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datander.c
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datander.c
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/*********************************************************************************************\
*
* Find all local self-alignment between long, noisy DNA reads:
* Compare sequences in each supplied blocks against themselves search for local alignments
* of MIN_OVERLAP or more above the diagonal (A start coord > B start coord). An output
* stream of 'Overlap' records (see align.h) is written in binary to a set of files, one
* per thread, each encoding a given found local alignment. The -v option turns on a verbose
* reporting mode that reports progress and gives statistics on each major stage.
*
* The filter operates by looking for a pair of diagonal bands of width 2^'s' that contain
* a collection of exact matching 'k'-mers between positions of a sequence, such that the total
* number of bases covered by 'k'-mer hits is 'h'. k cannot be larger than 15 in the
* current implementation.
*
* For each subject, say XXX, the program outputs a file containing LAs of the form
* XXX.XXX.T#.las where # is the thread that detected and wrote out the collection of LAs.
* For example, if NTHREAD in the program is 4, then 4 files are output for each subject block.
*
* Author: Gene Myers
* Date : March 27, 2016
*
*********************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdint.h>
#include <ctype.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <dirent.h>
#include <sys/param.h>
#if defined(BSD)
#include <sys/sysctl.h>
#endif
#include "DB.h"
#include "tandem.h"
static char *Usage[] =
{ "[-v] [-k<int(12)>] [-w<int(4)>] [-h<int(35)>] [-T<int(4)>] [-P<dir(/tmp)>]",
" [-e<double(.70)] [-l<int(500)>] [-s<int(100)>] <subject:db|dam> ...",
};
int VERBOSE; // Globally visible to tandem.c
char *SORT_PATH;
int MINOVER;
static int read_DB(DAZZ_DB *block, char *name, int kmer)
{ int i, isdam;
isdam = Open_DB(name,block);
if (isdam < 0)
Clean_Exit(1);
Trim_DB(block);
if (block->cutoff < kmer)
{ for (i = 0; i < block->nreads; i++)
if (block->reads[i].rlen < kmer)
{ fprintf(stderr,"%s: Block %s contains reads < %dbp long ! Run DBsplit.\n",
Prog_Name,name,kmer);
Clean_Exit(1);
}
}
Load_All_Reads(block,0);
return (isdam);
}
static char *CommandBuffer(char *bname, char *spath)
{ static char *cat = NULL;
static int max = -1;
int len;
len = 2*(strlen(bname) + strlen(spath)) + 200;
if (len > max)
{ max = ((int) (1.2*len)) + 100;
if ((cat = (char *) realloc(cat,max+1)) == NULL)
{ fprintf(stderr,"%s: Out of memory (Making path name)\n",Prog_Name);
Clean_Exit(1);
}
}
return (cat);
}
void Clean_Exit(int val)
{ char *command;
command = CommandBuffer("",SORT_PATH);
sprintf(command,"rm -r %s",SORT_PATH);
if (system(command) != 0)
{ fprintf(stderr,"%s: Command Failed:\n%*s %s\n",
Prog_Name,(int) strlen(Prog_Name),"",command);
exit (1);
}
exit (val);
}
int main(int argc, char *argv[])
{ DAZZ_DB _bblock;
DAZZ_DB *bblock = &_bblock;
char *bfile;
char *broot;
Align_Spec *settings;
int isdam;
char *command;
int KMER_LEN;
int BIN_SHIFT;
int HIT_MIN;
double AVE_ERROR;
int SPACING;
int NTHREADS;
{ int i, j, k;
int flags[128];
char *eptr;
DIR *dirp;
ARG_INIT("datander")
KMER_LEN = 12;
HIT_MIN = 35;
BIN_SHIFT = 4;
AVE_ERROR = .70;
SPACING = 100;
MINOVER = 500; // Globally visible to filter.c
NTHREADS = 4;
SORT_PATH = "/tmp";
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("v")
break;
case 'k':
ARG_POSITIVE(KMER_LEN,"K-mer length")
if (KMER_LEN > 32)
{ fprintf(stderr,"%s: K-mer length must be 32 or less\n",Prog_Name);
exit (1);
}
break;
case 'w':
ARG_POSITIVE(BIN_SHIFT,"Log of bin width")
break;
case 'h':
ARG_POSITIVE(HIT_MIN,"Hit threshold (in bp.s)")
break;
case 'e':
ARG_REAL(AVE_ERROR)
if (AVE_ERROR < .6 || AVE_ERROR >= 1.)
