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|
/*********************************************************************************************\
*
* Produce a script to compute overlaps for all block pairs between two DBs, and then sort
* and merge * them into as many .las files as their are blocks of the 1st DB.
*
* Author: Gene Myers
* Date : December 31, 2014
*
*********************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <ctype.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "DB.h"
#undef LSF // define if want a directly executable LSF script
#undef SLURM // define if want a directly executable SLURM script
static char *Usage[] =
{ "[-vpzCN] [-k<int(20)>] [-t<int>] [-M<int>] [-e<double(.85)] [-s<int(100)]",
" [-n<double(1.)] [-m<track>]+ [-B<int( 4)>] [-T<int(4)>] [-f<name>]",
" <ref:db|dam> <reads:db|dam> [<first:int>[-<last:int>]]"
};
#ifdef LSF
#define HPC
#define HPC_ALIGN "bsub -q medium -n 4 -o DAMAPPER.out -e DAMAPPER.err -R span[hosts=1] -J map#%d"
#endif
#ifdef SLURM
#define HPC
#define HPC_ALIGN \
"srun -p batch -n 1 -c %d --mem_per_cpu=%d -o DALIGNER.out -e DALIGNER.err -J map#%d"
#endif
int main(int argc, char *argv[])
{ int nblocks2;
int useblock2;
int usepath1, usepath2;
int fblock, lblock;
#ifdef HPC
int jobid;
#endif
FILE *out;
char name[100];
char *pwd1, *root1;
char *pwd2, *root2;
int FORWARD, REVERSE;
int BUNIT;
int VON, PON, CON, NON, ZON;
int TINT, KINT, SINT, MINT;
int NTHREADS;
double EREL, NEIGHBOR;
int MMAX, MTOP;
char **MASK;
char *ONAME;
{ int i, j, k; // Process options
int flags[128];
char *eptr;
ARG_INIT("HPC.damapper")
BUNIT = 4;
KINT = 20;
TINT = 0;
EREL = 0.;
SINT = 100;
MINT = -1;
NEIGHBOR = 1.;
NTHREADS = 4;
MTOP = 0;
MMAX = 10;
MASK = (char **) Malloc(MMAX*sizeof(char *),"Allocating mask track array");
if (MASK == NULL)
exit (1);
ONAME = NULL;
out = stdout;
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("vbpzCN");
break;
case 'e':
ARG_REAL(EREL)
if (EREL < .7 || EREL >= 1.)
{ fprintf(stderr,"%s: Average correlation must be in [.7,1.) (%g)\n",Prog_Name,EREL);
exit (1);
}
break;
case 'k':
ARG_POSITIVE(KINT,"K-mer length")
break;
case 'm':
if (MTOP >= MMAX)
{ MMAX = 1.2*MTOP + 10;
MASK = (char **) Realloc(MASK,MMAX*sizeof(char *),"Reallocating mask track array");
if (MASK == NULL)
exit (1);
}
MASK[MTOP++] = argv[i]+2;
break;
case 'n':
ARG_REAL(NEIGHBOR)
if (NEIGHBOR < .7 || NEIGHBOR > 1.)
