROUTE_LENGTH_MAX];
char unikmer_g[ROUTE_LENGTH_MAX];
char unioff_g[ROUTE_LENGTH_MAX];
char unichr[ROUTE_LENGTH_MAX];
char N_route[ROUTE_LENGTH_MAX];
char unisize[ROUTE_LENGTH_MAX];
char vcf_file_name[ROUTE_LENGTH_MAX];
char chr_names[MAX_CHR_NUM][MAX_CHR_NAME_LENGTH];
char chr_line_content[MAX_CHR_NAME_LENGTH];
//files
FILE* fp_ref_seq = NULL;
FILE* fp_us_b = NULL;
FILE* fp_usf_b = NULL;
FILE* fp_ub = NULL;
//FILE* fp_ue = NULL;
FILE* fp_up = NULL;
FILE* fp_upp = NULL;
FILE* fp_pu = NULL;
FILE* fp_sta = NULL;
FILE* fp_chr = NULL;
FILE* fp_uh = NULL;
FILE* fp_uf = NULL;
FILE* fp_hash = NULL;
FILE* fp_kmer = NULL;
FILE* fp_off = NULL;
FILE* fp_n = NULL;
FILE* fp_us = NULL;
FILE* fp_num = NULL;
FILE* unipath_debug = NULL;
int** chr_res_buffer = NULL;
char** xa_d1s_buffer = NULL;
char** xa_d2s_buffer = NULL;
uint32_t** sam_pos1s_buffer = NULL;
uint32_t** sam_pos2s_buffer = NULL;
int** lv_re1s_buffer = NULL;
int** lv_re2s_buffer = NULL;
const uint8_t f = 4;
const uint8_t k = 14;
uint8_t k_t = 22;
uint32_t chr_file_n = 1;
uint8_t thread_n = 1;
uint32_t upper_ins = 700;
uint32_t floor_ins = 300;
uint16_t readlen_max = 512;//252
uint16_t seed_l_max = 0;
uint8_t seed_l_l = 5;
uint16_t seed_step = 5;
uint8_t cir_fix_n = 4;
uint16_t pos_n_max = 300;
uint16_t length_reduce = 22;
float va_ra = 0.02;
//important parameter
float mis_match_r = 0.04;
float lv_rate = 0.06;//0.1
float last_circle_rate = 0;
//
float max_pair_score_r = 0.05;//0.06 0.2
float mis_match_r_single = 0.05;//0.04 0.4
float lv_rate_anchor = 0.05;
uint8_t anchor_ext_flag = 0;
uint8_t flag_std = 0;
uint8_t local_ksw = 0;
uint8_t mgn_flag = 1;
uint8_t tree_flag = 0;
uint16_t cus_ali_n = 20; //150
uint16_t cus_max_output_ali = 150;//300 anchor
float max_single_score_r = 0.06;
uint16_t pr_single_outputn = 1000;
uint16_t seed_filter_pos_numn = 100;
uint16_t seed_filter_pos_num_singlen = 100;//
int8_t mat_score = 1, mis_score = 4, gapo_score = 6, gape_score = 1;
static int index_build_usage()
{
fprintf(stderr, "\n");
fprintf(stderr, "Program: de Brijn Graph-based mapping system index building\n");
fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
fprintf(stderr, "Contact: Hongzhe Guo <hzguo@hit.edu>\n\n");
fprintf(stderr, "Usage: deBGA index [options] reference.fasta <index_route> \n\n");
fprintf(stderr, "Options: -k INT the k-mer length of the vertices of RdBG [20-28]\n");
fprintf(stderr, " --ext-alt STR (default: not set) vcf-info-based alignment\n");
fprintf(stderr, "\n");
return 1;
}
static int load_input_usage()
{
fprintf(stderr, "\n");
fprintf(stderr, "Program: de Brijn Graph-based mapping system seed reduction and alignment\n");
fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
fprintf(stderr, "Contact: Hongzhe Guo <hzguo@hit.edu>\n\n");
fprintf(stderr, "Usage: deBGA aln [options] <index_route> <read pair-end1.fq> [read pair-end2.fq] <result_file.sam>\n\nOptions:\n");
fprintf(stderr, " -k INT the minimum length of a valid Uni-MEM seed [21-28]\n");
fprintf(stderr, " -s INT the number of iterations of re-seeding [%u]\n", cir_fix_n);
fprintf(stderr, " -i INT the minimum interval of seeding [%u]\n", seed_step);
fprintf(stderr, " -n INT the maximum allowed number of hits per seed [%u]\n", pos_n_max);
