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HPCdaligner.c
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HPCdaligner.c
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/************************************************************************************\
* *
* Copyright (c) 2014, Dr. Eugene W. Myers (EWM). All rights reserved. *
* *
* Redistribution and use in source and binary forms, with or without modification, *
* are permitted provided that the following conditions are met: *
* *
* · Redistributions of source code must retain the above copyright notice, this *
* list of conditions and the following disclaimer. *
* *
* · Redistributions in binary form must reproduce the above copyright notice, this *
* list of conditions and the following disclaimer in the documentation and/or *
* other materials provided with the distribution. *
* *
* · The name of EWM may not be used to endorse or promote products derived from *
* this software without specific prior written permission. *
* *
* THIS SOFTWARE IS PROVIDED BY EWM ”AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, *
* INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND *
* FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL EWM BE LIABLE *
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES *
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS *
* OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY *
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING *
* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN *
* IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. *
* *
* For any issues regarding this software and its use, contact EWM at: *
* *
* Eugene W. Myers Jr. *
* Bautzner Str. 122e *
* 01099 Dresden *
* GERMANY *
* Email: [email protected] *
* *
\************************************************************************************/
/*********************************************************************************************\
*
* 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 "DB.h"
#include "filter.h"
#undef LSF // define if want a directly executable LSF script
static char *Usage[] =
{ "[-vbAI] [-k<int(14)>] [-w<int(6)>] [-h<int(35)>] [-t<int>] [-M<int>]",
" [-e<double(.70)] [-l<int(1000)>] [-s<int(100)] [-H<int>]",
" [-m<track>]+ [-dal<int(4)>] [-deg<int(25)>]",
" <path:db|dam> [<block:int>[-<range:int>]"
};
static int power(int base, int exp)
{ int i, pow;
pow = 1;
for (i = 0; i < exp; i++)
pow *= base;
return (pow);
}
#define LSF_ALIGN "bsub -q medium -n 4 -o ALIGN.out -e ALIGN.err -R span[hosts=1] -J align#%d"
#define LSF_MERGE "bsub -q short -n 12 -o MERGE.out -e MERGE.err -R span[hosts=1] -J merge#%d"
int main(int argc, char *argv[])
{ int nblocks;
int useblock;
int fblock, lblock;
#ifdef LSF
int jobid;
#endif
char *pwd, *root;
int MUNIT, DUNIT;
int VON, BON, AON, ION;
int WINT, TINT, HGAP, HINT, KINT, SINT, LINT, MINT;
double EREL;
int MMAX, MTOP;
char **MASK;
{ int i, j, k; // Process options
int flags[128];
char *eptr;
ARG_INIT("HPCdaligner")
DUNIT = 4;
MUNIT = 25;
KINT = 14;
WINT = 6;
HINT = 35;
TINT = 0;
HGAP = 0;
EREL = 0.;
LINT = 1000;
SINT = 100;
MINT = -1;
MTOP = 0;
MMAX = 10;
MASK = (char **) Malloc(MMAX*sizeof(char *),"Allocating mask track array");
if (MASK == NULL)
exit (1);
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("vbAI");
break;
case 'k':
ARG_POSITIVE(KINT,"K-mer length")
break;
case 'w':
ARG_POSITIVE(WINT,"Log of bin width")
break;
case 'h':
ARG_POSITIVE(HINT,"Hit threshold (in bp.s)")
break;
case 't':