{ fprintf(stderr,"%s: Average correlation must be in [.6,1.) (%g)\n",
Prog_Name,AVE_ERROR);
exit (1);
}
break;
case 'l':
ARG_POSITIVE(MINOVER,"Minimum alignment length")
break;
case 's':
ARG_POSITIVE(SPACING,"Trace spacing")
break;
case 'P':
SORT_PATH = argv[i]+2;
if ((dirp = opendir(SORT_PATH)) == NULL)
{ fprintf(stderr,"%s: -P option: cannot open directory %s\n",Prog_Name,SORT_PATH);
exit (1);
}
closedir(dirp);
break;
case 'T':
ARG_POSITIVE(NTHREADS,"Number of threads")
break;
}
else
argv[j++] = argv[i];
argc = j;
VERBOSE = flags['v']; // Globally declared in filter.h
if (argc <= 1)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage[0]);
fprintf(stderr," %*s %s\n",(int) strlen(Prog_Name),"",Usage[1]);
fprintf(stderr,"\n");
fprintf(stderr," -v: Verbose mode, output statistics as proceed.\n");
fprintf(stderr," -k: k-mer size (must be <= 32).\n");
fprintf(stderr," -w: Look for k-mers in averlapping bands of size 2^-w.\n");
fprintf(stderr," -h: A seed hit if the k-mers in band cover >= -h bps in the");
fprintf(stderr," targest read.\n");
fprintf(stderr,"\n");
fprintf(stderr," -e: Look for alignments with -e percent similarity.\n");
fprintf(stderr," -l: Look for alignments of length >= -l.\n");
fprintf(stderr," -s: Use -s as the trace point spacing for encoding alignments.\n");
fprintf(stderr,"\n");
fprintf(stderr," -T: Use -T threads.\n");
fprintf(stderr," -P: Do first level sort and merge in directory -P.\n");
exit (1);
}
}
MINOVER *= 2;
if (Set_Filter_Params(KMER_LEN,BIN_SHIFT,HIT_MIN,NTHREADS))
{ fprintf(stderr,"Illegal combination of filter parameters\n");
exit (1);
}
{ float freq[4] = { .25, .25, .25, .25};
settings = New_Align_Spec( AVE_ERROR, SPACING, freq, 0);
}
// Create directory in SORT_PATH for file operations
{ char *newpath;
newpath = (char *) Malloc(strlen(SORT_PATH)+30,"Allocating sort path");
if (newpath == NULL)
exit (1);
sprintf(newpath,"%s/datander.%d",SORT_PATH,getpid());
if (mkdir(newpath,S_IRWXU) != 0)
{ fprintf(stderr,"%s: Could not create directory %s\n",Prog_Name,newpath);
exit (1);
}
SORT_PATH = newpath;
}
// Compare each block against itself
{ int i;
broot = NULL;
for (i = 1; i < argc; i++)
{ bfile = argv[i];
isdam = read_DB(bblock,bfile,KMER_LEN);
if (isdam)
broot = Root(bfile,".dam");
else
broot = Root(bfile,".db");
Match_Self(broot,bblock,settings);
Close_DB(bblock);
command = CommandBuffer(broot,SORT_PATH);
#define SYSTEM_CHECK(command) \
if (VERBOSE) \
printf("%s\n",command); \
if (system(command) != 0) \
{ fprintf(stderr,"\n%s: Command Failed:\n%*s %s\n", \
Prog_Name,(int) strlen(Prog_Name),"",command); \
Clean_Exit(1); \
}
sprintf(command,"LAsort %s/%s.T%c.las",SORT_PATH,broot,BLOCK_SYMBOL);
SYSTEM_CHECK(command)
sprintf(command,"LAmerge TAN.%s.las %s/%s.T%c.S.las",broot,SORT_PATH,broot,BLOCK_SYMBOL);
SYSTEM_CHECK(command)
}
}
Clean_Exit(0);
exit (0);
}