fprintf(stderr, " -c NUM the threshold on the edit distance for early stop [%.2f]\n", max_pair_score_r);
fprintf(stderr, " --cl NUM the adjusted threshold on the edit distance for early stop [%.2f]\n", last_circle_rate);
fprintf(stderr, " --local the local alignment option for confident alignment\n");
fprintf(stderr, " --local-match NUM the score for a matched base in the local alignment [%d]\n", mat_score);
fprintf(stderr, " --local-mismatch NUM the penalty for a mismatched base in the local alignment [%d]\n", mis_score);
fprintf(stderr, " --local-gap-open NUM the penalty for a gap open in the local alignment [%d]\n", gapo_score);
fprintf(stderr, " --local-gap-extension NUM the penalty for gap extension in the local alignment [%d]\n", gape_score);
fprintf(stderr, " --ext-alt-aln (default: not set) vcf-info-based alignment\n");
fprintf(stderr, " --stdout (default: not set) output alignments by stdout\n");
fprintf(stderr, " -u INT the upper limit of insert size (only for pair-end reads) [%u] \n", upper_ins);
fprintf(stderr, " -f INT the lower limit of insert size (only for pair-end reads) [%u] \n", floor_ins);
fprintf(stderr, " -o INT the maximum number of alignment output [%u]\n", cus_ali_n);
fprintf(stderr, " -x INT the maximum number of alignment output for anchoring alignment [%u]\n", cus_max_output_ali);
fprintf(stderr, " -l INT the maximum allowed read length [%u]\n", readlen_max);
fprintf(stderr, " -e INT the budget for single-end alignment [%u]\n", seed_filter_pos_numn);
fprintf(stderr, " -p INT the number of threads [%u]\n", thread_n);
//fprintf(stderr, " --mg use the mode of multi-genomes\n");
fprintf(stderr, " Please refer to the following link for more detailed information about the options: https://github.com/HIT-Bioinformatics/deBGA\n");
fprintf(stderr, "\n");
return 1;
}
int help_usage()
{
fprintf(stderr, "\n");
fprintf(stderr, "Program: deBGA (De bruijn graph nucleotide alignment)\n");
fprintf(stderr, "Usage: deBGA <command> [options]\n\n");
fprintf(stderr, "Command: index index sequences in the FASTA format\n");
fprintf(stderr, " aln pair-end and single-end reads seed reduction and alignment based on De bruijn graph\n");
fprintf(stderr, "\n");
fprintf(stderr, "Usage: deBGA index [options] reference.fasta <index_route> \n\n");
fprintf(stderr, "Options: -k INT the k-mer length of the vertices of RdBG [20-28]\n");
fprintf(stderr, "\n");
fprintf(stderr, "Usage: deBGA aln [options] <index_route> <read pair-end1.fq> [read pair-end2.fq] <result_file.sam>\n\nOptions:\n");
fprintf(stderr, " -k INT the minimum length of a valid Uni-MEM seed [21-28]\n");
fprintf(stderr, " -s INT the number of iterations of re-seeding [%u]\n", cir_fix_n);
fprintf(stderr, " -i INT the minimum interval of seeding [%u]\n", seed_step);
fprintf(stderr, " -n INT the maximum allowed number of hits per seed [%u]\n", pos_n_max);
fprintf(stderr, " -c NUM the threshold on the edit distance for early stop [%.2f]\n", max_pair_score_r);
fprintf(stderr, " --cl NUM the adjusted threshold on the edit distance for early stop [%.2f]\n", last_circle_rate);
fprintf(stderr, " --local the local alignment option for confident alignment\n");
