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command_dist.c
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command_dist.c
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// Copyright 2019 Huiguang Yi. All Rights Reservered.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
#include "command_dist.h"
#include "command_shuffle.h"
#include "iseq2comem.h"
#include "co2mco.h"
#include "mytime.h"
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <dirent.h>
#include <err.h>
#include <errno.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <sys/sysinfo.h>
#include <math.h>
#include <tgmath.h>
#include <time.h>
#include <unistd.h>
#include <zlib.h>
#include <stdbool.h>
#include <malloc.h>
#include <libgen.h>
#ifdef _OPENMP
#include <omp.h>
#endif
mem_dispatch_t mem_dispatch = {0,0,0,0,0,0,0, OBJ_TRADITION , STD , MAKE_REF ,0};
mem_usage_stat_t mem_usage_stat = { 0, 0, 1e7 };
static llint real_time_mem;
const char co_dstat[] = "cofiles.stat";
const char mco_dstat[] = "mcofiles.stat";
const char distoutdir[] = "dist";
typedef int mco_co_dist_t[BIN_SZ];
static inline unsigned int * mco_co_mmpdist_core(gidobj_t** unit_arrmco, char *co_fcode_in, unsigned int *ctx_obj_ct_in );
static inline void mco_co_dist_core(gidobj_t** unit_arrmco, char *co_fcode_in, int bin_sz, mco_co_dist_t shared_ctx_num_in);
#define LINE_LEN 1024
typedef struct prt_line { int len; char line[LINE_LEN]; } prt_line_t ;
static inline void output_ctrl (unsigned int X_size, unsigned int XnY_size, print_ctrl_t* outfield, char *rname, prt_line_t* linebuf ) ;
int dist_dispatch(dist_opt_val_t *opt_val)
{
if( opt_val->mmry == 0 )
opt_val->mmry = get_sys_mmry();
llint base_mem = (llint)( (opt_val->mmry - get_sys_mmry()) * BBILLION ) - mem_usage_stat.others ;
real_time_mem = base_mem + (llint)(get_sys_mmry()*BBILLION) ;
int p_fit_mem = 1;
if( ( opt_val->refpath[0] != '\0' ) )
{
const char *refco_dstat_fpath = test_get_fullpath(opt_val->refpath,co_dstat);
const char *refmco_dstat_fpath = test_get_fullpath(opt_val->refpath,mco_dstat);
if( (refco_dstat_fpath == NULL ) && ( refmco_dstat_fpath == NULL) ){
infile_tab_t *ref_stat = dist_organize_refpath(opt_val);
if(ref_stat->infile_num == 0)
err(errno,"no valid input .fas/.fq file or absent %s | %s in %s \n", co_dstat, mco_dstat, opt_val->refpath ) ;
infile_fmt_count_t* ref_fmt_count;
ref_fmt_count = infile_fmt_count(ref_stat);
if( (ref_stat->infile_num == 0) || (ref_fmt_count->fasta + ref_fmt_count->fastq != ref_stat->infile_num ))
err(errno,"not a valid input files: make sure input files are .fas/.fq format"
"or .co.num |.mco.num files with %s | %s in %s \n", co_dstat, mco_dstat, opt_val->refpath );
const char *dist_refco_dir = opt_val->outdir;
mkdir(dist_refco_dir,0777);
int *shuffled_refname_ind = shuffleN( ref_stat->infile_num, 0 );
mem_usage_stat.input_file_name_sz = ref_stat->infile_num * ( sizeof(llong) + PATHLEN*sizeof(char) );
real_time_mem -= mem_usage_stat.input_file_name_sz;
dim_shuffle = get_dim_shuffle(opt_val);
hashsize = get_hashsz(dim_shuffle);
seq2co_global_var_initial();
mem_usage_stat.shuffled_subctx_arr_sz = (1LLU << 4*( dim_shuffle->dim_shuffle_stat.subk) )*sizeof(int);
real_time_mem -= mem_usage_stat.shuffled_subctx_arr_sz;
p_fit_mem = real_time_mem / ( (hashsize + 1) * sizeof(llong));
if( opt_val->p < p_fit_mem )
p_fit_mem = opt_val->p;
else if(p_fit_mem < 1)
err(errno,"dist_dispatch():\n"
" Kmer hashing need mem.(%lf G) exceed the mem. system or user provide (%lf G)\n"
" user can either consider specify more mem.(-m ) or use smaller k value ( -k)\n"
" or increase dimension reduction level ( -L)\n",
(double)hashsize * sizeof(llong)/1e9, opt_val->mmry);
size_t phash_mem = (llong)p_fit_mem * (hashsize + 1) * sizeof(llong);
real_time_mem -= phash_mem;
opt_val->abundance = false;
const char *refcostat = run_stageI(opt_val, ref_stat, shuffled_refname_ind, dist_refco_dir, p_fit_mem);
run_stageII(refcostat, opt_val->outdir , opt_val->p);
free(dim_shuffle->shuffled_dim);
real_time_mem += mem_usage_stat.shuffled_subctx_arr_sz;
}
else if ( refco_dstat_fpath != NULL) {
if (refmco_dstat_fpath == NULL)
run_stageII(refco_dstat_fpath, opt_val->refpath ,opt_val->p);
}
else if(refmco_dstat_fpath != NULL) {;}
free((char*)refco_dstat_fpath);
free((char*)refmco_dstat_fpath);
}
if ( (opt_val->num_remaining_args >0) || (opt_val->fpath[0] != '\0' ) )
{
const char *qryco_dstat_fpath = NULL;
const char *qrymco_dstat_fpath = NULL;
if((opt_val->pipecmd[0]=='\0') && (opt_val->num_remaining_args >0)){
qryco_dstat_fpath = test_get_fullpath(opt_val->remaining_args[0],co_dstat);
qrymco_dstat_fpath = test_get_fullpath(opt_val->remaining_args[0],mco_dstat);
}
if(opt_val->refpath[0] != '\0'){
const char *ref_db = test_get_fullpath(opt_val->refpath, mco_dstat);
if(ref_db==NULL) err(errno,"need speficy the ref-sketch path for -r to run the query-ref search model");
FILE * ref_mco_stat_fp;
if ((ref_mco_stat_fp = fopen(ref_db,"rb")) == NULL) err(errno,"mco stat file:%s",ref_db );
mco_dstat_t mco_ref_dstat;
fread( &mco_ref_dstat, sizeof(mco_dstat_t),1,ref_mco_stat_fp );
fclose(ref_mco_stat_fp);
if( qryco_dstat_fpath != NULL ){
FILE *qry_co_stat_fp;
if (( qry_co_stat_fp = fopen(qryco_dstat_fpath,"rb")) == NULL) err(errno,"qry co stat file:%s",qryco_dstat_fpath);
co_dstat_t co_qry_dstat;
fread( &co_qry_dstat, sizeof(co_dstat_t), 1, qry_co_stat_fp);
if(co_qry_dstat.shuf_id != mco_ref_dstat.shuf_id )
err(errno, "qry shuf_id: %d not match ref shuf_id: %d\ntry regenerate .co dir and feed -s the .shuf"
"file used to generated ref database",co_qry_dstat.shuf_id,mco_ref_dstat.shuf_id);
else if(co_qry_dstat.comp_num != mco_ref_dstat.comp_num)
err(errno, "qry comp_num: %d not match ref comp_num: %d",co_qry_dstat.comp_num, mco_ref_dstat.comp_num);