{ fprintf(stderr,"%s: Near optimal threshold must be in [.7,1.] (%g)\n",
Prog_Name,NEIGHBOR);
exit (1);
}
break;
case 's':
ARG_POSITIVE(SINT,"Trace spacing")
break;
case 't':
ARG_POSITIVE(TINT,"Tuple suppression frequency")
break;
case 'B':
ARG_NON_NEGATIVE(BUNIT,"Blocks per command")
break;
case 'f':
ONAME = argv[i]+2;
break;
case 'M':
ARG_NON_NEGATIVE(MINT,"Memory allocation (in Gb)")
break;
case 'T':
ARG_POSITIVE(NTHREADS,"Number of threads")
break;
}
else
argv[j++] = argv[i];
argc = j;
VON = flags['v'];
PON = flags['p'];
ZON = flags['z'];
CON = flags['C'];
NON = flags['N'];
if (argc < 3 || argc > 4)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage[0]);
fprintf(stderr," %*s %s\n",(int) strlen(Prog_Name),"",Usage[1]);
fprintf(stderr," %*s %s\n",(int) strlen(Prog_Name),"",Usage[2]);
fprintf(stderr,"\n");
fprintf(stderr," Passed through to damapper.\n");
fprintf(stderr," -k: k-mer size (must be <= 32).\n");
fprintf(stderr," -t: Ignore k-mers that occur >= -t times in a block.\n");
fprintf(stderr," -M: Use only -M GB of memory by ignoring most frequent k-mers.\n");
fprintf(stderr,"\n");
fprintf(stderr," -e: Look for alignments with -e percent similarity.\n");
fprintf(stderr," -s: Use -s as the trace point spacing for encoding alignments.\n");
fprintf(stderr," -n: Output all matches within this %% of the best\n");
fprintf(stderr,"\n");
fprintf(stderr," -T: Use -T threads.\n");
fprintf(stderr," -P: Do sorts and merges in directory -P.\n");
fprintf(stderr," -m: Soft mask the blocks with the specified mask.\n");
fprintf(stderr," -b: For AT/GC biased data, compensate k-mer counts (deprecated).\n");
fprintf(stderr,"\n");
fprintf(stderr," -z: sort .las by A,B-read pairs (overlap piles)\n");
fprintf(stderr," off => sort .las by A-read,A-position pairs");
fprintf(stderr," (default for mapping)\n");
fprintf(stderr," -p: Output repeat profile track\n");
fprintf(stderr," -C: Output reference vs reads .las.\n");
fprintf(stderr," -N: Do not output reads vs reference .las.\n");
fprintf(stderr,"\n");
fprintf(stderr," Script control.\n");
fprintf(stderr," -v: Verbose mode, output statistics as proceed.\n");
fprintf(stderr," -B: # of block compares per daligner job\n");
fprintf(stderr," -f: Place script bundles in separate files with prefix <name>\n");
exit (1);
}
if (CON)
if (NON)
{ FORWARD = 0;
REVERSE = 1;
}
else
{ FORWARD = 1;
REVERSE = 1;
}
else
if (NON)
{ fprintf(stderr,"%s: Cannot specify both C and N flags together\n",Prog_Name);
exit (1);
}
else
{ FORWARD = 1;
REVERSE = 0;
}
for (j = 1; 2*j <= NTHREADS; j *= 2)
;
NTHREADS = j;
}
// Make sure DAM and DB exist and the DB is partitioned, get number of blocks in partition
pwd1 = PathTo(argv[1]);
if (strcmp(argv[1]+(strlen(argv[1])-4),".dam") == 0)
root1 = Root(argv[1],".dam");
else
root1 = Root(argv[1],".db");
{ int i, nfiles;
FILE *dbvis;
dbvis = fopen(Catenate(pwd1,"/",root1,".dam"),"r");