fprintf(stderr, " --local-match NUM the score for a matched base in the local alignment [%d]\n", mat_score);
fprintf(stderr, " --local-mismatch NUM the penalty for a mismatched base in the local alignment [%d]\n", mis_score);
fprintf(stderr, " --local-gap-open NUM the penalty for a gap open in the local alignment [%d]\n", gapo_score);
fprintf(stderr, " --local-gap-extension NUM the penalty for gap extension in the local alignment [%d]\n", gape_score);
fprintf(stderr, " --anchor-ext (default: not set) deBGA do anchor alignment if the tree-extension do not output an alignment record\n");
fprintf(stderr, " --stdout (default: not set) output alignments by stdout\n");
fprintf(stderr, " -u INT the upper limit of insert size (only for pair-end reads) [%u] \n", upper_ins);
fprintf(stderr, " -f INT the lower limit of insert size (only for pair-end reads) [%u] \n", floor_ins);
fprintf(stderr, " -o INT the maximum number of alignment output [%u]\n", cus_ali_n);
fprintf(stderr, " -x INT the maximum number of alignment output for anchoring alignment [%u]\n", cus_max_output_ali);
fprintf(stderr, " -l INT the maximum allowed read length [%u]\n", readlen_max);
fprintf(stderr, " -e INT the budget for single-end alignment [%u]\n", seed_filter_pos_numn);
fprintf(stderr, " -p INT the number of threads [%u]\n", thread_n);
//fprintf(stderr, " --mg use the mode of multi-genomes\n");
fprintf(stderr, " Please refer to the following link for more detailed information about the options: https://github.com/hitbc/deBGA2\n");
fprintf(stderr, "\n");
return 1;
}
enum {
PAR_LOCAL_KSW,
PAR_LAST_CIRCLE,
PAR_MULTI_GENOMES,
PAR_MAT_SCORE,
PAR_MIS_SCORE,
PAR_GAPO_SCORE,
PAR_GAPE_SCORE,
PAR_A_ANCHOR,
PAR_LV_ANCHOR,
PAR_EXT_ALT,
PAR_EXT_ALT_ALN,
PAR_HELP,
PAR_ANCHOR_EXT,
PAR_STD_OUT
};
static const char *short_option = "k:p:u:f:l:r:i:s:n:o:x:a:c:g:e:v:";
static struct option long_option[] = {
{(char*)"local", no_argument, 0, PAR_LOCAL_KSW},
{(char*)"cl", required_argument, 0, PAR_LAST_CIRCLE},
{(char*)"mg", no_argument, 0, PAR_MULTI_GENOMES},
{(char*)"local-match", required_argument, 0, PAR_MAT_SCORE},
{(char*)"local-mismatch", required_argument, 0, PAR_MIS_SCORE},
{(char*)"local-gap-open", required_argument, 0, PAR_GAPO_SCORE},
{(char*)"local-gap-extension", required_argument, 0, PAR_GAPE_SCORE},
{(char*)"aanchor", required_argument, 0, PAR_A_ANCHOR},
{(char*)"vanchor", required_argument, 0, PAR_LV_ANCHOR},
{(char*)"ext-alt", required_argument, 0, PAR_EXT_ALT},
{(char*)"help", no_argument, 0, PAR_HELP},
{(char*)"anchor-ext", no_argument, 0, PAR_ANCHOR_EXT},
{(char*)"stdout", no_argument, 0, PAR_STD_OUT},
{(char*)"ext-alt-aln", no_argument, 0, PAR_EXT_ALT_ALN},
{(char*)0, 0, 0, 0}
};
int load_input_index(int argc, char *argv[])
{
int c = 0;
//while ((c = getopt(argc, argv, "k:")) >= 0) {
while((c = getopt_long(argc, argv, short_option, long_option, NULL)) != -1){
switch (c) {
case 'k': k_t = atoi(optarg); break;
case PAR_EXT_ALT: strcpy(vcf_file_name, optarg); tree_flag = 1; break;
case PAR_HELP: return index_build_usage();
//default: return index_build_usage();
}
}
if (argc - optind < 2) return index_build_usage();
memset(filename_ref, 0, ROUTE_LENGTH_MAX);
