command_dist.h

//	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.
   
#ifndef COMMAND_DIST
#define COMMAND_DIST 
#include "global_basic.h"
#include "command_dist_wrapper.h"
#include "command_shuffle.h"
#include <string.h>
#define DISM_MEM_PCT 0.25
#define CO_MEM_PCT 0.125
extern const char co_dstat[];
typedef struct mem_dispatch
{
  bool has_ref;
  bool has_arg;
  bool dm_inmem;
  bool keep_coindisk;
  bool keep_mcoinmem;
  bool alphabet_group;
  bool multiple_composition;
  enum{
    OBJ_COMPATIBLE = 4096,
    OBJ_TRADITION = 16384,
    OBJ_GROUP = 65536,
  } enum_bin_sz ;
  enum{
     SLIM,
     STD,
     ALL,
  } gbin ;
  enum {
    MAKE_REF,
    REF_QRY,
    DIST,
  } usage_mode;
  bool mco_info;
} mem_dispatch_t ;
typedef struct mem_usage_stat
{
  llong shuffled_subctx_arr_sz;
  llong input_file_name_sz;
  llong others;
} mem_usage_stat_t;
typedef long long int llint;
typedef struct mco_dirstat
{
 unsigned int shuf_id;
 int kmerlen;
 int dim_rd_len;
  int comp_num;
  int infile_num;
} mco_dstat_t;
typedef struct output
{
 int X_size;
 int Y_size;
 int XnY_size;
 double metric;
 double dist;
  double CI95_mtrc_1;
 double CI95_mtrc_2;
 double CI95_dist_1;
 double CI95_dist_2;
 double pv;
} output_t;
typedef struct print_ctrl
{
 MTRIC metric;
 PFIELD pfield;
 bool correction;
 double dthreshold ;
  unsigned int Y_size;
  llong cmprsn_num;
  char *qname ;
 int qry_len;
} print_ctrl_t;
extern dim_shuffle_t* dim_shuffle;
extern unsigned int hashsize;
extern int component_num;
int dist_dispatch(struct dist_opt_val* opt_val);
infile_tab_t* dist_organize_infiles (dist_opt_val_t *opt_val);
infile_tab_t* dist_organize_refpath (dist_opt_val_t *opt_val);
dim_shuffle_t *get_dim_shuffle( dist_opt_val_t *opt_val_in );
int get_hashsz(dim_shuffle_t *dim_shuffle_in );
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);
void run_stageII(const char * co_dstat_fpath, const char* dist_mco_dir, int p_fit_mem);
void mco_cbdco_nobin_dist(dist_opt_val_t *opt_val_in);
void mco_co_dist( char *refmco_dname, char *qryco_dname, const char *distout_dir, int p_fit_mem);
void mco_cbd_co_dist(dist_opt_val_t *opt_val_in);
void mco_cbd_koc_compatible_dist (dist_opt_val_t *opt_val_in);
void dist_print( const char *distf, FILE *dist_fp );
void fname_dist_print(int ref_bin_code, int qry_fcode, const char *distout_dir, unsigned int*ref_ctx_ct_list,
      unsigned int*qry_ctx_ct_list, char (*refname)[PATHLEN], char (*qryfname)[PATHLEN], FILE *dout_fp);
void dist_print_nobin ( const char *distout_dir,unsigned int ref_num, unsigned int qry_num, unsigned int*ref_ctx_ct_list,
      unsigned int*qry_ctx_ct_list, int num_cof_batch, char (*refname)[PATHLEN], char (*qryfname)[PATHLEN],dist_opt_val_t *opt_val);
void koc_dist_print_nobin ( const char *distout_dir,unsigned int ref_num, unsigned int qry_num, unsigned int*ref_ctx_ct_list,
      unsigned int*qry_ctx_ct_list, int num_cof_batch, char (*refname)[PATHLEN], char (*qryfname)[PATHLEN]);
const char * combine_queries(dist_opt_val_t *opt_val);
#endif