ARG_POSITIVE(TINT,"Tuple suppression frequency")
break;
case 'H':
ARG_POSITIVE(HGAP,"HGAP threshold (in bp.s)")
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 'l':
ARG_POSITIVE(LINT,"Minimum ovlerap length")
break;
case 's':
ARG_POSITIVE(SINT,"Trace spacing")
break;
case 'M':
ARG_NON_NEGATIVE(MINT,"Memory allocation (in Gb)")
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 'd':
if (argv[i][2] == 'e' && argv[i][3] == 'g')
{ MUNIT = strtol(argv[i]+4,&eptr,10);
if (*eptr != '\0' || argv[i][4] == '\0')
{ fprintf(stderr,"%s: -mrg argument is not an integer\n",Prog_Name);
exit (1);
}
if (MUNIT <= 0)
{ fprintf(stderr,"%s: Files per merge must be positive (%d)\n",
Prog_Name,MUNIT);
exit (1);
}
if (MUNIT < 3)
{ fprintf(stderr,"%s: Files per merge must be at least 3 (%d)\n",
Prog_Name,MUNIT);
exit (1);
}
}
else if (argv[i][2] == 'a' && argv[i][3] == 'l')
{ DUNIT = strtol(argv[i]+4,&eptr,10);
if (*eptr != '\0' || argv[i][4] == '\0')
{ fprintf(stderr,"%s: -dal argument is not an integer\n",Prog_Name);
exit (1);
}
if (DUNIT <= 0)
{ fprintf(stderr,"%s: Blocks per daligner call must be positive (%d)\n",
Prog_Name,DUNIT);
exit (1);
}
}
else
{ fprintf(stderr,"%s: -%.3s is an illegal option\n",Prog_Name,argv[i]+1);
exit (1);
}
break;
}
else
argv[j++] = argv[i];
argc = j;
VON = flags['v'];
BON = flags['b'];
AON = flags['A'];
ION = flags['I'];
if (argc < 2 || argc > 3)
{ 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," %*s %s\n",(int) strlen(Prog_Name),"",Usage[3]);
exit (1);
}
}
// 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",NULL),"r");
if (dbvis == NULL)
{ dbvis = Fopen(Catenate(pwd,"/",root,".db",NULL),"r");
if (dbvis == NULL)
exit (1);
}
if (fscanf(dbvis,"files = %d\n",&nfiles) != 1)
SYSTEM_ERROR
for (i = 0; i < nfiles; i++)
{ char buffer[30001];
if (fgets(buffer,30000,dbvis) == NULL)
SYSTEM_ERROR
}
useblock = 1;
if (fscanf(dbvis,"blocks = %d\n",&nblocks) != 1)
{ useblock = 0;
nblocks = 1;
}
}
// 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);
}
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(root,".",Int_To_Str(fblock-1),".las",NULL),"r");
if (file == NULL)
{ fprintf(stderr,"%s: File %s.%d.las should already be present!\n",
Prog_Name,root,fblock-1);
exit (1);
}
else
fclose(file);
}
file = fopen(Catenate(root,".",Int_To_Str(fblock),".las",NULL),"r");
if (file != NULL)
{ fprintf(stderr,"%s: File %s.%d.las should not yet exist!\n",
Prog_Name,root,fblock);
exit (1);
}
}
{ int level, njobs;
int i, j, k;
int usepath;
// Produce all necessary daligner jobs ...
usepath = (strcmp(pwd,".") != 0);
njobs = 0;
for (i = fblock; i <= lblock; i++)
njobs += (i-1)/DUNIT+1;
printf("# Daligner jobs (%d)\n",njobs);
#ifdef LSF
jobid = 1;
#endif
for (i = fblock; i <= lblock; i++)
{ int bits;
int low, hgh;
bits = (i-1)/DUNIT+1;
low = 1;
for (j = 1; j <= bits; j++)
{
#ifdef LSF
printf(LSF_ALIGN,jobid++);
printf(" \"");
#endif
printf("daligner");
if (VON)
printf(" -v");
if (BON)
printf(" -b");
if (AON)
printf(" -A");
if (ION)
printf(" -I");
if (KINT != 14)
printf(" -k%d",KINT);
if (WINT != 6)
printf(" -w%d",WINT);
if (HINT != 35)
printf(" -h%d",HINT);
if (TINT > 0)
printf(" -t%d",TINT);
if (HGAP > 0)
printf(" -H%d",HGAP);
if (EREL > .1)
printf(" -e%g",EREL);
if (LINT != 1000)
printf(" -l%d",LINT);
if (SINT != 100)
printf(" -s%d",SINT);
if (MINT >= 0)
printf(" -M%d",MINT);
for (k = 0; k < MTOP; k++)
printf(" -m%s",MASK[k]);
if (useblock)
if (usepath)
printf(" %s/%s.%d",pwd,root,i);
else
printf(" %s.%d",root,i);
else
if (usepath)
printf(" %s/%s",pwd,root);
else
printf(" %s",root);
hgh = (i*j)/bits + 1;