memset(index_route, 0, ROUTE_LENGTH_MAX);
strcpy(filename_ref, argv[optind]);
strcpy(index_route, argv[optind + 1]);
if(index_route[strlen(index_route) - 1] != '/') strcat(index_route, "/");
fprintf(stderr, "reference file: %s\nindex route: %s\n", filename_ref, index_route);
memset(ref_seq, 0, ROUTE_LENGTH_MAX);
strcpy(ref_seq, index_route);
strcat(ref_seq, refseqs);
memset(uniseq, 0, ROUTE_LENGTH_MAX);
strcpy(uniseq, index_route);
strcat(uniseq, uniseqs);
memset(uniseq_b, 0, ROUTE_LENGTH_MAX);
strcpy(uniseq_b, index_route);
strcat(uniseq_b, uniseq_bs);
memset(uniseqf_b, 0, ROUTE_LENGTH_MAX);
strcpy(uniseqf_b, index_route);
strcat(uniseqf_b, uniseqf_bs);
memset(uniedge, 0, ROUTE_LENGTH_MAX);
strcpy(uniedge, index_route);
strcat(uniedge, uniedges);
memset(unipu, 0, ROUTE_LENGTH_MAX);
strcpy(unipu, index_route);
strcat(unipu, unipus);
memset(unipos, 0, ROUTE_LENGTH_MAX);
strcpy(unipos, index_route);
strcat(unipos, uniposs);
memset(uniposp, 0, ROUTE_LENGTH_MAX);
strcpy(uniposp, index_route);
strcat(uniposp, uniposps);
/*
memset(unista, 0, ROUTE_LENGTH_MAX);
strcpy(unista, index_route);
strcat(unista, unistas);
*/
memset(unihash_g, 0, ROUTE_LENGTH_MAX);
strcpy(unihash_g, index_route);
strcat(unihash_g, unihash_gs);
memset(unikmer_g, 0, ROUTE_LENGTH_MAX);
strcpy(unikmer_g, index_route);
strcat(unikmer_g, unikmer_gs);
memset(unioff_g, 0, ROUTE_LENGTH_MAX);
strcpy(unioff_g, index_route);
strcat(unioff_g, unioff_gs);
memset(unichr, 0, ROUTE_LENGTH_MAX);
strcpy(unichr, index_route);
strcat(unichr, unichrs);
memset(N_route, 0, ROUTE_LENGTH_MAX);
strcpy(N_route, index_route);
strcat(N_route, f_n);
memset(filename_div, 0, ROUTE_LENGTH_MAX);
strcpy(filename_div, index_route);
strcat(filename_div, divs);
memset(filename_sta, 0, ROUTE_LENGTH_MAX);
strcpy(filename_sta, filename_div);
strcat(filename_sta, graph);
memset(unisize, 0, ROUTE_LENGTH_MAX);
strcpy(unisize, index_route);
strcat(unisize, f_size);
if(tree_flag)
{
fprintf(stderr, "use the VCF-info-based extension and VCF file is %s\n", vcf_file_name);
memset(vcf_rpos, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_rpos, index_route);
strcat(vcf_rpos, vcf_rposs);
memset(vcf_aindex, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_aindex, index_route);
strcat(vcf_aindex, vcf_aindexs);
memset(vcf_apos, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_apos, index_route);
strcat(vcf_apos, vcf_aposs);
memset(vcf_aseq, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_aseq, index_route);
strcat(vcf_aseq, vcf_aseqs);
memset(vcf_rpos_end, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_rpos_end, index_route);
strcat(vcf_rpos_end, vcf_rpos_ends);
memset(ref_vcf, 0, ROUTE_LENGTH_MAX);
strcpy(ref_vcf, index_route);
strcat(ref_vcf, ref_vcfs);
memset(vcf_size, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_size, index_route);
strcat(vcf_size, vcf_sizes);
memset(vcf_type, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_type, index_route);
strcat(vcf_type, vcf_types);
memset(vcf_rpos_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_rpos_rev, index_route);
strcat(vcf_rpos_rev, vcf_rposs_rev);
memset(vcf_aindex_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_aindex_rev, index_route);
