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HPC.daligner.c
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HPC.daligner.c
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/*********************************************************************************************\
*
* Produce a script to compute overlaps for all block pairs of a DB, and then sort and merge
* them into as many .las files as their are blocks.
*
* Author: Gene Myers
* Date : June 1, 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 <dirent.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[] =
{ "[-vad] [-l<int(1500)>] [-s<int(100)] [-t<int>] [-M<int>]",
" [-P<dir(/tmp)>] [-B<int(4)>] [-T<int(4)>] [-f<name>]",
" ( [-k<int(16)>] [-h<int(50)>] [-w<int(6)>] [-e<double(.75)>] [-H<int>]",
" [-k<int(20)>] [-h<int(50)>] [-w<int(6)>] [-e<double(.85)>] <ref:db|dam> )",
" [-m<track>]+ <reads:db|dam> [<first:int>[-<last:int>]]"
};
// Command Options
static int BUNIT;
static int VON, CON, DON;
static int WINT, TINT, HGAP, HINT, KINT, SINT, LINT, MINT;
static int NTHREADS;
static double EREL;
static int MMAX, MTOP;
static char **MASK;
static char *ONAME;
static char *PDIR;
#ifdef LSF
#define HPC
#define HPC_ALIGN \
"bsub -q medium -n %d -o DALIGNER.out -e DALIGNER.err -R span[hosts=1] -J align#%d"
#define HPC_MERGE \
"bsub -q short -n 12 -o MERGE.DAL.out -e MERGE.DAL.err -R span[hosts=1] -J merge#%d"
#define HPC_CHECK \
"bsub -q short -n 12 -o CHECK.DAL.out -e CHECK.DAL.err -R span[hosts=1] -J check#%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 align#%d"
#define HPC_MERGE \
"srun -p batch -n 1 -c 12 -t 00:05:00 -o MERGE.DAL.out -e MERGE.DAL.err -J merge#%d"
#define HPC_CHECK \
"srun -p batch -n 1 -c 12 -t 00:05:00 -o CHECK.DAL.out -e CHECK.DAL.err -J check#%d"
#endif
void daligner_script(int argc, char *argv[])
{ int nblocks;
int usepath;
int useblock;
int fblock, lblock;
#ifdef HPC
int jobid;
#endif
FILE *out;
char name[100];
char *pwd, *root;
// Make sure DB exists and is partitioned, get number of blocks in partition
pwd = PathTo(argv[1]);
if (strcmp(argv[1]+(strlen(argv[1])-4),".dam") == 0)
root = Root(argv[1],".dam");
else
root = Root(argv[1],".db");
{ int i, nfiles;
FILE *dbvis;
dbvis = fopen(Catenate(pwd,"/",root,".dam"),"r");
if (dbvis == NULL)
{ dbvis = Fopen(Catenate(pwd,"/",root,".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
}
useblock = 1;
if (fscanf(dbvis,"blocks = %d\n",&nblocks) != 1 || nblocks == 1)
{ useblock = 0;
nblocks = 1;
}
usepath = (strcmp(pwd,".") != 0);
fclose(dbvis);
}
// Set range fblock-lblock checking that DB.<fblock-1>.las exists & DB.<fblock>.las does not
{ char *eptr, *fptr;
FILE *file;
if (argc == 3)
{ fblock = strtol(argv[2],&eptr,10);
if (*eptr != '\0' && *eptr != '-')
{ fprintf(stderr,"%s: final argument '%s' does not start with an integer\n",
Prog_Name,argv[2]);
exit (1);
}
useblock = 1;
if (*eptr == '-')
{ lblock = strtol(eptr+1,&fptr,10);
if (*fptr != '\0')
{ 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 > nblocks || 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 = nblocks;
}
if (fblock > 1)
{ file = fopen(Catenate(pwd,"/",root,Numbered_Suffix(".",fblock-1,".las")),"r");
if (file == NULL)
{ if (usepath)