for (k = low; k < hgh; k++)
if (useblock)
if (usepath)
printf(" %s/%s.%d",pwd,root,k);
else
printf(" %s.%d",root,k);
else
if (usepath)
printf(" %s/%s",pwd,root);
else
printf(" %s",root);
#ifdef LSF
printf("\"");
#endif
printf("\n");
low = hgh;
}
}
// ... and then all the initial sort & merge jobs for each block pair
printf("# Initial sort jobs (%d)\n", lblock*lblock - (fblock-1)*(fblock-1) );
#ifdef LSF
jobid = 1;
#endif
for (i = 1; i <= lblock; i++)
for (j = (i < fblock ? fblock : 1); j <= lblock; j++)
{
#ifdef LSF
printf(LSF_MERGE,jobid++);
printf(" \"");
#endif
printf("LAsort");
if (VON)
printf(" -v");
for (k = 0; k < NTHREADS; k++)
if (useblock)
{ printf(" %s.%d.%s.%d.C%d",root,i,root,j,k);
printf(" %s.%d.%s.%d.N%d",root,i,root,j,k);
}
else
{ printf(" %s.%s.C%d",root,root,k);
printf(" %s.%s.N%d",root,root,k);
}
printf(" && LAmerge");
if (VON)
printf(" -v");
if (lblock == 1)
printf(" %s.%d",root,i);
else if (i < fblock)
printf(" L1.%d.%d",i,(j-fblock)+1);
else
printf(" L1.%d.%d",i,j);
for (k = 0; k < NTHREADS; k++)
if (useblock)
{ printf(" %s.%d.%s.%d.C%d.S",root,i,root,j,k);
printf(" %s.%d.%s.%d.N%d.S",root,i,root,j,k);
}
else
{ printf(" %s.%s.C%d.S",root,root,k);
printf(" %s.%s.N%d.S",root,root,k);
}
printf(" && rm");
for (k = 0; k < NTHREADS; k++)
if (useblock)
{ printf(" %s.%d.%s.%d.C%d.S.las",root,i,root,j,k);
printf(" %s.%d.%s.%d.N%d.S.las",root,i,root,j,k);
}
else
{ printf(" %s.%s.C%d.S.las",root,root,k);
printf(" %s.%s.N%d.S.las",root,root,k);
}
#ifdef LSF
printf("\"");
#endif
printf("\n");
}
// Higher level merges (if lblock > 1)
if (lblock > 1)
{ int pow, mway;
// Determine most balance mway for merging in ceil(log_mrg lblock) levels
pow = 1;
for (level = 0; pow < lblock; level++)
pow *= MUNIT;
for (mway = MUNIT; mway >= 3; mway--)
if (power(mway,level) < lblock)
break;
mway += 1;
// Issue the commands for each merge level
{ int p, cnt, dnt;
cnt = lblock;
dnt = (lblock-fblock)+1;
for (i = 1; i <= level; i++)
{ int bits, dits;
int low, hgh;
bits = (cnt-1)/mway+1;
dits = (dnt-1)/mway+1;
// Incremental update merges
#ifdef LSF
jobid = 1;
#endif
if (dnt >= 1)
{ int last;
last = (dnt == 1 || i == level);
printf("# Level %d jobs (%d)\n",i,bits*((lblock-fblock)+1) + dits*(fblock-1));
for (j = 1; j < fblock; j++)
{
#ifdef LSF
printf(LSF_MERGE,jobid++);
printf(" \"");
#endif
if (last)
printf("mv %s.%d.las L%d.%d.0.las && ",root,j,i,j);
low = 1;
for (p = 1; p <= dits; p++)
{ hgh = (dnt*p)/dits;
#ifdef LSF
if (p > 1)
{ printf(LSF_MERGE,jobid++);
printf(" \"");
}
#endif
printf("LAmerge");
if (VON)
printf(" -v");
if (last)
printf(" %s.%d L%d.%d.0",root,j,i,j);
else
printf(" L%d.%d.%d",i+1,j,p);
for (k = low; k <= hgh; k++)
printf(" L%d.%d.%d",i,j,k);
printf(" && rm");
if (last)
printf(" L%d.%d.0.las",i,j);
for (k = low; k <= hgh; k++)
printf(" L%d.%d.%d.las",i,j,k);
#ifdef LSF
printf("\"");
#endif
printf("\n");
low = hgh+1;
}
}
if (dnt > 1)
dnt = dits;
else
dnt = 0;
}
else
printf("# Level %d jobs (%d)\n",i,bits*((lblock-fblock)+1));
// New block merges
for (j = fblock; j <= lblock; j++)
{ low = 1;
for (p = 1; p <= bits; p++)
{ hgh = (cnt*p)/bits;
#ifdef LSF
printf(LSF_MERGE,jobid++);
printf(" \"");
#endif
printf("LAmerge");
if (VON)
printf(" -v");
if (i == level)
printf(" %s.%d",root,j);
else
printf(" L%d.%d.%d",i+1,j,p);
for (k = low; k <= hgh; k++)
printf(" L%d.%d.%d",i,j,k);
printf(" && rm");
for (k = low; k <= hgh; k++)
printf(" L%d.%d.%d.las",i,j,k);
#ifdef LSF
printf("\"");
#endif
printf("\n");
low = hgh+1;
}
}
cnt = bits;
}
}
}
}
free(root);
free(pwd);
exit (0);
}