strcat(vcf_aindex_rev, vcf_aindexs_rev);
memset(vcf_apos_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_apos_rev, index_route);
strcat(vcf_apos_rev, vcf_aposs_rev);
memset(vcf_aseq_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_aseq_rev, index_route);
strcat(vcf_aseq_rev, vcf_aseqs_rev);
memset(vcf_rpos_end_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_rpos_end_rev, index_route);
strcat(vcf_rpos_end_rev, vcf_rpos_ends_rev);
memset(ref_vcf_rev, 0, ROUTE_LENGTH_MAX);
strcpy(ref_vcf_rev, index_route);
strcat(ref_vcf_rev, ref_vcfs_rev);
memset(vcf_size_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_size_rev, index_route);
strcat(vcf_size_rev, vcf_sizes_rev);
memset(vcf_type_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_type_rev, index_route);
strcat(vcf_type_rev, vcf_types_rev);
memset(vcf_chr_rpos, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_chr_rpos, index_route);
strcat(vcf_chr_rpos, vcf_chr_rposs);
}
chr_end_n = (uint64_t* )calloc(MAX_CHR_NUM, 8);
#ifdef HANDLE_DIR
char create_route[ROUTE_LENGTH_MAX];
char rm_route[ROUTE_LENGTH_MAX];
DIR* directory_pointer = NULL;
#ifndef DEBUG_VCF
if((directory_pointer = opendir(index_route)) != NULL)//filename_div
{
memset(rm_route, 0, ROUTE_LENGTH_MAX);
strcpy(rm_route, sys_c_rm);
strcat(rm_route, index_route);
system(rm_route);
}
#endif
memset(create_route, 0, ROUTE_LENGTH_MAX);
strcpy(create_route, sys_c_mkdir);
strcat(create_route, index_route);
if((directory_pointer = opendir(index_route))==NULL)
system(create_route);
memset(create_route, 0, ROUTE_LENGTH_MAX);
strcpy(create_route, sys_c_mkdir);
strcat(create_route, filename_div);
if((directory_pointer = opendir(filename_div))==NULL)
system(create_route);
#endif
return 0;
}
int load_input_map(int argc, char *argv[])
{
int c = 0;
while((c = getopt_long(argc, argv, short_option, long_option, NULL)) != -1){
switch (c) {
case 'k': k_t = atoi(optarg); break;
case 'p': thread_n = atoi(optarg); break;
case 'u': upper_ins = atoi(optarg); break;
case 'f': floor_ins = atoi(optarg); break;
case 'l': readlen_max = atoi(optarg); break;
case 'r': length_reduce = atoi(optarg); break;
case 'i': seed_step = atoi(optarg); break;
case 's': cir_fix_n = atoi(optarg); break;
case 'n': pos_n_max = atoi(optarg); break;
case 'o': cus_ali_n = atoi(optarg); break;
case 'x': cus_max_output_ali = atoi(optarg); break;
case 'c': max_pair_score_r = atof(optarg); lv_rate_anchor = max_pair_score_r; mis_match_r_single = max_pair_score_r; break;
case 'e': seed_filter_pos_numn = atoi(optarg); break;
case 'v': lv_rate = atof(optarg); break;
case PAR_A_ANCHOR: mis_match_r_single = atof(optarg); break;
case PAR_LV_ANCHOR: lv_rate_anchor = atof(optarg); break;
case PAR_LAST_CIRCLE: last_circle_rate = atof(optarg); mis_match_r_single = last_circle_rate; break;
case PAR_LOCAL_KSW: local_ksw = 1; last_circle_rate = 0; mis_match_r_single = 0.4; break;
case PAR_MULTI_GENOMES: mgn_flag = 0;break;
case PAR_MAT_SCORE: mat_score = atoi(optarg); break;
case PAR_MIS_SCORE: mis_score = atoi(optarg); break;
case PAR_GAPO_SCORE: gapo_score = atoi(optarg); break;
case PAR_GAPE_SCORE: gape_score = atoi(optarg); break;
case PAR_ANCHOR_EXT: anchor_ext_flag = 1; break;