if (dbvis == NULL)
{ dbvis = Fopen(Catenate(pwd1,"/",root1,".db"),"r");
if (dbvis == NULL)
exit (1);
}
if (fscanf(dbvis,"files = %d\n",&nfiles) != 1)
SYSTEM_READ_ERROR
for (i = 0; i < nfiles; i++)
{ char buffer[30001];
if (fgets(buffer,30000,dbvis) == NULL)
SYSTEM_READ_ERROR
}
usepath1 = (strcmp(pwd1,".") != 0);
fclose(dbvis);
}
pwd2 = PathTo(argv[2]);
if (strcmp(argv[2]+(strlen(argv[2])-4),".dam") == 0)
root2 = Root(argv[2],".dam");
else
root2 = Root(argv[2],".db");
if (strcmp(root2,root1) == 0 && strcmp(pwd1,pwd2) == 0)
{ fprintf(stderr,"%s: Comparing the same data base %s/%s against itself, use HPCdaligner\n",
Prog_Name,pwd1,root1);
exit (1);
}
{ int i, nfiles;
FILE *dbvis;
dbvis = fopen(Catenate(pwd2,"/",root2,".dam"),"r");
if (dbvis == NULL)
{ dbvis = Fopen(Catenate(pwd2,"/",root2,".db"),"r");
if (dbvis == NULL)
exit (1);
}
if (fscanf(dbvis,"files = %d\n",&nfiles) != 1)
SYSTEM_READ_ERROR
for (i = 0; i < nfiles; i++)
{ char buffer[30001];
if (fgets(buffer,30000,dbvis) == NULL)
SYSTEM_READ_ERROR
}
useblock2 = 1;
if (fscanf(dbvis,"blocks = %d\n",&nblocks2) != 1 || nblocks2 == 1)
{ useblock2 = 0;
nblocks2 = 1;
}
usepath2 = (strcmp(pwd2,".") != 0);
fclose(dbvis);
}
// Set range fblock-lblock checking that DB.<fblock-1>.las exists & DB.<fblock>.las does not
{ char *eptr, *fptr, *src2;
FILE *file;
if (argc == 4)
{ fblock = strtol(argv[3],&eptr,10);
if ((*eptr != '\0' && *eptr != '-') || eptr <= argv[3])
{ fprintf(stderr,"%s: final argument '%s' does not start with an integer\n",
Prog_Name,argv[3]);
exit (1);
}
useblock2 = 1;
if (*eptr == '-')
{ lblock = strtol(eptr+1,&fptr,10);
if (*fptr != '\0' || fptr <= eptr+1)
{ fprintf(stderr,"%s: second part of range '%s' is not an integer\n",
Prog_Name,eptr+1);
exit (1);
}
}
else
lblock = fblock;
if (fblock < 1 || lblock > nblocks2 || fblock > lblock)
{ fprintf(stderr,"%s: range %d-%d is empty or out of bounds\n",Prog_Name,fblock,lblock);
exit (1);
}
}
else
{ fblock = 1;
lblock = nblocks2;
}
if (usepath2)
src2 = Strdup(Catenate(pwd2,"/",root2,""),"Allocating small string!");
else
src2 = Strdup(root2,"Allocating small string!");
if (src2 == NULL)
exit (1);
if (fblock > 1)
{ file = fopen(Catenate(src2,Numbered_Suffix(".",fblock-1,"."),root1,".las"),"r");
if (file == NULL)
{ fprintf(stderr,"%s: File %s.%d.%s.las should already be present!\n",
Prog_Name,src2,fblock-1,root1);
exit (1);
}
else
fclose(file);
}
if (useblock2)
{ file = fopen(Catenate(src2,Numbered_Suffix(".",fblock,"."),root1,".las"),"r");
if (file != NULL)
{ fprintf(stderr,"%s: File %s.%d.%s.las should not yet exist!\n",
Prog_Name,src2,fblock,root1);
exit (1);
}
}
else
{ file = fopen(Catenate(src2,".",root1,".las"),"r");
if (file != NULL)
{ fprintf(stderr,"%s: File %s.%s.las should not yet exist!\n",
Prog_Name,src2,root1);
exit (1);
}
}
free(src2);
}
{ int njobs;
int j, k;
// Produce all necessary daligner jobs ...