mco_cbdco_nobin_dist(opt_val);
}
else if (qrymco_dstat_fpath != NULL)
err(errno,"when -r specified, the query sould not be .mco format, the valid query format shoulde be .fas/.fq file or .co");
else{
infile_tab_t *infile_stat = dist_organize_infiles(opt_val);
infile_fmt_count_t* qry_fmt_count;
qry_fmt_count = infile_fmt_count(infile_stat);
bool is_valid_fas_fq_in = (infile_stat->infile_num != 0) &&
(qry_fmt_count->fasta + qry_fmt_count->fastq == infile_stat->infile_num );
if(is_valid_fas_fq_in){
}
else err(errno,"please specify valid query genomes seq or .co file for database search");
}
}
else if( qryco_dstat_fpath != NULL) {
if( opt_val->num_remaining_args == 1 ){
run_stageII(qryco_dstat_fpath,opt_val->outdir, opt_val->p);
}
else if (opt_val->num_remaining_args > 1){
combine_queries(opt_val);
}
}
else if ( (qrymco_dstat_fpath != NULL) && (opt_val->num_remaining_args > 1 )){
}
else {
infile_tab_t *infile_stat = dist_organize_infiles(opt_val);
infile_fmt_count_t* qry_fmt_count;
qry_fmt_count = infile_fmt_count(infile_stat);
bool is_valid_fas_fq_in = (infile_stat->infile_num != 0) &&
(qry_fmt_count->fasta + qry_fmt_count->fastq == infile_stat->infile_num );
if(is_valid_fas_fq_in || (opt_val->pipecmd[0] != '\0') ){
const char *dist_co_dir = opt_val->outdir;
mkdir(dist_co_dir,0777);
int *shuffled_refname_ind = shuffleN( infile_stat->infile_num, 0 );
mem_usage_stat.input_file_name_sz = infile_stat->infile_num * ( sizeof(llong) + PATHLEN*sizeof(char) );
real_time_mem -= mem_usage_stat.input_file_name_sz;
dim_shuffle = get_dim_shuffle(opt_val);
hashsize = get_hashsz(dim_shuffle);
seq2co_global_var_initial();
mem_usage_stat.shuffled_subctx_arr_sz = (1LLU << 4*( dim_shuffle->dim_shuffle_stat.subk) )*sizeof(int);
real_time_mem -= mem_usage_stat.shuffled_subctx_arr_sz;
p_fit_mem = real_time_mem / ( (hashsize + 1) * sizeof(llong));
if( opt_val->p < p_fit_mem ) p_fit_mem = opt_val->p;
else if(p_fit_mem < 1)
err(errno,"dist_dispatch():\n"
" Kmer hashing need mem.(%lf G) exceed the mem. system or user provide (%lf G)\n"
" user can either consider specify more mem.(-m ) or use smaller k value ( -k)\n"
" or increase dimension reduction level ( -L)\n",
(double)hashsize * sizeof(llong)/1e9, opt_val->mmry);
size_t phash_mem = (llong)p_fit_mem * (hashsize + 1) * sizeof(llong);
real_time_mem -= phash_mem ;
run_stageI(opt_val,infile_stat,shuffled_refname_ind,dist_co_dir,p_fit_mem);
}
else err(errno,"not valid raw seq format");
}
}
return 0;
};
dim_shuffle_t *get_dim_shuffle( dist_opt_val_t *opt_val_in )
{
char shuf_infile_name_prefix[PATHLEN+9];
char shuf_infile_name[PATHLEN];
strcpy(shuf_infile_name, opt_val_in->dr_file);
if( strcmp( shuf_infile_name, "" ) == 0 )
{
srand ( time(NULL) );
dim_shuffle_stat_t dim_shuffle_stat =
{
rand(),
opt_val_in->k,
opt_val_in->dr_level + add_len_drlevel2subk(),
opt_val_in->dr_level,
};
struct stat outd;
if( (stat(opt_val_in->outdir, &outd) != 0 ) || (! S_ISDIR(outd.st_mode) ) )
mkdir(opt_val_in->outdir,0777);
sprintf(shuf_infile_name_prefix, "%s/default",opt_val_in->outdir);
write_dim_shuffle_file( &dim_shuffle_stat,shuf_infile_name_prefix);
sprintf(shuf_infile_name,"%s.shuf",shuf_infile_name_prefix);
};
return read_dim_shuffle_file(shuf_infile_name);
};
int get_hashsz(dim_shuffle_t *dim_shuffle_in )
{
llong ctx_space_sz = 1LLU << 4*( dim_shuffle_in->dim_shuffle_stat.k - dim_shuffle_in->dim_shuffle_stat.drlevel );
int primer_ind = 4*( dim_shuffle_in->dim_shuffle_stat.k - dim_shuffle_in->dim_shuffle_stat.drlevel ) - CTX_SPC_USE_L - 7;
if(primer_ind < 0 || primer_ind > 24 ){
int k_add = primer_ind < 0 ? (1 + (0-primer_ind)/4) : - (1 + ( primer_ind - 24 )/4) ;
err(errno,"get_hashsz(): primer_ind: %d out of range(0 ~ 24), by formula:\n"
"int primer_ind = 4*(opt_val->k - dim_shuffle->dim_shuffle_stat.drlevel) - CTX_SPC_USE_L - 7\n"
"this might caused by too small or too large k\n"
"kmer length = %d\n"
"dim reduction level = %d\n"
"ctx_space size = %llu\n"
"CTX space usage limit = %lf\n\n"
"try rerun the program with option -k = %d",
primer_ind, dim_shuffle_in->dim_shuffle_stat.k, dim_shuffle_in->dim_shuffle_stat.drlevel,ctx_space_sz,
(double)1/(1 << CTX_SPC_USE_L),dim_shuffle_in->dim_shuffle_stat.k + k_add );
};
int hashsize_get = primer[primer_ind];
return hashsize_get ;
}
const char* test_get_fullpath(const char *parent_path, const char *dstat_f)
{
struct stat path_stat;
if( stat(parent_path, &path_stat) < 0 )
err(errno,"test_get_fullpath()::%s",parent_path);
if( S_ISDIR(path_stat.st_mode) ){
char* fullpath = malloc(PATHLEN+1);
sprintf((char *)fullpath,"%s/%s", parent_path, dstat_f);
FILE *fp;
if ( (fp = fopen(fullpath,"rb")) != NULL ){
fclose(fp);
return fullpath;
}
else{
free((char*)fullpath);
return NULL;
}
}
else
return NULL;
};
const char * run_stageI (dist_opt_val_t *opt_val, infile_tab_t *seqfile_stat,
int* shuffled_seqfname_ind, const char *co_dir, int p_fit_mem)
{
llong **CO = malloc( p_fit_mem * sizeof(llong *) );
for(int i = 0; i< p_fit_mem; i++ ){
CO[i] = (llong *)malloc(hashsize * sizeof(llong) );
}
llong all_ctx_ct = 0 ;
ctx_obj_ct_t *ctx_ct_list = malloc(sizeof(ctx_obj_ct_t) * seqfile_stat->infile_num);
if(opt_val->byread){
for(int i = 0; i< seqfile_stat->infile_num; i++){
char* seqfname = seqfile_stat->organized_infile_tab[ shuffled_seqfname_ind[i] ].fpath;
printf("decomposing %s by reads\n",seqfname) ;
reads2mco(seqfname, co_dir, opt_val->pipecmd);
}
}
else {
int num_threads = seqfile_stat->infile_num > p_fit_mem ? p_fit_mem : 1;
int fcount = 0;
#pragma omp parallel for num_threads(num_threads) reduction(+:all_ctx_ct) schedule(guided)
for(int i = 0; i< seqfile_stat->infile_num; i++){
int tid = 0;
#ifdef _OPENMP
tid = omp_get_thread_num();