fprintf(stderr,"%s: File %s/%s.%d.las should already be present!\n",
Prog_Name,pwd,root,fblock-1);
else
fprintf(stderr,"%s: File %s.%d.las should already be present!\n",
Prog_Name,root,fblock-1);
exit (1);
}
else
fclose(file);
}
if (useblock)
file = fopen(Catenate(pwd,"/",root,Numbered_Suffix(".",fblock,".las")),"r");
else
file = fopen(Catenate(pwd,"/",root,".las"),"r");
if (file != NULL)
{ if (usepath)
if (useblock)
fprintf(stderr,"%s: File %s/%s.%d.las should not yet exist!\n",
Prog_Name,pwd,root,fblock);
else
fprintf(stderr,"%s: File %s/%s.las should not yet exist!\n",Prog_Name,pwd,root);
else
if (useblock)
fprintf(stderr,"%s: File %s.%d.las should not yet exist!\n",Prog_Name,root,fblock);
else
fprintf(stderr,"%s: File %s.las should not yet exist!\n",Prog_Name,root);
exit (1);
}
DON = (DON && (lblock > 1));
out = stdout;
}
{ int njobs;
int i, j, k;
// Create all work subdirectories if DON
if (DON && lblock > 1)
{ if (ONAME != NULL)
{ sprintf(name,"%s.00.MKDIR",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Create work subdirectories\n");
for (i = 1; i <= lblock; i++)
fprintf(out,"mkdir -p work%d\n",i);
if (ONAME != NULL)
fclose(out);
}
// Produce all necessary daligner jobs
if (ONAME != NULL)
{ sprintf(name,"%s.01.OVL",ONAME);
out = fopen(name,"w");
}
njobs = 0;
for (i = fblock; i <= lblock; i++)
njobs += (i-1)/BUNIT+1;
fprintf(out,"# Daligner jobs (%d)\n",njobs);
#ifdef HPC
jobid = 1;
#endif
for (i = fblock; i <= lblock; i++)
{ int bits;
int low, hgh;
bits = (i-1)/BUNIT+1;
low = 1;
for (j = 1; j <= bits; j++)
{
#ifdef LSF
fprintf(out,HPC_ALIGN,NTHREADS,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,"daligner");
if (VON)
fprintf(out," -v");
if (CON)
fprintf(out," -a");
if (KINT != 16)
fprintf(out," -k%d",KINT);
if (WINT != 6)
fprintf(out," -w%d",WINT);
if (HINT != 50)
fprintf(out," -h%d",HINT);
if (TINT > 0)
fprintf(out," -t%d",TINT);
if (HGAP > 0)
fprintf(out," -H%d",HGAP);
if (EREL > 0.)
fprintf(out," -e%g",EREL);
if (LINT != 1500)
fprintf(out," -l%d",LINT);
if (SINT != 100)
fprintf(out," -s%d",SINT);
if (MINT >= 0)
fprintf(out," -M%d",MINT);
if (PDIR != NULL)
fprintf(out," -P%s",PDIR);
if (NTHREADS != 4)
fprintf(out," -T%d",NTHREADS);
for (k = 0; k < MTOP; k++)
fprintf(out," -m%s",MASK[k]);
if (useblock)
if (usepath)
fprintf(out," %s/%s.%d",pwd,root,i);
else
fprintf(out," %s.%d",root,i);
else
if (usepath)
fprintf(out," %s/%s",pwd,root);
else
fprintf(out," %s",root);
hgh = (i*j)/bits + 1;
if (useblock)
if (usepath)
fprintf(out," %s/%s.@%d-%d",pwd,root,low,hgh-1);
else
fprintf(out," %s.@%d-%d",root,low,hgh-1);
else
if (usepath)
fprintf(out," %s/%s",pwd,root);
else
fprintf(out," %s",root);
if (lblock == 1) // ==> i = 1, [low,hgh) = [1,2)
{ fprintf(out," && mv");
if (useblock)
fprintf(out," %s.1.%s.1.las",root,root);
else
fprintf(out," %s.%s.las",root,root);
if (usepath)
fprintf(out," %s/",pwd);
else
fprintf(out," ");
if (useblock)
fprintf(out,"%s.1.las",root);
else
fprintf(out,"%s.las",root);
}
else if (DON)
{ fprintf(out," && mv");
for (k = low; k < hgh; k++)
fprintf(out," %s.%d.%s.%d.las",root,i,root,k);
fprintf(out," work%d",i);
for (k = low; k < hgh; k++)
if (k != i)
fprintf(out," && mv %s.%d.%s.%d.las work%d",root,k,root,i,k);
}
#ifdef HPC