case PAR_STD_OUT: flag_std = 1; break;
case PAR_EXT_ALT_ALN: tree_flag = 1; break;
case PAR_HELP: return load_input_usage();
default: return load_input_usage();
}
}
if (argc - optind < 3) return load_input_usage();
if((k_t < 21) || (k_t > 28))
{
fprintf(stderr, "Input error: -k cannot be less than 21 or more than 28\n");
exit(1);
}
if((thread_n < 1) || (thread_n > 32))
{
fprintf(stderr, "Input error: -p cannot be less than 1 or more than 32\n");
exit(1);
}
if(upper_ins <= floor_ins)
{
fprintf(stderr, "Input error: -u should be more than floor limit\n");
exit(1);
}
if(readlen_max > 2048)
{
fprintf(stderr, "Input error: -l cannot be more than 2048\n");
exit(1);
}
if(length_reduce > 50)
{
fprintf(stderr, "Input error: -r cannot be more than 50\n");
exit(1);
}
if((seed_step < 1) || (seed_step > 20))//5 20
{
fprintf(stderr, "Input error: -i cannot be more than 20 or less than 5\n");
exit(1);
}
if(cir_fix_n > 10)
{
fprintf(stderr, "Input error: -s cannot be more than 10\n");
exit(1);
}
if(cus_ali_n > 1000)//300
{
fprintf(stderr, "Input error: -o cannot be more than 1000\n");//300
exit(1);
}
if(cus_max_output_ali > 1000)//500
{
fprintf(stderr, "Input error: -x cannot be more than 1000\n");//500
exit(1);
}
if(max_pair_score_r > 0.35)//0.5
{
fprintf(stderr, "Input error: -c cannot be more than 0.5\n");
exit(1);
}
if(seed_filter_pos_numn > 2000)
{
fprintf(stderr, "Input error: -e cannot be more than 2000\n");
exit(1);
}
if(lv_rate > 0.5)
{
fprintf(stderr, "Input error: -v cannot be more than 0.5\n");
exit(1);
}
if(last_circle_rate > 0.5)
{
fprintf(stderr, "Input error: --cl cannot be more than 0.5\n");
exit(1);
}
memset(index_route, 0, ROUTE_LENGTH_MAX);
strcpy(index_route, argv[optind]);
if(index_route[strlen(index_route) - 1] != '/') strcat(index_route, "/");
memset(read_fastq1, 0, ROUTE_LENGTH_MAX);
strcpy(read_fastq1, argv[optind + 1]);
memset(ref_seq, 0, ROUTE_LENGTH_MAX);
strcpy(ref_seq, index_route);
strcat(ref_seq, refseqs);
memset(uniseq_b, 0, ROUTE_LENGTH_MAX);
strcpy(uniseq_b, index_route);
strcat(uniseq_b, uniseq_bs);
memset(uniseqf_b, 0, ROUTE_LENGTH_MAX);
strcpy(uniseqf_b, index_route);
strcat(uniseqf_b, uniseqf_bs);
memset(uniedge, 0, ROUTE_LENGTH_MAX);
strcpy(uniedge, index_route);
strcat(uniedge, uniedges);
memset(unipu, 0, ROUTE_LENGTH_MAX);
strcpy(unipu, index_route);
strcat(unipu, unipus);
memset(unipos, 0, ROUTE_LENGTH_MAX);
strcpy(unipos, index_route);
strcat(unipos, uniposs);
memset(uniposp, 0, ROUTE_LENGTH_MAX);
strcpy(uniposp, index_route);
strcat(uniposp, uniposps);
/*
memset(unista, 0, ROUTE_LENGTH_MAX);
strcpy(unista, index_route);
strcat(unista, unistas);
*/
memset(unihash_g, 0, ROUTE_LENGTH_MAX);
strcpy(unihash_g, index_route);
strcat(unihash_g, unihash_gs);
memset(unikmer_g, 0, ROUTE_LENGTH_MAX);
strcpy(unikmer_g, index_route);
strcat(unikmer_g, unikmer_gs);
memset(unioff_g, 0, ROUTE_LENGTH_MAX);
strcpy(unioff_g, index_route);
strcat(unioff_g, unioff_gs);
memset(unichr, 0, ROUTE_LENGTH_MAX);
strcpy(unichr, index_route);
strcat(unichr, unichrs);
memset(N_route, 0, ROUTE_LENGTH_MAX);
strcpy(N_route, index_route);
strcat(N_route, f_n);
memset(filename_div, 0, ROUTE_LENGTH_MAX);
strcpy(filename_div, index_route);