#endif
char* seqfname = seqfile_stat->organized_infile_tab[ shuffled_seqfname_ind[i] ].fpath;
char cofname[PATHLEN];
sprintf(cofname,"%s/%d.co",co_dir,i);
llong *co;
if(isOK_fmt_infile(seqfname,fastq_fmt,FQ_FMT_SZ) || opt_val->pipecmd[0]!='\0'){
if(opt_val->abundance){
co = mt_shortreads2koc(seqfname,CO[tid],opt_val->pipecmd, p_fit_mem);
ctx_ct_list[i] = write_fqkoc2files(cofname,co);
}
else{
co = fastq2co(seqfname,CO[tid],opt_val->pipecmd,opt_val->kmerqlty,opt_val->kmerocrs);
ctx_ct_list[i] = write_fqco2file(cofname,co);
}
}
else{
if(opt_val->abundance) {
opt_val->abundance = 0;
printf("Warning: close abundance mode (-A) since non-fastq file input.\n");
}
if(opt_val->u)
co = uniq_fasta2co(seqfname,CO[tid],opt_val->pipecmd);
else
co = fasta2co(seqfname,CO[tid],opt_val->pipecmd);
ctx_ct_list[i] = wrt_co2cmpn_use_inn_subctx(cofname,co);
}
all_ctx_ct += ctx_ct_list[i] ;
#pragma omp atomic
fcount++;
printf("%d/%d decomposing %s\r",fcount,seqfile_stat->infile_num,seqfname) ;
}
printf("\n");
#pragma omp parallel for num_threads(p_fit_mem) schedule(guided)
for(int c = 0; c < component_num; c++){
size_t *cof_index_in_cbdco = malloc( (seqfile_stat->infile_num + 1) * sizeof(size_t) );
char tmpfname[PATHLEN];
FILE *com_cofp,*indexfp, *com_abund_fp;
sprintf(tmpfname,"%s/%s.%d",co_dir,skch_prefix,c);
if( (com_cofp = fopen(tmpfname,"wb")) == NULL) err(errno,"%s",tmpfname);
sprintf(tmpfname,"%s/%s.%d",co_dir,idx_prefix,c);
if( (indexfp = fopen(tmpfname,"wb")) == NULL) err(errno,"%s",tmpfname);
if(opt_val->abundance) {
sprintf(tmpfname,"%s/%s.%d.a",co_dir,skch_prefix,c);
com_abund_fp = fopen(tmpfname,"wb");
if( com_abund_fp == NULL) err(errno,"%s",tmpfname);
}
void *tmp_mem = malloc( LD_FCTR * 2 * (1LLU << (4*COMPONENT_SZ - CTX_SPC_USE_L)) *sizeof(unsigned int) );
struct stat tmpstat;
FILE *tmpfp;
cof_index_in_cbdco[0] = 0;
for(int i = 0; i< seqfile_stat->infile_num; i++){
sprintf(tmpfname,"%s/%d.co.%d", co_dir, i, c);
if( (tmpfp = fopen(tmpfname,"rb")) == NULL) err(errno,"%s",tmpfname);
stat(tmpfname,&tmpstat);
int tmpkmerct = tmpstat.st_size/sizeof(unsigned int);
cof_index_in_cbdco[i+1] = (size_t)cof_index_in_cbdco[i] + tmpkmerct;
fread(tmp_mem,tmpstat.st_size,1,tmpfp);
fwrite(tmp_mem,tmpstat.st_size,1,com_cofp);
fclose(tmpfp);
remove(tmpfname);
if(opt_val->abundance) {
sprintf(tmpfname,"%s/%d.co.%d.a", co_dir, i, c);
if( (tmpfp = fopen(tmpfname,"rb")) == NULL) err(errno,"%s",tmpfname);
fread(tmp_mem, sizeof(unsigned short)*tmpkmerct, 1 , tmpfp);
fwrite(tmp_mem, sizeof(unsigned short)*tmpkmerct, 1 , com_abund_fp );
fclose(tmpfp);
remove(tmpfname);
}
}
fclose(com_cofp);
if(opt_val->abundance) fclose(com_abund_fp) ;
free(tmp_mem);
fwrite(cof_index_in_cbdco,sizeof(size_t), seqfile_stat->infile_num + 1, indexfp);
fclose(indexfp);
free(cof_index_in_cbdco);
}
}
for(int i = 0; i< p_fit_mem; i++ ) free(CO[i]);
free(CO);
co_dstat_t co_dstat_wrout;
co_dstat_wrout.shuf_id = dim_shuffle->dim_shuffle_stat.id ;
co_dstat_wrout.koc = opt_val->abundance ;
co_dstat_wrout.kmerlen = dim_shuffle->dim_shuffle_stat.k * 2;
co_dstat_wrout.dim_rd_len = dim_shuffle->dim_shuffle_stat.drlevel * 2 ;
co_dstat_wrout.comp_num = component_num ;
co_dstat_wrout.infile_num = seqfile_stat->infile_num;
co_dstat_wrout.all_ctx_ct = all_ctx_ct;
char *co_dstat_fullname = malloc(PATHLEN*sizeof(char) );
sprintf(co_dstat_fullname, "%s/%s",co_dir,co_dstat);
FILE *coutfp;
if ( ( coutfp = fopen(co_dstat_fullname,"wb")) == NULL ) err(errno,"%s",co_dstat_fullname);
fwrite(&co_dstat_wrout,sizeof(co_dstat_wrout),1,coutfp);
fwrite(ctx_ct_list,sizeof(ctx_obj_ct_t),co_dstat_wrout.infile_num,coutfp);
free(ctx_ct_list);
for(int i = 0; i< co_dstat_wrout.infile_num; i++)
fwrite(seqfile_stat->organized_infile_tab[ shuffled_seqfname_ind[i] ].fpath,PATHLEN,1,coutfp);
fclose(coutfp);
return (const char *)co_dstat_fullname;
}
void run_stageII(const char * co_dstat_fpath, const char* dist_mco_dir, int p_fit_mem)
{
const char* dist_co_dir = get_pathname(co_dstat_fpath,co_dstat);
if ( mkdir(dist_mco_dir, 0700) ) {
if(errno == EEXIST)
printf("Warning: write mco file to an exists outdir:%s\n",dist_mco_dir);
else
err(errno,"run_stageII(): mkdir %s error", dist_mco_dir);
}
const char* mco_dstat_fpath = malloc(PATHLEN*sizeof(char));
sprintf((char*)mco_dstat_fpath,"%s/%s",dist_mco_dir,mco_dstat);
FILE *co_stat_fp,*mco_stat_fp;
if( ( co_stat_fp = fopen(co_dstat_fpath,"rb")) == NULL ) err(errno,"run_stageII(():%s",co_dstat_fpath);
co_dstat_t co_dstat_readin;
fread( &co_dstat_readin, sizeof(co_dstat_t),1,co_stat_fp );
if( ( mco_stat_fp = fopen(mco_dstat_fpath,"wb")) == NULL ) err(errno,"run_stageII(():%s",mco_dstat_fpath);
mco_dstat_t mco_dstat_writeout;
mco_dstat_writeout.shuf_id = co_dstat_readin.shuf_id;
mco_dstat_writeout.kmerlen = co_dstat_readin.kmerlen ;
mco_dstat_writeout.dim_rd_len = co_dstat_readin.dim_rd_len ;
mco_dstat_writeout.infile_num = co_dstat_readin.infile_num;
mco_dstat_writeout.comp_num = co_dstat_readin.comp_num ;
fwrite(&mco_dstat_writeout,sizeof(mco_dstat_writeout),1, mco_stat_fp );
ctx_obj_ct_t *tmp_ctx_ct = malloc(sizeof(ctx_obj_ct_t)*co_dstat_readin.infile_num);
fread(tmp_ctx_ct,sizeof(ctx_obj_ct_t),co_dstat_readin.infile_num,co_stat_fp);
fwrite(tmp_ctx_ct,sizeof(ctx_obj_ct_t),co_dstat_readin.infile_num,mco_stat_fp);
char (*tmpname)[PATHLEN] = malloc( PATHLEN * co_dstat_readin.infile_num );
fread(tmpname,PATHLEN,co_dstat_readin.infile_num,co_stat_fp);
fwrite(tmpname,PATHLEN,co_dstat_readin.infile_num,mco_stat_fp);
free(tmp_ctx_ct);
free(tmpname);
fclose(co_stat_fp);
fclose(mco_stat_fp);
combco2mco(dist_mco_dir,dist_co_dir,co_dstat_readin.infile_num,co_dstat_readin.comp_num,p_fit_mem);
free((char*)dist_co_dir );
free((char*)mco_dstat_fpath);
}
int alp_size = 4 ;
