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DBstats.c
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DBstats.c
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/*******************************************************************************************
*
* Display statistics about the contents of a .db and a histogram of its read lengths.
*
* Author: Gene Myers
* Date : July 2013
* Mod : April 2014
*
********************************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include "DB.h"
static char *Usage = " [-a] [-x<int>] [-b<int(1000)>] <name:db>";
int main(int argc, char *argv[])
{ HITS_DB db;
HITS_READ *reads;
int ALL;
int CUTOFF;
int BIN;
{ int i, j, k;
int flags[128];
char *eptr;
ARG_INIT("DBstats")
CUTOFF = 0;
BIN = 1000;
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("a")
break;
case 'x':
ARG_NON_NEGATIVE(CUTOFF,"Min read length cutoff")
break;
case 'b':
ARG_POSITIVE(BIN,"Bin size")
break;
}
else
argv[j++] = argv[i];
argc = j;
ALL = flags['a'];
if (argc != 2)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
exit (1);
}
}
if (Open_DB(argv[1],&db))
exit (1);
reads = db.reads;
{ int nbin, *hist;
int64 totlen, *bsum;
int nreads;
int i;
nbin = (db.maxlen-1)/BIN + 1;
hist = (int *) Malloc(sizeof(int)*nbin,"Allocating histograms");
bsum = (int64 *) Malloc(sizeof(int64)*nbin,"Allocating histograms");
if (hist == NULL || bsum == NULL)
exit (1);
for (i = 0; i < nbin; i++)
{ hist[i] = 0;
bsum[i] = 0;
}
{ int64 ave, dev;
if ( ! ALL)
{ for (i = 0; i < db.nreads; i++)
if ((reads[i].flags & DB_BEST) == 0)
{ reads[i].beg = 1;
reads[i].end = 0;
}
}
totlen = 0;
nreads = 0;
for (i = 0; i < db.nreads; i++)
{ int rlen = ((int) reads[i].end) - reads[i].beg;
if (rlen >= CUTOFF)
{ totlen += rlen;
nreads += 1;
hist[rlen/BIN] += 1;
bsum[rlen/BIN] += rlen;
}
}
ave = totlen/nreads;
dev = 0;
for (i = 0; i < db.nreads; i++)
{ int rlen = ((int) reads[i].end) - reads[i].beg;
if (rlen >= CUTOFF)
dev += (rlen-ave)*(rlen-ave);
}
dev = sqrt(dev/nreads);
if (CUTOFF == 0 && ALL)
{ printf("\nStatistics over all reads in the data set\n\n");
Print_Number((int64) nreads,15,stdout);
printf(" reads\n");
Print_Number(totlen,15,stdout);
printf(" base pairs\n");
}
else
{ if (ALL)
printf("\nStatistics for all reads");
else
printf("\nStatistics for all wells");
if (CUTOFF > 0)
{ printf(" of length ");
Print_Number(CUTOFF,0,stdout);
printf(" bases or more\n\n");
}
else
printf(" in the data set\n\n");
Print_Number((int64) nreads,15,stdout);
printf(" reads out of ");
Print_Number((int64 ) db.nreads,15,stdout);
printf(" %5.1f%% loss\n",100.-(100.*nreads)/db.nreads);
Print_Number(totlen,15,stdout);
printf(" base pairs out of ");
Print_Number(db.totlen,15,stdout);
printf(" %5.1f%% loss\n",100.-(100.*totlen)/db.totlen);
}
printf("\nBase composition: %.3f(A) %.3f(C) %.3f(G) %.3f(T)\n\n",
db.freq[0],db.freq[1],db.freq[2],db.freq[3]);
Print_Number(ave,15,stdout);
printf(" average read length\n");
Print_Number(dev,15,stdout);
printf(" standard deviation\n");
}
{ int64 btot;
int cum;
printf("\nDistribution of Read Lengths (Bin size = ");
Print_Number((int64) BIN,0,stdout);
printf(")\n\n Bin: Count %% Reads %% Bases Average\n");
cum = 0;
btot = 0;
for (i = nbin-1; i >= 0; i--)
{ cum += hist[i];
btot += bsum[i];
Print_Number((int64) (i*BIN),7,stdout);
printf(":");
Print_Number((int64) hist[i],11,stdout);
printf(" %5.1f %5.1f %5lld\n",(100.*cum)/nreads,(100.*btot)/totlen,btot/cum);
if (cum == nreads) break;
}
printf("\n");
}
}
{ HITS_TRACK *dust;
dust = Load_Track(&db,"dust");
if (dust == NULL && db.part > 0)
{ db.oreads = db.nreads;
db.ofirst = 0;
dust = Load_Track(&db,Numbered_Suffix("",db.part,".dust"));
}
if (dust != NULL)
{ void *data = dust->data;
int *anno = (int *) dust->anno;
int i, rlen;
int *idata, *edata;
int64 numint, totlen;
totlen = 0;
numint = 0;
for (i = 0; i < db.nreads; i++)
{ rlen = reads[i].end - reads[i].beg;
if (rlen >= CUTOFF)
{ edata = (int *) (data + anno[i+1]);
for (idata = (int *) (data + anno[i]); idata < edata; idata += 2)
{ numint += 1;
totlen += (idata[1] - *idata) + 1;
}
}
}
Print_Number(numint,0,stdout);
printf(" low-complexity intervals totaling ");
Print_Number(totlen,0,stdout);
printf(" bases\n\n");
}
Close_Track(&db,"dust");
}
Close_DB(&db);
exit (0);
}