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/*******************************************************************************************
*
* Read the .covr track of each db or db block on the command line and output a histogram
* of the coverage of the unmasked portions and an estimate of the coverage of the
* underlying genome
*
* Author: Gene Myers
* Date : January 2017
*
*******************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdint.h>
#include <math.h>
#include "DB.h"
// Command format and global parameter variables
static char *Usage = "<source:db> ...";
int main(int argc, char *argv[])
{ int c;
// Process arguments
Prog_Name = Strdup("REPcover","");
if (argc < 2)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
exit (1);
}
// Open trimmed DB and the qual-track
for (c = 1; c < argc; c++)
{ DAZZ_DB _DB, *DB = &_DB;
DAZZ_EXTRA ex_hgap, ex_covr;
// Load DB
{ int status;
status = Open_DB(argv[c],DB);
if (status < 0)
exit (1);
if (status == 1)
{ fprintf(stderr,"%s: Cannot be called on a .dam index: %s\n",Prog_Name,argv[1]);
exit (1);
}
Trim_DB(DB);
}
// Get .covr track extras
{ FILE *afile;
char *aname;
int extra;
afile = NULL;
if (DB->part)
{ aname = Strdup(Catenate(DB->path,Numbered_Suffix(".",DB->part,"."),"covr",".anno"),
"Allocating anno file");
if (aname == NULL)
exit (1);
afile = fopen(aname,"r");
if (afile == NULL)
{ fprintf(stderr,"%s: Must have a 'covr.%d' track, run DAScover\n",Prog_Name,DB->part);
exit (1);
}
}
else
{ aname = Strdup(Catenate(DB->path,".","covr",".anno"),"Allocating anno file");
if (aname == NULL)
exit (1);
afile = fopen(aname,"r");
if (afile == NULL)
{ fprintf(stderr,"%s: Must have a 'covr' track, run DAScover\n",Prog_Name);
exit (1);
}
}
fseeko(afile,0,SEEK_END);
extra = ftell(afile) - sizeof(int)*2;
fseeko(afile,-extra,SEEK_END);
ex_covr.nelem = 0;
if (Read_Extra(afile,aname,&ex_covr) != 0)
{ fprintf(stderr,"%s: Histogram extra missing from .covr track?\n",Prog_Name);
exit (1);
}
ex_hgap.nelem = 0;
if (Read_Extra(afile,aname,&ex_hgap) != 0)
{ fprintf(stderr,"%s: Hgap threshold extra missing from .covr track?\n",Prog_Name);
exit (1);
}
fclose(afile);
}
// Generate display
{ char *root;
int i, cmax, hgap_min, cover;
int64 nreads, totlen;
int64 *cgram;
int64 ssum, stotal;
root = Root(argv[c],".db");
nreads = DB->nreads;
totlen = DB->totlen;
hgap_min = (int) ((int64 *) (ex_hgap.value))[0];
cgram = (int64 *) (ex_covr.value);
cmax = ex_covr.nelem - 1;
printf("\nDAScover");
if (hgap_min > 0)
printf(" -H%d",hgap_min);
printf(" %s\n\n",root);
if (hgap_min > 0)
{ for (i = 0; i < DB->nreads; i++)
if (DB->reads[i].rlen < hgap_min)
{ nreads -= 1;
totlen -= DB->reads[i].rlen;
}
}
// Display histogram
printf("\nInput: ");
Print_Number(nreads,7,stdout);
printf("reads, ");
Print_Number(totlen,12,stdout);
printf(" bases");
if (hgap_min > 0)
{ printf(" (another ");
Print_Number(DB->nreads-nreads,0,stdout);
printf(" were < H-length)");
}
printf("\n");
stotal = 0;
for (i = 0; i <= cmax; i++)
stotal += cgram[i];
printf("\nCoverage Histogram\n\n");
ssum = cgram[cmax];
if (ssum > 0)
printf(" %4d: %9lld %5.1f%%\n\n",
cmax,cgram[cmax],(100.*ssum)/stotal);
stotal -= ssum;
ssum = 0;
for (i = cmax-1; i >= 0; i--)
if (cgram[i] > 0)
{ ssum += cgram[i];
printf(" %4d: %9lld %5.1f%%\n",
i,cgram[i],(100.*ssum)/stotal);
}
i = 0;
while (cgram[i+1] < cgram[i])
i += 1;
for (cover = i++; i < cmax; i++)
if (cgram[cover] < cgram[i])
cover = i;
printf("\n Coverage is estimated at %d\n\n",cover);
free(root);
Close_DB(DB);
}
}
free(Prog_Name);
exit (0);
}
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