static ctx_obj_ct_t initial_dist[BIN_SZ];
static int ref_seq_num,qry_seq_num,kmerlen,dim_reduct_len ;
void mco_co_dist( char *refmco_dname, char *qryco_dname, const char *distout_dir, int p_fit_mem)
{
FILE *refmco_dstat_fp, *qryco_dstat_fp;
char *refmco_dstat_fpath = malloc(PATHLEN*sizeof(char));
char *qryco_dstat_fpath = malloc(PATHLEN*sizeof(char));
sprintf(refmco_dstat_fpath,"%s/%s",refmco_dname,mco_dstat);
sprintf(qryco_dstat_fpath,"%s/%s",qryco_dname,co_dstat);
if( (refmco_dstat_fp = fopen(refmco_dstat_fpath,"rb")) == NULL )
err(errno,"need provied mco dir path for mco_co_dist() arg 1. refmco_dstat_fpath");
if( (qryco_dstat_fp = fopen(qryco_dstat_fpath,"rb")) == NULL )
err(errno,"need provied co dir path for mco_co_dist() arg 2. qryco_dstat_fpath");
mco_dstat_t mco_dstat_readin ;
co_dstat_t co_dstat_readin ;
fread(&mco_dstat_readin,sizeof(mco_dstat_readin),1,refmco_dstat_fp);
fread(&co_dstat_readin,sizeof(co_dstat_readin),1,qryco_dstat_fp);
unsigned int * qry_ctx_ct_list = malloc(co_dstat_readin.infile_num * sizeof(unsigned int));
unsigned int * ref_ctx_ct_list = malloc(mco_dstat_readin.infile_num * sizeof(unsigned int));
fread(qry_ctx_ct_list,sizeof(unsigned int),co_dstat_readin.infile_num,qryco_dstat_fp);
fread(ref_ctx_ct_list,sizeof(unsigned int),mco_dstat_readin.infile_num,refmco_dstat_fp);
char (*cofname)[PATHLEN] = malloc(co_dstat_readin.infile_num * PATHLEN);
char (*mcofname)[PATHLEN] = malloc(mco_dstat_readin.infile_num * PATHLEN);
fread(cofname,PATHLEN,co_dstat_readin.infile_num,qryco_dstat_fp);
fread(mcofname,PATHLEN,mco_dstat_readin.infile_num,refmco_dstat_fp);
fclose(refmco_dstat_fp);
fclose(qryco_dstat_fp);
if( !(mco_dstat_readin.comp_num == co_dstat_readin.comp_num) )
err(errno,"query args not match ref args: ref.comp_num = %d vs. %d = qry.comp_num",
mco_dstat_readin.comp_num, co_dstat_readin.comp_num);
if(!(mco_dstat_readin.shuf_id == co_dstat_readin.shuf_id))
err(errno,"query args not match ref args: ref.shuf_id = %d vs. %d = qry.shuf_id",
mco_dstat_readin.shuf_id, co_dstat_readin.shuf_id);
int ref_bin_num = mco_dstat_readin.infile_num / BIN_SZ;
int binsz;
for(int i=0; i<=ref_bin_num;i++ ){
if( i == ref_bin_num ){
binsz = mco_dstat_readin.infile_num % BIN_SZ;
if(binsz == 0) continue;
}else binsz = BIN_SZ;
#pragma omp parallel for num_threads(p_fit_mem) schedule(guided)
for( int k=0; k< co_dstat_readin.infile_num; k++){
if(qry_ctx_ct_list[k]==0){
warnx("%dth co file is empty",k);
continue;
}
char dist_fcode[PATHLEN];
sprintf(dist_fcode,"%s/%d.%d.dist", distout_dir, i, k );
FILE *distfp;
if ( (distfp = fopen(dist_fcode,"wb")) == NULL) err(errno,"mco_co_dist()::%s",dist_fcode);
fwrite(initial_dist, sizeof(ctx_obj_ct_t), binsz, distfp);
fclose(distfp);
}
for ( int j = 0; j < mco_dstat_readin.comp_num; j++ ){
char mco_fcode[PATHLEN];
sprintf(mco_fcode,"%s/%d.mco.%d",refmco_dname,i,j);
gidobj_t** unit_arrmco_readin = read_unit_arrmco_file(mco_fcode);
#pragma omp parallel for num_threads(p_fit_mem) schedule(guided)
for(int k=0; k< co_dstat_readin.infile_num; k++){
if(qry_ctx_ct_list[k]==0) continue;
int tid = 0;
#ifdef _OPENMP
tid = omp_get_thread_num();
#endif
char co_fcode[PATHLEN]; char dist_fcode[PATHLEN];
sprintf(co_fcode,"%s/%d.%d.co.%d",qryco_dname,k/BIN_SZ, k % BIN_SZ, j);
sprintf(dist_fcode,"%s/%d.%d.dist",distout_dir, i , k );
int fd;
if( ( (fd = open(dist_fcode,O_RDWR, 0600) ) == -1) )
err(errno,"mco_co_dist()::distfile = %s[tid = %d]",dist_fcode,tid);
ctx_obj_ct_t * ctx_obj_ct = mmap(NULL, binsz*(sizeof(ctx_obj_ct_t)), PROT_READ | PROT_WRITE, MAP_SHARED, fd, 0);
if(ctx_obj_ct == MAP_FAILED) err(errno,"ctx_obj_ct mmap error");
ctx_obj_ct = mco_co_mmpdist_core(unit_arrmco_readin,co_fcode,ctx_obj_ct);
if ( msync( ctx_obj_ct, binsz*(sizeof(ctx_obj_ct_t)), MS_SYNC ) < 0 )
err(errno,"mco_co_dist()::ctx_obj_ct msync failed");
munmap(ctx_obj_ct,binsz*(sizeof(ctx_obj_ct_t)));
close(fd);
}
free_unit_arrmco(unit_arrmco_readin);
}
}
ref_seq_num = mco_dstat_readin.infile_num ;
qry_seq_num = co_dstat_readin.infile_num ;
kmerlen = co_dstat_readin.kmerlen;
dim_reduct_len = co_dstat_readin.dim_rd_len;
char distf[PATHLEN];
sprintf(distf, "%s/distance.out", distout_dir);
FILE *distfp;
if( (distfp = fopen(distf,"a")) == NULL ) err(errno,"mco_co_dist():%s",distf);
for(int i=0; i<=ref_bin_num;i++ ){
for ( int k = 0; k < co_dstat_readin.infile_num; k++ ){
if(qry_ctx_ct_list[k]>0)
fname_dist_print(i,k,distout_dir,ref_ctx_ct_list,qry_ctx_ct_list,mcofname,cofname,distfp);
}
}
fclose(distfp);
free(ref_ctx_ct_list);
free(qry_ctx_ct_list);
free(mcofname);
free(cofname);
}
void mco_cbd_co_dist(dist_opt_val_t *opt_val_in)
{
int p_fit_mem = opt_val_in->p;
llong mem_limit = (llong)opt_val_in->mmry*BBILLION;
char *refmco_dname = opt_val_in->refpath;
char *qryco_dname = opt_val_in->remaining_args[0];
const char *distout_dir = opt_val_in->outdir;
printf("run mco_cbd_co_dist(), %fG memory used\t%d threads used\n",opt_val_in->mmry,p_fit_mem);
FILE *refmco_dstat_fp, *qryco_dstat_fp;
char *refmco_dstat_fpath = malloc(PATHLEN*sizeof(char));
char *qryco_dstat_fpath = malloc(PATHLEN*sizeof(char));
sprintf(refmco_dstat_fpath,"%s/%s",refmco_dname,mco_dstat);
sprintf(qryco_dstat_fpath,"%s/%s",qryco_dname,co_dstat);
if( (refmco_dstat_fp = fopen(refmco_dstat_fpath,"rb")) == NULL )
err(errno,"need provied mco dir path for mco_co_dist() arg 1. refmco_dstat_fpath");
if( (qryco_dstat_fp = fopen(qryco_dstat_fpath,"rb")) == NULL )
err(errno,"need provied co dir path for mco_co_dist() arg 2. qryco_dstat_fpath");
mco_dstat_t mco_dstat_readin ;
co_dstat_t co_dstat_readin ;
fread(&mco_dstat_readin,sizeof(mco_dstat_readin),1,refmco_dstat_fp);
fread(&co_dstat_readin,sizeof(co_dstat_readin),1,qryco_dstat_fp);