fprintf(out,"\"");
#endif
fprintf(out,"\n");
low = hgh;
}
}
// Check .las files (optional)
if (ONAME != NULL)
{ fclose(out);
sprintf(name,"%s.02.CHECK.OPT",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Check initial .las files jobs (%d) (optional but recommended)\n",lblock);
#ifdef HPC
jobid = 1;
#endif
for (i = 1; i <= lblock; i++)
{
#ifdef HPC
fprintf(out,HPC_CHECK,jobid++);
fprintf(out," \"");
#endif
fprintf(out,"LAcheck -v%sS",CON?"a":"");
if (usepath)
fprintf(out," %s/%s",pwd,root);
else
fprintf(out," %s",root);
if (lblock == 1)
{ if (usepath)
if (useblock)
fprintf(out," %s/%s.1",pwd,root);
else
fprintf(out," %s/%s",pwd,root);
else
if (useblock)
fprintf(out," %s.1",root);
else
fprintf(out," %s",root);
}
else if (i < fblock)
{ if (DON)
fprintf(out," work%d/%s.%d.%s.%c%d",i,root,i,root,BLOCK_SYMBOL,fblock);
else
fprintf(out," %s.%d.%s.%c%d",root,i,root,BLOCK_SYMBOL,fblock);
}
else
{ if (DON)
fprintf(out," work%d/%s.%d.%s.%c",i,root,i,root,BLOCK_SYMBOL);
else
fprintf(out," %s.%d.%s.%c",root,i,root,BLOCK_SYMBOL);
}
#ifdef HPC
fprintf(out,"\"");
#endif
fprintf(out,"\n");
}
if (ONAME != NULL)
fclose(out);
// Merges required if lblock > 1
if (lblock > 1)
{ if (ONAME != NULL)
{ sprintf(name,"%s.03.MERGE",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Merge jobs (%d)\n",lblock);
// Incremental update merges
#ifdef HPC
jobid = 1;
#endif
for (j = 1; j < fblock; j++)
{
#ifdef HPC
fprintf(out,HPC_MERGE,jobid++);
fprintf(out," \"");
#endif
if (DON)
{ if (usepath)
fprintf(out,"mv %s/%s.%d.las work%d/_%s.%d.las && ",
pwd,root,j,j,root,j);
else
fprintf(out,"mv %s.%d.las work%d/_%s.%d.las && ",root,j,j,root,j);
}
else
{ if (usepath)
fprintf(out,"mv %s/%s.%d.las _%s.%d.las && ",pwd,root,j,root,j);
else
fprintf(out,"mv %s.%d.las _%s.%d.las && ",root,j,root,j);
}
fprintf(out,"LAmerge");
if (VON)
fprintf(out," -v");
if (CON)
fprintf(out," -a");
if (usepath)
fprintf(out," %s/%s.%d",pwd,root,j);
else
fprintf(out," %s.%d",root,j);
if (DON)
fprintf(out," work%d/_%s.%d",j,root,j);
else
fprintf(out," _%s.%d",root,j);
if (DON)
fprintf(out," work%d/%s.%d.%s.%c%d-%d",j,root,j,root,BLOCK_SYMBOL,fblock,lblock);
else
fprintf(out," %s.%d.%s.%c%d-%d",root,j,root,BLOCK_SYMBOL,fblock,lblock);
if (usepath)
fprintf(out," && LAcheck -v%sS %s/%s %s/%s.%d",CON?"a":"",pwd,root,pwd,root,j);
else
fprintf(out," && LAcheck -v%sS %s %s.%d",CON?"a":"",root,root,j);
if (DON)
fprintf(out," && rm work%d/_%s.%d.las",j,root,j);
else
fprintf(out," && rm _%s.%d.las",root,j);
#ifdef HPC
fprintf(out,"\"");
#endif
fprintf(out,"\n");
}
// New block merges
for (j = fblock; j <= lblock; j++)
{
#ifdef HPC
fprintf(out,HPC_MERGE,jobid++);
fprintf(out," \"");
#endif
fprintf(out,"LAmerge");
if (VON)
fprintf(out," -v");
if (CON)
fprintf(out," -a");
if (usepath)
fprintf(out," %s/%s.%d",pwd,root,j);
else
fprintf(out," %s.%d",root,j);
if (DON)
fprintf(out," work%d/%s.%d.%s.%c",j,root,j,root,BLOCK_SYMBOL);
else
fprintf(out," %s.%d.%s.%c",root,j,root,BLOCK_SYMBOL);
if (usepath)
fprintf(out," && LAcheck -v%sS %s/%s %s/%s.%d",CON?"a":"",pwd,root,pwd,root,j);
else
fprintf(out," && LAcheck -v%sS %s %s.%d",CON?"a":"",root,root,j);
#ifdef HPC
fprintf(out,"\"");
#endif
fprintf(out,"\n");
}
// Cleanup (optional)