if (ONAME != NULL)
{ sprintf(name,"%s.01.OVL",ONAME);
out = fopen(name,"w");
}
njobs = (lblock-fblock)/BUNIT + 1;
fprintf(out,"# Damapper jobs (%d)\n",njobs);
#ifdef HPC
jobid = 1;
#endif
{ int bits;
int low, hgh;
bits = (lblock-fblock)/BUNIT+1;
low = fblock;
for (j = 1; j <= bits; j++)
{
#ifdef LSM
fprintf(out,HPC_ALIGN,jobid++);
fprintf(out," \"");
#endif
#ifdef SLURM
if (MINT >= 0)
fprintf(out,HPC_ALIGN,NTHREADS,(MINT*1024)/NTHREADS,jobid++);
else
fprintf(out,HPC_ALIGN,NTHREADS,(16*1024)/NTHREADS,jobid++);
fprintf(out," \"");
#endif
fprintf(out,"damapper");
if (VON)
fprintf(out," -v");
if (PON)
fprintf(out," -p");
if (ZON)
fprintf(out," -z");
if (CON)
fprintf(out," -C");
if (NON)
fprintf(out," -N");
if (KINT != 20)
fprintf(out," -k%d",KINT);
if (TINT > 0)
fprintf(out," -t%d",TINT);
if (EREL > 0.)
fprintf(out," -e%g",EREL);
if (SINT != 100)
fprintf(out," -s%d",SINT);
if (NEIGHBOR > 0.)
fprintf(out," -n%g",NEIGHBOR);
if (MINT >= 0)
fprintf(out," -M%d",MINT);
if (NTHREADS != 4)
fprintf(out," -T%d",NTHREADS);
for (k = 0; k < MTOP; k++)
fprintf(out," -m%s",MASK[k]);
if (usepath1)
fprintf(out," %s/%s",pwd1,root1);
else
fprintf(out," %s",root1);
hgh = fblock + (((lblock-fblock)+1)*j)/bits;
for (k = low; k < hgh; k++)
if (useblock2)
if (usepath2)
fprintf(out," %s/%s.%d",pwd2,root2,k);
else
fprintf(out," %s.%d",root2,k);
else
if (usepath2)
fprintf(out," %s/%s",pwd2,root2);
else
fprintf(out," %s",root2);
#ifdef HPC
fprintf(out,"\"");
#endif
fprintf(out,"\n");
low = hgh;
}
}
// Check .las (optional)
if (ONAME != NULL)
{ fclose(out);
sprintf(name,"%s.02.CHECK.OPT",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Check all .las files (optional but recommended)\n");
if (FORWARD)
{ fprintf(out,"LAcheck -v%sS",ZON?"":"a");
if (usepath2)
fprintf(out," %s/%s",pwd2,root2);
else
fprintf(out," %s",root2);
if (usepath1)
fprintf(out," %s/%s",pwd1,root1);
else
fprintf(out," %s",root1);
if (usepath2)
if (useblock2)
fprintf(out," %s/%s.%c%d-%d.%s",pwd2,root2,BLOCK_SYMBOL,fblock,lblock,root1);
else
fprintf(out," %s/%s.%s",pwd2,root2,root1);
else
if (useblock2)
fprintf(out," %s.%c%d-%d.%s",root2,BLOCK_SYMBOL,fblock,lblock,root1);
else
fprintf(out," %s.%s",root2,root1);
fprintf(out,"\n");
}
if (REVERSE)
{ fprintf(out,"LAcheck -v%sS",ZON?"":"a");
if (usepath1)
fprintf(out," %s/%s",pwd1,root1);
else
fprintf(out," %s",root1);
if (usepath2)
fprintf(out," %s/%s",pwd2,root2);
else
fprintf(out," %s",root2);
if (usepath2)
if (useblock2)
fprintf(out," %s/%s.%s.%c%d-%d",pwd2,root1,root2,BLOCK_SYMBOL,fblock,lblock);
else
fprintf(out," %s/%s.%s",pwd2,root1,root2);
else
if (useblock2)
fprintf(out," %s.%s.%c%d-%d",root1,root2,BLOCK_SYMBOL,fblock,lblock);
else
fprintf(out," %s.%s",root1,root2);
fprintf(out,"\n");
}
if (ONAME != NULL)
fclose(out);
}
free(root2);
free(pwd2);
free(root1);
free(pwd1);
exit (0);
}
|