ctx_obj_ct_t * qry_ctx_ct_list = malloc(co_dstat_readin.infile_num * sizeof(ctx_obj_ct_t));
ctx_obj_ct_t * ref_ctx_ct_list = malloc(mco_dstat_readin.infile_num * sizeof(ctx_obj_ct_t));
fread(qry_ctx_ct_list,sizeof(ctx_obj_ct_t),co_dstat_readin.infile_num,qryco_dstat_fp);
fread(ref_ctx_ct_list,sizeof(ctx_obj_ct_t),mco_dstat_readin.infile_num,refmco_dstat_fp);
char (*cofname)[PATHLEN] = malloc(co_dstat_readin.infile_num * PATHLEN);
char (*mcofname)[PATHLEN] = malloc(mco_dstat_readin.infile_num * PATHLEN);
fread(cofname,PATHLEN,co_dstat_readin.infile_num,qryco_dstat_fp);
fread(mcofname,PATHLEN,mco_dstat_readin.infile_num,refmco_dstat_fp);
fclose(refmco_dstat_fp);
fclose(qryco_dstat_fp);
if( !(mco_dstat_readin.comp_num == co_dstat_readin.comp_num) )
err(errno,"query args not match ref args: ref.comp_num = %d vs. %d = qry.comp_num",
mco_dstat_readin.comp_num, co_dstat_readin.comp_num);
if(!(mco_dstat_readin.shuf_id == co_dstat_readin.shuf_id))
err(errno,"query args not match ref args: ref.shuf_id = %d vs. %d = qry.shuf_id",
mco_dstat_readin.shuf_id, co_dstat_readin.shuf_id);
int ref_bin_num = mco_dstat_readin.infile_num / BIN_SZ;
if( mco_dstat_readin.infile_num % BIN_SZ > 0 ) ref_bin_num +=1;
char onedist[PATHLEN];
sprintf(onedist,"%s/sharedk_ct.dat",distout_dir);
int dist_bfp = open(onedist,O_RDWR,0600) ;
if (dist_bfp == -1) {
close(dist_bfp);
dist_bfp = open(onedist,O_RDWR|O_CREAT, 0600) ;
if (dist_bfp == -1) err(errno,"mco_cbd_co_dist()::%s",onedist);
}
else{
errno = EEXIST;
err(errno,"mco_cbd_co_dist()::%s",onedist);
}
size_t disf_sz = (size_t)mco_dstat_readin.infile_num*co_dstat_readin.infile_num*sizeof(ctx_obj_ct_t) ;
if(ftruncate(dist_bfp, disf_sz) == -1) err(errno,"mco_cbd_co_dist()::ftruncate");
close(dist_bfp);
dist_bfp = open(onedist,O_RDWR, 0600);
if (dist_bfp == -1) err(errno,"mco_cbd_co_dist()::%s",onedist);
ctx_obj_ct_t *ctx_obj_ct = mmap(NULL,disf_sz,PROT_READ | PROT_WRITE,MAP_SHARED ,dist_bfp,0);
if(ctx_obj_ct == MAP_FAILED) err(errno,"ctx_obj_ct mmap error");
close(dist_bfp);
int page_sz = sysconf(_SC_PAGESIZE);
size_t comp_sz = (1LLU << 4*COMPONENT_SZ);
if( comp_sz % page_sz != 0 ) err(errno,"comp_sz %d is not multiple of page_sz %d ",comp_sz,page_sz );
int num_unit_mem = mem_limit / (mco_dstat_readin.infile_num*sizeof(ctx_obj_ct_t) * page_sz);
if(num_unit_mem < 1) err(errno,"at least %fG memory needed to map ./onedist, specify more memory use -m",
(float)mco_dstat_readin.infile_num*sizeof(ctx_obj_ct_t) * page_sz/1073741824 );
int num_cof_batch = num_unit_mem*page_sz;
size_t unitsz_distf_mapped = (size_t)num_cof_batch * mco_dstat_readin.infile_num * sizeof(ctx_obj_ct_t) ;
int num_mapping_distf = co_dstat_readin.infile_num / num_cof_batch ;
size_t maplength;
int bnum_infile;
FILE *cbd_fcode_comp_fp,*cbd_fcode_comp_index_fp;
struct stat cbd_fcode_stat;
size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1) );
size_t *mco_offset_index = malloc(sizeof(size_t) * comp_sz);
unsigned int *mco_bin_index = malloc( sizeof(unsigned int) * comp_sz * ref_bin_num );
gidobj_t* mco_mem = malloc( sizeof(gidobj_t) * 442317172 );
char mco_fcode[PATHLEN]; char mco_index_fcode[PATHLEN];
char co_cbd_fcode[PATHLEN];char co_cbd_index_fcode[PATHLEN];
for(int b=0;b<=num_mapping_distf;b++){
if(b==num_mapping_distf){
bnum_infile = co_dstat_readin.infile_num % num_cof_batch ;
if( bnum_infile == 0 ) continue;
}else bnum_infile = num_cof_batch;
maplength = (size_t)bnum_infile * mco_dstat_readin.infile_num * sizeof(ctx_obj_ct_t);
printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n",
disf_sz,mco_dstat_readin.infile_num,co_dstat_readin.infile_num,num_mapping_distf,bnum_infile,maplength,(size_t)b*unitsz_distf_mapped);
for ( int j = 0; j < mco_dstat_readin.comp_num; j++ ) {
sprintf(mco_index_fcode,"%s/mco.index.%d",refmco_dname,j);
sprintf(mco_fcode,"%s/mco.%d",refmco_dname,j);
FILE *indexfp, *mcofp;
if( (indexfp = fopen(mco_index_fcode,"rb"))==NULL) err(errno,"mco_cbd_co_dist()::%s",mco_index_fcode);
fread(mco_offset_index,sizeof(size_t),comp_sz,indexfp);
fread(mco_bin_index,sizeof(unsigned int),comp_sz * ref_bin_num,indexfp);
fclose(indexfp);
struct stat s;
if( (mcofp = fopen(mco_fcode,"rb"))==NULL) err(errno,"mco_cbd_co_dist()::%s",mco_fcode);
stat(mco_fcode, &s);
fread(mco_mem,sizeof(gidobj_t),s.st_size/sizeof(gidobj_t),mcofp);
fclose(mcofp);
sprintf(co_cbd_fcode,"%s/combco.%d",qryco_dname,j);
if( (cbd_fcode_comp_fp = fopen(co_cbd_fcode,"rb"))==NULL) err(errno,"mco_cbd_co_dist()::%s",co_cbd_fcode);
stat(co_cbd_fcode, &cbd_fcode_stat);
if(co_dstat_readin.koc){
}
unsigned int *cbd_fcode_mem = malloc(cbd_fcode_stat.st_size);
fread(cbd_fcode_mem,sizeof(unsigned int),cbd_fcode_stat.st_size/sizeof(unsigned int),cbd_fcode_comp_fp);
fclose(cbd_fcode_comp_fp);
sprintf(co_cbd_index_fcode,"%s/combco.index.%d",qryco_dname,j);
if( (cbd_fcode_comp_index_fp = fopen(co_cbd_index_fcode,"rb"))==NULL)
err(errno,"mco_cbd_co_dist()::%s",co_cbd_index_fcode);
fread(fco_pos,sizeof(size_t),co_dstat_readin.infile_num + 1 ,cbd_fcode_comp_index_fp);
fclose(cbd_fcode_comp_index_fp);
#pragma omp parallel for num_threads(p_fit_mem) schedule(guided)
for(int kind = 0; kind < bnum_infile; kind++){
int k = b*num_cof_batch + kind;
if(qry_ctx_ct_list[k]==0) continue;
unsigned int ind, mcogid, pos;
llong distf_offset = (size_t)k * mco_dstat_readin.infile_num;
for(int n = 0; n < fco_pos[k+1] - fco_pos[k]; n++){
ind = cbd_fcode_mem[ fco_pos[k] + n ];
pos = 0;
for(int bin=0; bin < ref_bin_num; bin++){
int bin_gnum = mco_bin_index[ ind *ref_bin_num + bin];
for(int g = 0; g < bin_gnum ; g++ ){
mcogid = bin*BIN_SZ + mco_mem[ mco_offset_index[ind] + pos ];
ctx_obj_ct[distf_offset + mcogid ]++ ;
pos++;
}
}
}
}
free(cbd_fcode_mem);
munmap(mco_offset_index, comp_sz * sizeof(size_t));