strcat(filename_div, divs);
memset(filename_sta, 0, ROUTE_LENGTH_MAX);
strcpy(filename_sta, filename_div);
strcat(filename_sta, graph);
memset(unisize, 0, ROUTE_LENGTH_MAX);
strcpy(unisize, index_route);
strcat(unisize, f_size);
if(tree_flag)
{
fprintf(stderr, "use the VCF-info-based extension\n");
memset(vcf_rpos, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_rpos, index_route);
strcat(vcf_rpos, vcf_rposs);
memset(vcf_aindex, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_aindex, index_route);
strcat(vcf_aindex, vcf_aindexs);
memset(vcf_apos, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_apos, index_route);
strcat(vcf_apos, vcf_aposs);
memset(vcf_aseq, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_aseq, index_route);
strcat(vcf_aseq, vcf_aseqs);
memset(vcf_rpos_end, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_rpos_end, index_route);
strcat(vcf_rpos_end, vcf_rpos_ends);
memset(ref_vcf, 0, ROUTE_LENGTH_MAX);
strcpy(ref_vcf, index_route);
strcat(ref_vcf, ref_vcfs);
memset(vcf_size, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_size, index_route);
strcat(vcf_size, vcf_sizes);
memset(vcf_type, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_type, index_route);
strcat(vcf_type, vcf_types);
memset(vcf_rpos_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_rpos_rev, index_route);
strcat(vcf_rpos_rev, vcf_rposs_rev);
memset(vcf_aindex_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_aindex_rev, index_route);
strcat(vcf_aindex_rev, vcf_aindexs_rev);
memset(vcf_apos_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_apos_rev, index_route);
strcat(vcf_apos_rev, vcf_aposs_rev);
memset(vcf_aseq_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_aseq_rev, index_route);
strcat(vcf_aseq_rev, vcf_aseqs_rev);
memset(vcf_rpos_end_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_rpos_end_rev, index_route);
strcat(vcf_rpos_end_rev, vcf_rpos_ends_rev);
memset(ref_vcf_rev, 0, ROUTE_LENGTH_MAX);
strcpy(ref_vcf_rev, index_route);
strcat(ref_vcf_rev, ref_vcfs_rev);
memset(vcf_size_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_size_rev, index_route);
strcat(vcf_size_rev, vcf_sizes_rev);
memset(vcf_type_rev, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_type_rev, index_route);
strcat(vcf_type_rev, vcf_types_rev);
memset(vcf_chr_rpos, 0, ROUTE_LENGTH_MAX);
strcpy(vcf_chr_rpos, index_route);
strcat(vcf_chr_rpos, vcf_chr_rposs);
}
if ((argc - optind < 4) && (flag_std == 0))
{
max_single_score_r = max_pair_score_r;
seed_filter_pos_num_singlen = seed_filter_pos_numn;
if(strcmp(argv[optind + 2] + strlen(argv[optind + 2]) - 3, ".fq") || strcmp(argv[optind + 2] + strlen(argv[optind + 2]) - 6, ".fastq"))
{
fprintf(stderr, "result file cannot be .fq or .fastq\n");
exit(1);
}
strcpy(sam_result, argv[optind + 2]);
seed_ali_single_end();
}else{
memset(read_fastq2, 0, ROUTE_LENGTH_MAX);
strcpy(read_fastq2, argv[optind + 2]);
if(flag_std == 0)
strcpy(sam_result, argv[optind + 3]);
seed_ali();
}
return 0;
}
void load_index_file()
{
uint64_t a_size = 0;
uint64_t us_n = 0;
uint64_t usf_n = 0;
uint64_t ue_n = 0;
uint64_t up_n = 0;
uint64_t upp_n = 0;
uint64_t hash_n = 0;
uint64_t kmer_n = 0;