if (ONAME != NULL)
{ fclose(out);
sprintf(name,"%s.04.RM.OPT",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Remove block .las files (optional)\n");
for (i = 1; i <= lblock; i++)
{ if (DON)
fprintf(out,"cd work%d; ",i);
fprintf(out,"rm %s.%d.%s.*.las",root,i,root);
if (DON)
fprintf(out,"; cd ..");
fprintf(out,"\n");
}
if (ONAME != NULL)
fclose(out);
}
}
free(root);
free(pwd);
}
/*********************************************************************************************\
*
* 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
*
*********************************************************************************************/
#ifdef LSF
#define HPC_MALIGN \
"bsub -q medium -n %d -o MAP.ALL.out -e MAP.ALL.err -R span[hosts=1] -J malign#%d"
#define HPC_MMERGE \
"bsub -q short -n 12 -o MERGE.ALL.out -e MERGE.ALL.err -R span[hosts=1] -J mmerge#%d"
#define HPC_MCHECK \
"bsub -q short -n 12 -o CHECK.ALL.out -e CHECK.ALL.err -R span[hosts=1] -J mcheck#%d"
#endif
#ifdef SLURM
#define HPC_MALIGN \
"srun -p batch -n 1 -c %d --mem_per_cpu=%d -o MAP.ALL.out -e MAP.ALL.err -J malign#%d"
#define HPC_MMERGE \
"srun -p batch -n 1 -c 12 -t 00:05:00 -o MERGE.ALL.out -e MERGE.ALL.err -J mmerge#%d"
#define HPC_MCHECK \
"srun -p batch -n 1 -c 12 -t 00:05:00 -o CHECK.ALL.out -e CHECK.DAL.err -J mcheck#%d"
#endif
void mapper_script(int argc, char *argv[])
{ int nblocks1, nblocks2;
int useblock1, useblock2;
int usepath1, usepath2;
int fblock, lblock;
#ifdef HPC
int jobid;
#endif
FILE *out;
char name[100];
char *pwd1, *root1;
char *pwd2, *root2;
// 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
}
useblock1 = 1;
if (fscanf(dbvis,"blocks = %d\n",&nblocks1) != 1 || nblocks1 == 1)
{ useblock1 = 0;
nblocks1 = 1;
}
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,".",root1,Numbered_Suffix(".",fblock-1,".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,".",root1,Numbered_Suffix(".",fblock,".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);
DON = (DON && (nblocks1 > 1));
out = stdout;
}
{ int njobs;
int i, j, k;
// Create all work subdirectories if DON
if (DON && nblocks1 > 1)
{ if (ONAME != NULL)
{ sprintf(name,"%s.00.MKDIR",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Create work subdirectories\n");
for (i = fblock; i <= lblock; i++)
fprintf(out,"mkdir -p work%d\n",i);
if (ONAME != NULL)
fclose(out);
}
// Produce all necessary daligner jobs ...
if (ONAME != NULL)
{ sprintf(name,"%s.01.CMP",ONAME);
out = fopen(name,"w");
}
njobs = nblocks1 * ( (lblock-fblock)/BUNIT + 1);
fprintf(out,"# Daligner jobs (%d)\n",njobs);
#ifdef HPC
jobid = 1;
#endif
for (i = fblock; i <= lblock; i++)
{ int bits;
int low, hgh;
bits = (nblocks1-1)/BUNIT+1;
low = 1;
for (j = 1; j <= bits; j++)
{
#ifdef LSF
fprintf(out,HPC_MALIGN,NTHREADS,jobid++);
#endif
#ifdef SLURM
if (MINT >= 0)
fprintf(out,HPC_MALIGN,NTHREADS,(MINT*1024)/NTHREADS,jobid++);
else
fprintf(out,HPC_MALIGN,NTHREADS,(16*1024)/NTHREADS,jobid++);
#endif
#ifdef HPC
fprintf(out," \"");
#endif
fprintf(out,"daligner -A");
if (VON)
fprintf(out," -v");
if (CON)
fprintf(out," -a");
fprintf(out," -k%d",KINT);
if (WINT != 6)
fprintf(out," -w%d",WINT);
fprintf(out," -h%d",HINT);
if (TINT > 0)
fprintf(out," -t%d",TINT);
if (EREL > 0.)