munmap(mco_bin_index,comp_sz*ref_bin_num*sizeof(unsigned int) );
}
if ( msync( ctx_obj_ct + (size_t)b*num_cof_batch*mco_dstat_readin.infile_num, maplength, MS_SYNC ) < 0 )
err(errno,"mco_cbd_co_dist()::ctx_obj_ct msync failed");
munmap(ctx_obj_ct + (size_t)b*num_cof_batch*mco_dstat_readin.infile_num, maplength);
}
free(fco_pos);
ref_seq_num = mco_dstat_readin.infile_num ;
qry_seq_num = co_dstat_readin.infile_num ;
kmerlen = co_dstat_readin.kmerlen;
dim_reduct_len = co_dstat_readin.dim_rd_len;
dist_print_nobin(distout_dir,ref_seq_num, qry_seq_num, ref_ctx_ct_list, qry_ctx_ct_list,num_cof_batch,mcofname, cofname, opt_val_in);
free(ref_ctx_ct_list);
free(qry_ctx_ct_list);
free(mcofname);
free(cofname);
}
void mco_cbdco_nobin_dist(dist_opt_val_t *opt_val_in)
{
int p_fit_mem = opt_val_in->p;
llong mem_limit = (llong)opt_val_in->mmry*BBILLION;
char *refmco_dname = opt_val_in->refpath;
char *qryco_dname = opt_val_in->remaining_args[0];
const char *distout_dir = opt_val_in->outdir;
mkdir(distout_dir,0700);
FILE *refmco_dstat_fp, *qryco_dstat_fp;
char *refmco_dstat_fpath = malloc(PATHLEN*sizeof(char));
char *qryco_dstat_fpath = malloc(PATHLEN*sizeof(char));
sprintf(refmco_dstat_fpath,"%s/%s",refmco_dname,mco_dstat);
sprintf(qryco_dstat_fpath,"%s/%s",qryco_dname,co_dstat);
if( (refmco_dstat_fp = fopen(refmco_dstat_fpath,"rb")) == NULL )
err(errno,"need provied mco dir path for mco_co_dist() arg 1. refmco_dstat_fpath");
if( (qryco_dstat_fp = fopen(qryco_dstat_fpath,"rb")) == NULL )
err(errno,"need provied co dir path for mco_co_dist() arg 2. qryco_dstat_fpath");
mco_dstat_t mco_dstat_readin ;
co_dstat_t co_dstat_readin ;
fread(&mco_dstat_readin,sizeof(mco_dstat_readin),1,refmco_dstat_fp);
fread(&co_dstat_readin,sizeof(co_dstat_readin),1,qryco_dstat_fp);
ctx_obj_ct_t * qry_ctx_ct_list = malloc(co_dstat_readin.infile_num * sizeof(ctx_obj_ct_t));
ctx_obj_ct_t * ref_ctx_ct_list = malloc(mco_dstat_readin.infile_num * sizeof(ctx_obj_ct_t));
fread(qry_ctx_ct_list,sizeof(ctx_obj_ct_t),co_dstat_readin.infile_num,qryco_dstat_fp);
fread(ref_ctx_ct_list,sizeof(ctx_obj_ct_t),mco_dstat_readin.infile_num,refmco_dstat_fp);
char (*cofname)[PATHLEN] = malloc(co_dstat_readin.infile_num * PATHLEN);
char (*mcofname)[PATHLEN] = malloc(mco_dstat_readin.infile_num * PATHLEN);
fread(cofname,PATHLEN,co_dstat_readin.infile_num,qryco_dstat_fp);
fread(mcofname,PATHLEN,mco_dstat_readin.infile_num,refmco_dstat_fp);
fclose(refmco_dstat_fp);
fclose(qryco_dstat_fp);
if( !(mco_dstat_readin.comp_num == co_dstat_readin.comp_num) )
err(errno,"query args not match ref args: ref.comp_num = %d vs. %d = qry.comp_num",
mco_dstat_readin.comp_num, co_dstat_readin.comp_num);
if(!(mco_dstat_readin.shuf_id == co_dstat_readin.shuf_id))
err(errno,"query args not match ref args: ref.shuf_id = %d vs. %d = qry.shuf_id",
mco_dstat_readin.shuf_id, co_dstat_readin.shuf_id);
char onedist[PATHLEN];
sprintf(onedist,"%s/sharedk_ct.dat",distout_dir);
int dist_bfp = open(onedist,O_RDWR,0600) ;
if (dist_bfp == -1) {
close(dist_bfp);
dist_bfp = open(onedist,O_RDWR|O_CREAT, 0600) ;
if (dist_bfp == -1) err(errno," mco_cbdco_nobin_dist()::%s",onedist);
}else err(EEXIST," mco_cbdco_nobin_dist():%s",onedist);
int page_sz = sysconf(_SC_PAGESIZE);
size_t comp_sz = (1LLU << 4*COMPONENT_SZ);
if( comp_sz % page_sz != 0 ) err(errno,"comp_sz %d is not multiple of page_sz %d ",comp_sz,page_sz );
size_t maplength;
int bnum_infile;
size_t *mco_offset_index = malloc(sizeof(size_t) * comp_sz);
#define MCOMM_SZ 442317172
gidobj_t* mco_mem = malloc( sizeof(gidobj_t) * MCOMM_SZ );
char mco_fcode[PATHLEN]; char mco_index_fcode[PATHLEN];
char co_cbd_fcode[PATHLEN];char co_cbd_index_fcode[PATHLEN];
ref_seq_num = mco_dstat_readin.infile_num ;
qry_seq_num = co_dstat_readin.infile_num ;
kmerlen = co_dstat_readin.kmerlen;
dim_reduct_len = co_dstat_readin.dim_rd_len;
char distf[PATHLEN];
sprintf(distf, "%s/distance.out", distout_dir);
int num_unit_mem = mem_limit / (mco_dstat_readin.infile_num*sizeof(ctx_obj_ct_t) * page_sz);
if(num_unit_mem < 1) err(errno,"at least %fG memory needed to map ./onedist, specify more memory use -m",
(float)mco_dstat_readin.infile_num*sizeof(ctx_obj_ct_t) * page_sz/1073741824 );
int num_cof_batch = num_unit_mem*page_sz;
if( opt_val_in->shared_kmerpath[0] != '\0'){
dist_print_nobin(distout_dir,ref_seq_num, qry_seq_num, ref_ctx_ct_list, qry_ctx_ct_list,num_cof_batch,mcofname, cofname,opt_val_in);
return;
}
size_t unitsz_distf_mapped = (size_t)num_cof_batch * mco_dstat_readin.infile_num * sizeof(ctx_obj_ct_t) ;
int num_mapping_distf = co_dstat_readin.infile_num / num_cof_batch ;
size_t disf_sz = (size_t)mco_dstat_readin.infile_num*co_dstat_readin.infile_num*sizeof(ctx_obj_ct_t) ;
if(ftruncate(dist_bfp, disf_sz) == -1) err(errno,"mco_cbdco_nobin_dist()::ftruncate");
close(dist_bfp);
dist_bfp = open(onedist,O_RDWR, 0600);
if (dist_bfp == -1) err(errno,"mco_cbdco_nobin_dist()::%s",onedist);
ctx_obj_ct_t *ctx_obj_ct = mmap(NULL,disf_sz,PROT_READ | PROT_WRITE,MAP_SHARED,dist_bfp,0);
if(ctx_obj_ct == MAP_FAILED) err(errno,"ctx_obj_ct mmap error");
close(dist_bfp);
mmp_any_t* mco_offset_index_comps = malloc(sizeof( mmp_any_t) * mco_dstat_readin.comp_num);
mmp_any_t* mco_mem_comps = malloc(sizeof( mmp_any_t) * mco_dstat_readin.comp_num);
mmp_any_t* fco_pos_comps = malloc(sizeof( mmp_any_t) * mco_dstat_readin.comp_num);
mmp_any_t* cbd_fcode_mem_comps = malloc(sizeof( mmp_any_t) * mco_dstat_readin.comp_num);
for ( int j = 0; j < mco_dstat_readin.comp_num; j++ ) {
sprintf(mco_index_fcode,"%s/%s.%d",refmco_dname,mco_idx_prefix,j);
mco_offset_index_comps[j] = mmp_any(mco_index_fcode);
sprintf(mco_fcode,"%s/%s.%d",refmco_dname,mco_gids_prefix,j);
mco_mem_comps[j] = mmp_any(mco_fcode);