uint64_t off_n = 0;
uint64_t pu_n = 0;
uint64_t ref_seq_n = 0;
uint64_t file_size = 0;
//read index file size
fp_num = fopen(unisize, "rb");
if (fp_num == NULL)
{
fputs ("File error opening the size of index file: wrong index route or wrong index file name\n",stderr);
exit (1);
}
fread(&us_n, 8, 1, fp_num);
fread(&usf_n, 8, 1, fp_num);
fread(&ue_n, 8, 1, fp_num);
fread(&up_n, 8, 1, fp_num);
fread(&upp_n, 8, 1, fp_num);
fread(&hash_n, 8, 1, fp_num);
fread(&kmer_n, 8, 1, fp_num);
fread(&off_n, 8, 1, fp_num);
fread(&pu_n, 8, 1, fp_num);
fread(&ref_seq_n, 8, 1, fp_num);
if(tree_flag) fread(&ref_length_p, 8, 1, fp_num);
fclose(fp_num);
//read ref seq file
fprintf(stderr, "Load ref seq\n");
fp_ref_seq = fopen(ref_seq, "rb");
if (fp_ref_seq == NULL)
{
fputs ("File error opening the seq file\n",stderr);
exit (1);
}
fseek(fp_ref_seq, 0, SEEK_END);// non-portable
file_size = ftell(fp_ref_seq);
rewind(fp_ref_seq);
ref_seq_n = file_size;
buffer_ref_seq = (uint64_t* )calloc(ref_seq_n + 536, 1);//536 = (2048 >> 5 + 3) << 3
a_size = ref_seq_n >> 3;
result_ref_seq = fread(buffer_ref_seq, 8, a_size, fp_ref_seq);
if (result_ref_seq != a_size)
{
fprintf(stderr, "Reading error");
exit (3);
}
fclose(fp_ref_seq);
//read input unipath seq file
fprintf(stderr, "Load unipath seq\n");
fp_us_b = fopen (uniseq_b, "rb" );
if (fp_us_b == NULL)
{
fprintf(stderr, "File error opening the unipath seq file\n");
exit (1);
}
fseek(fp_us_b, 0, SEEK_END);// non-portable
file_size = ftell(fp_us_b);
rewind(fp_us_b);
us_n = file_size;
// allocate memory to contain the whole file:
#ifdef UNI_SEQ64
buffer_seq = (uint64_t* ) malloc (us_n);
#else
buffer_seq = (uint8_t* ) malloc (us_n);
#endif
if (buffer_seq == NULL)
{
fputs ("Memory error buffer_seq\n",stderr);
exit (2);
}
// copy the file into the buffer:
#ifdef UNI_SEQ64
a_size = us_n >> 3;
result_seq = fread (buffer_seq, 8, a_size, fp_us_b);
#else
a_size = us_n;
result_seq = fread (buffer_seq, 1, a_size, fp_us_b);
#endif
if (result_seq != a_size)
{
fputs ("Reading error",stderr);
exit (3);
}
fclose(fp_us_b);
//read input unipath offset file
fprintf(stderr, "Load unipath offset\n");
fp_usf_b = fopen(uniseqf_b, "rb");
if(fp_usf_b == NULL)
{
fputs ("File error opening the unipath offset file\n",stderr);
exit (1);
}
fseek(fp_usf_b, 0, SEEK_END);// non-portable
file_size = ftell(fp_usf_b);
rewind(fp_usf_b);
usf_n = file_size;
// allocate memory to contain the whole file:
// copy the file into the buffer:
#ifdef UNPIPATH_OFF_K20
buffer_seqf = (uint64_t* ) malloc (usf_n);
if (buffer_seqf == NULL)
{
fprintf(stderr, "Memory error buffer_seqf");
exit (2);
}
a_size = (usf_n >> 3);
result_seqf = fread (buffer_seqf, 8, a_size, fp_usf_b);
#else
buffer_seqf = (uint32_t* ) malloc (usf_n);
if (buffer_seqf == NULL)
{
fputs ("Memory error buffer_seqf",stderr);
exit (2);
}
a_size = (usf_n >> 2);
result_seqf = fread (buffer_seqf, 4, a_size, fp_usf_b);
#endif
if (result_seqf != a_size)
{
fputs ("Reading error",stderr);
exit (3);
}
fclose(fp_usf_b);
//read input unipath position file
fprintf(stderr, "Load unipath position\n");
fp_up = fopen(unipos, "rb");
if(fp_up == NULL)
{
fprintf(stderr, "File error opening the unipath position file\n");