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/*******************************************************************************************
*
* Split a .db into a set of sub-database blocks for use by the Dazzler:
* Divide the database <path>.db conceptually into a series of blocks referable to on the
* command line as <path>.1.db, <path>.2.db, ... If the -x option is set then all reads
* less than the given length are ignored, and if the -a option is not set then secondary
* reads from a given well are also ignored. The remaining reads are split amongst the
* blocks so that each block is of size -s * 1Mbp except for the last which necessarily
* contains a smaller residual. The default value for -s is 400Mbp because blocks of this
* size can be compared by our "overlapper" dalign in roughly 16Gb of memory. The blocks
* are very space efficient in that their sub-index of the master .idx is computed on the
* fly when loaded, and the .bps file of base pairs is shared with the master DB. Any
* tracks associated with the DB are also computed on the fly when loading a database block.
*
* Author: Gene Myers
* Date : September 2013
* Mod : New splitting definition to support incrementality, and new stub file format
* Date : April 2014
*
********************************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <errno.h>
#include "DB.h"
#ifdef HIDE_FILES
#define PATHSEP "/."
#else
#define PATHSEP "/"
#endif
static char *Usage = "<path:db>";
int main(int argc, char *argv[])
{ DAZZ_DB db;
int status;
Prog_Name = Strdup("DBwipe","Allocating Program Name");
if (argc != 2)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
exit (1);
}
// Open db
status = Open_DB(argv[1],&db);
if (status < 0)
exit (1);
if (db.part > 0)
{ fprintf(stderr,"%s: Cannot be called on a block: %s\n",Prog_Name,argv[1]);
exit (1);
}
if (status)
{ fprintf(stderr,"%s: Cannot be called on a .dam: %s\n",Prog_Name,argv[1]);
exit (1);
}
{ char *pwd, *root;
FILE *index;
char *index_name;
int i;
pwd = PathTo(argv[1]);
root = Root(argv[1],".db");
if (unlink(Catenate(pwd,PATHSEP,root,".arw")) < 0)
{ if (errno != ENOENT)
{ fprintf(stderr,"%s: [WARNING] Could not delete %s.arw\n",Prog_Name,root);
exit (1);
}
}
if (unlink(Catenate(pwd,PATHSEP,root,".qvs")) < 0)
{ if (errno != ENOENT)
{ fprintf(stderr,"%s: [WARNING] Could not delete %s.qvs\n",Prog_Name,root);
exit (1);
}
}
for (i = 0; i < db.nreads; i++)
db.reads[i].coff = -1;
db.allarr &= ~DB_ARROW;
index_name = Strdup(Catenate(pwd,PATHSEP,root,".idx"),"Allocating index file name");
index = Fopen(index_name,"w");
if (index_name == NULL || index == NULL)
exit (1);
FFWRITE(&db,sizeof(DAZZ_DB),1,index)
FFWRITE(db.reads,sizeof(DAZZ_READ),db.nreads,index)
FCLOSE(index);
}
Close_DB(&db);
exit (0);
}
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