sprintf(co_cbd_index_fcode,"%s/%s.%d",qryco_dname,idx_prefix,j);
fco_pos_comps[j] = mmp_any(co_cbd_index_fcode);
sprintf(co_cbd_fcode,"%s/%s.%d",qryco_dname,skch_prefix,j);
cbd_fcode_mem_comps[j] = mmp_any(co_cbd_fcode);
}
for(int b=0;b<=num_mapping_distf;b++){
if(b==num_mapping_distf) bnum_infile = co_dstat_readin.infile_num % num_cof_batch ;
else bnum_infile = num_cof_batch;
if( bnum_infile == 0 ) continue;
maplength = (size_t)bnum_infile * mco_dstat_readin.infile_num * sizeof(ctx_obj_ct_t);
printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n",disf_sz,mco_dstat_readin.infile_num,co_dstat_readin.infile_num,num_mapping_distf,bnum_infile,maplength,(size_t)b*unitsz_distf_mapped);
for ( int j = 0; j < mco_dstat_readin.comp_num; j++ ) {
size_t *mco_offset_index= (size_t *) mco_offset_index_comps[j].mmp;
gidobj_t* mco_mem = (gidobj_t*) mco_mem_comps[j].mmp;
size_t *fco_pos = (size_t *)fco_pos_comps[j].mmp;
unsigned int *cbd_fcode_mem = (unsigned int *)cbd_fcode_mem_comps[j].mmp;
#pragma omp parallel for num_threads(p_fit_mem) schedule(guided)
for(int kind = 0; kind < bnum_infile; kind++){
int k = b*num_cof_batch + kind;
if(qry_ctx_ct_list[k]==0) continue;
size_t distf_offset = (size_t)k * mco_dstat_readin.infile_num;
for(size_t n = fco_pos[k]; n < fco_pos[k+1]; n++){
unsigned int ind = cbd_fcode_mem[n];
size_t s = ind > 0 ? mco_offset_index[ind-1] : 0 ;
for(size_t g = s; g < mco_offset_index[ind] ; g++)
ctx_obj_ct[distf_offset + mco_mem[g]]++ ;
}
}
}
if ( msync( ctx_obj_ct + (size_t)b*num_cof_batch*mco_dstat_readin.infile_num, maplength, MS_SYNC ) < 0 )
err(errno,"mco_cbdco_nobin_dist()::ctx_obj_ct msync failed");
munmap(ctx_obj_ct + (size_t)b*num_cof_batch*mco_dstat_readin.infile_num, maplength);
}
for ( int j = 0; j < mco_dstat_readin.comp_num; j++ ){
munmap(mco_offset_index_comps[j].mmp,mco_offset_index_comps[j].fsize);
munmap(mco_mem_comps[j].mmp,mco_mem_comps[j].fsize);
munmap(fco_pos_comps[j].mmp,fco_pos_comps[j].fsize);
munmap(cbd_fcode_mem_comps[j].mmp,cbd_fcode_mem_comps[j].fsize);
}
free(mco_offset_index_comps);
free( mco_mem_comps);
free( fco_pos_comps);
free (cbd_fcode_mem_comps);
dist_print_nobin(distout_dir,ref_seq_num, qry_seq_num, ref_ctx_ct_list, qry_ctx_ct_list,num_cof_batch,mcofname,cofname,opt_val_in);
free(mco_offset_index);
free(mco_mem);
free(ref_ctx_ct_list);
free(qry_ctx_ct_list);
free(mcofname);
free(cofname);
}
typedef struct koc_dist {
llong shared_koc_ct;
ctx_obj_ct_t shared_k_ct;
} koc_dist_t;
void mco_cbd_koc_compatible_dist(dist_opt_val_t *opt_val_in)
{
int p_fit_mem = opt_val_in->p;
llong mem_limit = (llong)opt_val_in->mmry*BBILLION;
char *refmco_dname = opt_val_in->refpath;
char *qryco_dname = opt_val_in->remaining_args[0];
const char *distout_dir = opt_val_in->outdir;
mkdir(distout_dir,0700);
FILE *refmco_dstat_fp, *qryco_dstat_fp;
char *refmco_dstat_fpath = malloc(PATHLEN*sizeof(char));
char *qryco_dstat_fpath = malloc(PATHLEN*sizeof(char));
sprintf(refmco_dstat_fpath,"%s/%s",refmco_dname,mco_dstat);
sprintf(qryco_dstat_fpath,"%s/%s",qryco_dname,co_dstat);
if( (refmco_dstat_fp = fopen(refmco_dstat_fpath,"rb")) == NULL )
err(errno,"need provied mco dir path for mco_co_dist() arg 1. refmco_dstat_fpath");
if( (qryco_dstat_fp = fopen(qryco_dstat_fpath,"rb")) == NULL )
err(errno,"need provied co dir path for mco_co_dist() arg 2. qryco_dstat_fpath");
mco_dstat_t mco_dstat_readin ;
co_dstat_t co_dstat_readin ;
fread(&mco_dstat_readin,sizeof(mco_dstat_readin),1,refmco_dstat_fp);
fread(&co_dstat_readin,sizeof(co_dstat_readin),1,qryco_dstat_fp);
ctx_obj_ct_t * qry_ctx_ct_list = malloc(co_dstat_readin.infile_num * sizeof(ctx_obj_ct_t));
ctx_obj_ct_t * ref_ctx_ct_list = malloc(mco_dstat_readin.infile_num * sizeof(ctx_obj_ct_t));
fread(qry_ctx_ct_list,sizeof(ctx_obj_ct_t),co_dstat_readin.infile_num,qryco_dstat_fp);
fread(ref_ctx_ct_list,sizeof(ctx_obj_ct_t),mco_dstat_readin.infile_num,refmco_dstat_fp);
char (*cofname)[PATHLEN] = malloc(co_dstat_readin.infile_num * PATHLEN);
char (*mcofname)[PATHLEN] = malloc(mco_dstat_readin.infile_num * PATHLEN);
fread(cofname,PATHLEN,co_dstat_readin.infile_num,qryco_dstat_fp);
fread(mcofname,PATHLEN,mco_dstat_readin.infile_num,refmco_dstat_fp);
fclose(refmco_dstat_fp);
fclose(qryco_dstat_fp);
if( !(mco_dstat_readin.comp_num == co_dstat_readin.comp_num) )
err(errno,"query args not match ref args: ref.comp_num = %d vs. %d = qry.comp_num",
mco_dstat_readin.comp_num, co_dstat_readin.comp_num);
if(!(mco_dstat_readin.shuf_id == co_dstat_readin.shuf_id))
err(errno,"query args not match ref args: ref.shuf_id = %d vs. %d = qry.shuf_id",
mco_dstat_readin.shuf_id, co_dstat_readin.shuf_id);
int ref_bin_num = mco_dstat_readin.infile_num / BIN_SZ;
if( mco_dstat_readin.infile_num % BIN_SZ > 0 ) ref_bin_num +=1;
char onedist[PATHLEN];
sprintf(onedist,"%s/sharedk_ct.dat",distout_dir);
int dist_bfp = open(onedist,O_RDWR,0600) ;
if (dist_bfp == -1) {
close(dist_bfp);
dist_bfp = open(onedist,O_RDWR|O_CREAT, 0600) ;
if (dist_bfp == -1) err(errno,"mco_cbd_co_dist()::%s",onedist);
}else err(EEXIST,"mco_cbd_koc_compatible_dist:%s",onedist);
int page_sz = sysconf(_SC_PAGESIZE);
size_t comp_sz = (1LLU << 4*COMPONENT_SZ);
if( comp_sz % page_sz != 0 ) err(errno,"comp_sz %d is not multiple of page_sz %d ",comp_sz,page_sz );
size_t maplength;
int bnum_infile;
FILE *cbd_fcode_comp_fp,*cbd_fcode_comp_index_fp;
struct stat cbd_fcode_stat;
size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1) );
size_t *mco_offset_index = malloc(sizeof(size_t) * comp_sz);
unsigned int *mco_bin_index = malloc( (size_t)comp_sz * sizeof(unsigned int) * ref_bin_num );
#define MCOMM_SZ 442317172
gidobj_t* mco_mem = malloc( sizeof(gidobj_t) * MCOMM_SZ );
char mco_fcode[PATHLEN]; char mco_index_fcode[PATHLEN];