fprintf(out," -e%g",EREL);
else
fprintf(out," -e.85");
if (LINT != 1000)
fprintf(out," -l%d",LINT);
if (SINT != 100)
fprintf(out," -s%d",SINT);
if (NTHREADS != 4)
fprintf(out," -T%d",NTHREADS);
if (MINT >= 0)
fprintf(out," -M%d",MINT);
if (PDIR != NULL)
fprintf(out," -P%s",PDIR);
for (k = 0; k < MTOP; k++)
fprintf(out," -m%s",MASK[k]);
fprintf(out," ");
if (usepath2)
fprintf(out,"%s/",pwd2);
fprintf(out,"%s",root2);
if (useblock2)
fprintf(out,".%d",i);
hgh = 1 + (nblocks1*j)/bits;
for (k = low; k < hgh; k++)
{ fprintf(out," ");
if (usepath1)
fprintf(out,"%s/",pwd1);
fprintf(out,"%s",root1);
if (useblock1)
fprintf(out,".%d",k);
}
if (nblocks1 == 1)
{ if (usepath2)
{ fprintf(out," && mv %s",root2);
if (useblock2)
fprintf(out,".%d",i);
fprintf(out,".%s.las %s",root1,pwd2);
}
}
else if (DON)
{ fprintf(out," && mv");
for (k = low; k < hgh; k++)
{ fprintf(out," %s",root2);
if (useblock2)
fprintf(out,".%d",i);
fprintf(out,".%s.%d.las",root1,k);
}
fprintf(out," work%d",i);
}
#ifdef HPC
fprintf(out,"\"");
#endif
fprintf(out,"\n");
low = hgh;
}
}
// Check .las files (optional)
if (ONAME != NULL)
{ fclose(out);
sprintf(name,"%s.02.CHECK.OPT",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Check initial .las files jobs (%d) (optional but recommended)\n",
(lblock-fblock)+1);
#ifdef HPC
jobid = 1;
#endif
for (j = fblock; j <= lblock; j++)
{
#ifdef HPC
fprintf(out,HPC_MCHECK,jobid++);
fprintf(out," \"");
#endif
fprintf(out,"LAcheck -v%sS",CON?"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);
fprintf(out," ");
if (nblocks1 == 1)
{ if (usepath2)
fprintf(out,"%s/",pwd2);
fprintf(out,"%s",root2);
if (useblock2)
fprintf(out,".%d",j);
fprintf(out,".%s",root1);
}
else
{ if (DON)
fprintf(out,"work%d/",j);
fprintf(out,"%s",root2);
if (useblock2)
fprintf(out,".%d",j);
fprintf(out,".%s.%c",root1,BLOCK_SYMBOL);
}
#ifdef HPC
fprintf(out,"\"");
#endif
fprintf(out,"\n");
}
if (ONAME != NULL)
fclose(out);
// Higher level merges (if lblock > 1)
if (nblocks1 > 1)
{ if (ONAME != NULL)
{ sprintf(name,"%s.03.MERGE",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Merge jobs (%d)\n",(lblock-fblock)+1);
#ifdef HPC
jobid = 1;
#endif
for (j = fblock; j <= lblock; j++)
{
#ifdef HPC
fprintf(out,HPC_MMERGE,jobid++);
fprintf(out," \"");
#endif
fprintf(out,"LAmerge ");
if (VON)
fprintf(out,"-v ");
if (CON)
fprintf(out,"-a ");
if (usepath2)
fprintf(out,"%s/",pwd2);
fprintf(out,"%s",root2);
if (useblock2)
fprintf(out,".%d",j);
fprintf(out,".%s",root1);
if (DON)
fprintf(out," work%d/",j);
else
fprintf(out," ");
fprintf(out,"%s",root2);
if (useblock2)
fprintf(out,".%d",j);
fprintf(out,".%s.%c",root1,BLOCK_SYMBOL);
#ifdef HPC
fprintf(out,"\"");
#endif
fprintf(out,"\n");
}
// Cleanup (optional)
if (ONAME != NULL)
{ fclose(out);
sprintf(name,"%s.04.RM",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Remove temporary .las files\n");
for (j = fblock; j <= lblock; j++)
{ if (DON)
fprintf(out,"cd work%d; ",j);
fprintf(out,"rm %s",root2);
if (useblock2)
fprintf(out,".%d",j);
fprintf(out,".%s.*.las",root1);
if (DON)
fprintf(out,"; cd ..");
fprintf(out,"\n");
}
if (ONAME != NULL)
fclose(out);
}
}
free(root2);
free(pwd2);
free(root1);
free(pwd1);
exit (0);
}
int main(int argc, char *argv[])
{ int i, j, k;
int flags[128];
char *eptr;
int mapper;
// Process options and decide if its a overlap or mapper script
ARG_INIT("HPC.daligner")
KINT = 0;
HINT = 0;
HGAP = 0;
EREL = 0.;
BUNIT = 4;
TINT = 0;
WINT = 6;
LINT = 1500;
SINT = 100;
MINT = -1;
PDIR = NULL;
MTOP = 0;
MMAX = 10;
MASK = (char **) Malloc(MMAX*sizeof(char *),"Allocating mask track array");
if (MASK == NULL)
exit (1);
ONAME = NULL;
NTHREADS = 4;