char co_cbd_fcode[PATHLEN];char co_cbd_index_fcode[PATHLEN];
ref_seq_num = mco_dstat_readin.infile_num ;
qry_seq_num = co_dstat_readin.infile_num ;
kmerlen = co_dstat_readin.kmerlen;
dim_reduct_len = co_dstat_readin.dim_rd_len;
char distf[PATHLEN];
sprintf(distf, "%s/distance.out", distout_dir);
co_dstat_readin.koc = 0;
int num_unit_mem = mem_limit / (mco_dstat_readin.infile_num*sizeof(ctx_obj_ct_t) * page_sz);
if(num_unit_mem < 1) err(errno,"at least %fG memory needed to map ./onedist, specify more memory use -m",
(float)mco_dstat_readin.infile_num*sizeof(ctx_obj_ct_t) * page_sz/1073741824 );
int num_cof_batch = num_unit_mem*page_sz;
if( opt_val_in->shared_kmerpath[0] != '\0'){
dist_print_nobin(distout_dir,ref_seq_num, qry_seq_num, ref_ctx_ct_list, qry_ctx_ct_list,num_cof_batch,mcofname, cofname,opt_val_in);
return;
}
size_t unitsz_distf_mapped = (size_t)num_cof_batch * mco_dstat_readin.infile_num * sizeof(ctx_obj_ct_t) ;
int num_mapping_distf = co_dstat_readin.infile_num / num_cof_batch ;
size_t disf_sz = (size_t)mco_dstat_readin.infile_num*co_dstat_readin.infile_num*sizeof(ctx_obj_ct_t) ;
if(ftruncate(dist_bfp, disf_sz) == -1) err(errno,"mco_cbd_koc_compatible_dist()::ftruncate");
close(dist_bfp);
dist_bfp = open(onedist,O_RDWR, 0600);
if (dist_bfp == -1) err(errno,"mco_cbd_koc_compatible_dist()::%s",onedist);
ctx_obj_ct_t *ctx_obj_ct = mmap(NULL,disf_sz,PROT_READ | PROT_WRITE,MAP_SHARED,dist_bfp,0);
if(ctx_obj_ct == MAP_FAILED) err(errno,"ctx_obj_ct mmap error");
close(dist_bfp);
for(int b=0;b<=num_mapping_distf;b++){
if(b==num_mapping_distf){
bnum_infile = co_dstat_readin.infile_num % num_cof_batch ;
if( bnum_infile == 0 ) continue;
}else bnum_infile = num_cof_batch;
maplength = (size_t)bnum_infile * mco_dstat_readin.infile_num * sizeof(ctx_obj_ct_t);
printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n",
disf_sz,mco_dstat_readin.infile_num,co_dstat_readin.infile_num,num_mapping_distf,bnum_infile,maplength,(size_t)b*unitsz_distf_mapped);
for ( int j = 0; j < mco_dstat_readin.comp_num; j++ ) {
sprintf(mco_index_fcode,"%s/mco.index.%d",refmco_dname,j);
sprintf(mco_fcode,"%s/mco.%d",refmco_dname,j);
FILE *indexfp, *mcofp;
if( (indexfp = fopen(mco_index_fcode,"rb"))==NULL) err(errno,"mco_cbd_koc_compatible_dist()::%s",mco_index_fcode);
fread(mco_offset_index,sizeof(size_t),comp_sz,indexfp);
fread(mco_bin_index,sizeof(unsigned int),(size_t)comp_sz * ref_bin_num,indexfp);
fclose(indexfp);
struct stat s;
if( (mcofp = fopen(mco_fcode,"rb"))==NULL) err(errno,"mco_cbd_koc_compatible_dist()::%s",mco_fcode);
stat(mco_fcode, &s);
if(s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *)realloc(mco_mem, s.st_size );
fread(mco_mem,sizeof(gidobj_t),s.st_size/sizeof(gidobj_t),mcofp);
fclose(mcofp);
sprintf(co_cbd_fcode,"%s/combco.%d",qryco_dname,j);
if( (cbd_fcode_comp_fp = fopen(co_cbd_fcode,"rb"))==NULL) err(errno,"mco_cbd_koc_compatible_dis()::%s",co_cbd_fcode);
stat(co_cbd_fcode, &cbd_fcode_stat);
unsigned int *cbd_fcode_mem = malloc(cbd_fcode_stat.st_size);
fread(cbd_fcode_mem,sizeof(unsigned int),cbd_fcode_stat.st_size/sizeof(unsigned int),cbd_fcode_comp_fp);
fclose(cbd_fcode_comp_fp);
sprintf(co_cbd_index_fcode,"%s/combco.index.%d",qryco_dname,j);
if( (cbd_fcode_comp_index_fp = fopen(co_cbd_index_fcode,"rb"))==NULL)
err(errno,"mco_cbd_koc_compatible_dis()::%s",co_cbd_index_fcode);
fread(fco_pos,sizeof(size_t),co_dstat_readin.infile_num + 1, cbd_fcode_comp_index_fp);
fclose(cbd_fcode_comp_index_fp);
#pragma omp parallel for num_threads(p_fit_mem) schedule(guided)
for(int kind = 0; kind < bnum_infile; kind++){
int k = b*num_cof_batch + kind;
if(qry_ctx_ct_list[k]==0) continue;
size_t ind, mcogid,pos;
size_t distf_offset = (size_t)k * mco_dstat_readin.infile_num;
for(size_t n = 0; n < fco_pos[k+1] - fco_pos[k]; n++){
ind = cbd_fcode_mem[ fco_pos[k] + n ];
pos = 0;
for(int bin=0; bin < ref_bin_num; bin++){
int bin_gnum = mco_bin_index[ (size_t)ind *ref_bin_num + bin ];
for(int g = 0; g < bin_gnum ; g++ ){
mcogid = bin*BIN_SZ + mco_mem[ (size_t)mco_offset_index[ind] + pos ];
ctx_obj_ct[distf_offset + mcogid]++ ;
pos++;
}
}
}
}
free(cbd_fcode_mem);
}
if ( msync( ctx_obj_ct + (size_t)b*num_cof_batch*mco_dstat_readin.infile_num, maplength, MS_SYNC ) < 0 )
err(errno,"mco_cbd_co_dist()::ctx_obj_ct msync failed");
munmap(ctx_obj_ct + (size_t)b*num_cof_batch*mco_dstat_readin.infile_num, maplength);
}
free(fco_pos);
dist_print_nobin(distout_dir,ref_seq_num, qry_seq_num, ref_ctx_ct_list, qry_ctx_ct_list,num_cof_batch,mcofname, cofname,opt_val_in);
free(mco_offset_index);
free(mco_bin_index);
free(mco_mem);
free(ref_ctx_ct_list);
free(qry_ctx_ct_list);
free(mcofname);
free(cofname);
}
static inline ctx_obj_ct_t * mco_co_mmpdist_core(gidobj_t** unit_arrmco, char *co_fcode_in, ctx_obj_ct_t * ctx_obj_ct_in )
{
mmp_uint_t mmpcofile;
mmpcofile = mmp_uint_arr(co_fcode_in);
unsigned int ind,mcogid;
int ctx_num = mmpcofile.fsize/sizeof(unsigned int);
for(int n = 0; n < ctx_num; n++){
ind = mmpcofile.mmpco[n];
if(unit_arrmco[ind] != NULL){
for(unsigned int k = 1; k< unit_arrmco[ind][0] + 1; k++ ){
mcogid = unit_arrmco[ind][k] ;
ctx_obj_ct_in[mcogid]++ ;
}
}
}
munmap(mmpcofile.mmpco, mmpcofile.fsize);
return ctx_obj_ct_in;
}
static inline void mco_co_dist_core(gidobj_t** unit_arrmco, char *co_fcode_in, int bin_sz,
mco_co_dist_t shared_ctx_num_in )
{
mmp_uint_t mmpcofile;
mmpcofile = mmp_uint_arr(co_fcode_in);
memset(shared_ctx_num_in,0, bin_sz);
unsigned int ind,mcogid;
int ctx_num = mmpcofile.fsize/sizeof(unsigned int);
for(int n = 0; n < ctx_num; n++){
ind = mmpcofile.mmpco[n] ;
if(unit_arrmco[ind] != NULL){
for(int k = 1; k< unit_arrmco[ind][0] + 1; k++ ){
mcogid = unit_arrmco[ind][k];
shared_ctx_num_in[mcogid]++ ;
}
}