int main(int argc, char *argv[])
{ DAZZ_DB _ablock, _bblock;
DAZZ_DB *ablock = &_ablock, *bblock = &_bblock;
char *afile, *bfile;
char *aroot, *broot, *apwd;
void *aindex, *bindex;
int alen, blen;
int isdam, nblocks; // of reference (a-argument)
int mflag;
char *command;
Align_Spec *settings;
int COVER, NOMAP;
int KMER_LEN;
int MAX_REPS;
double AVE_ERROR;
int NTHREADS;
int MAP_ORDER;
int MMAX, MTOP, *MSTAT;
char **MASK;
{ int i, j, k;
int flags[128];
char *eptr;
DIR *dirp;
ARG_INIT("damapper")
KMER_LEN = 20;
MAX_REPS = 0;
AVE_ERROR = .85;
SPACING = 100; // Globally visible to map.c
BEST_TIE = 1.0;
NTHREADS = 4;
SORT_PATH = "/tmp";
MEM_PHYSICAL = getMemorySize();
MEM_LIMIT = MEM_PHYSICAL;
if (MEM_PHYSICAL == 0)
{ fprintf(stderr,"\nWarning: Could not get physical memory size\n");
fflush(stderr);
}
MTOP = 0;
MMAX = 10;
MASK = (char **) Malloc(MMAX*sizeof(char *),"Allocating mask track array");
MSTAT = (int *) Malloc(MMAX*sizeof(int),"Allocating mask status array");
if (MASK == NULL || MSTAT == NULL)
exit (1);
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(AVE_ERROR)
if (AVE_ERROR < .7 || AVE_ERROR >= 1.)
{ fprintf(stderr,"%s: Average correlation must be in [.7,1.) (%g)\n",
Prog_Name,AVE_ERROR);
exit (1);
}
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 'm':
if (MTOP >= MMAX)
{ MMAX = 1.2*MTOP + 10;
MASK = (char **) Realloc(MASK,MMAX*sizeof(char *),"Reallocating mask track array");
MSTAT = (int *) Realloc(MSTAT,MMAX*sizeof(int),"Reallocating mask status array");
if (MASK == NULL || MSTAT == NULL)
exit (1);
}
MASK[MTOP++] = argv[i]+2;
break;
case 'n':
ARG_REAL(BEST_TIE)
if (BEST_TIE < .7 || BEST_TIE > 1.)
{ fprintf(stderr,"%s: Near optimal threshold must be in [.7,1.] (%g)\n",
Prog_Name,BEST_TIE);
exit (1);
}
break;
case 's':
ARG_POSITIVE(SPACING,"Trace spacing")
break;
case 't':
ARG_POSITIVE(MAX_REPS,"Tuple supression frequency")
break;
case 'M':
{ int limit;
ARG_NON_NEGATIVE(limit,"Memory allocation (in Gb)")
MEM_LIMIT = limit * 0x40000000ll;
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 map.h
BIASED = flags['b'];
PROFILE = flags['p'];
COVER = flags['C'];
NOMAP = flags['N'];
MAP_ORDER = 1-flags['z'];
if (argc <= 2)
{ 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," -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," -v: Verbose mode, output statistics as proceed.\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");
exit (1);
}
if (COVER)
if (NOMAP)
mflag = FLAG_DOB;
else
mflag = FLAG_DOA | FLAG_DOB;
else
if (NOMAP)
{ fprintf(stderr,"%s: Cannot specify both C and N flags together\n",Prog_Name);
exit (1);
}
else
mflag = FLAG_DOA;
if (NOMAP && PROFILE)
{ fprintf(stderr,"%s: Cannot specify both N and p flags together\n",Prog_Name);
exit (1);
}
for (j = 0; j < MTOP; j++)
MSTAT[j] = -2;
}
int main(int argc, char *argv[])
{ HITS_DB _ablock, _bblock;
HITS_DB *ablock = &_ablock, *bblock = &_bblock;
char *afile, *bfile;
char *aroot, *broot;
void *aindex, *bindex;
int alen, blen;
Align_Spec *asettings;
int isdam;
int MMAX, MTOP, *MSTAT;
char **MASK;
int KMER_LEN;
int BIN_SHIFT;
int MAX_REPS;
int HIT_MIN;
double AVE_ERROR;
int SPACING;
{ int i, j, k;
int flags[128];
char *eptr;
ARG_INIT("daligner")
KMER_LEN = 14;
HIT_MIN = 35;
BIN_SHIFT = 6;
MAX_REPS = 0;
HGAP_MIN = 0;
AVE_ERROR = .70;
SPACING = 100;
MINOVER = 1000; // Globally visible to filter.c
MEM_PHYSICAL = getMemorySize();
MEM_LIMIT = MEM_PHYSICAL;
if (MEM_PHYSICAL == 0)
{ fprintf(stderr,"\nWarning: Could not get physical memory size\n");
fflush(stderr);
}
MTOP = 0;
MMAX = 10;
MASK = (char **) Malloc(MMAX*sizeof(char *),"Allocating mask track array");
MSTAT = (int *) Malloc(MMAX*sizeof(int),"Allocating mask status array");
if (MASK == NULL || MSTAT == 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(KMER_LEN,"K-mer length")
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 't':
ARG_POSITIVE(MAX_REPS,"Tuple supression frequency")
break;
case 'H':
ARG_POSITIVE(HGAP_MIN,"HGAP threshold (in bp.s)")
break;
case 'e':
ARG_REAL(AVE_ERROR)
if (AVE_ERROR < .7 || AVE_ERROR >= 1.)
{ fprintf(stderr,"%s: Average correlation must be in [.7,1.) (%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 'M':
{ int limit;
ARG_NON_NEGATIVE(limit,"Memory allocation (in Gb)")
MEM_LIMIT = limit * 0x40000000ll;
break;
}
case 'm':
if (MTOP >= MMAX)
{ MMAX = 1.2*MTOP + 10;
MASK = (char **) Realloc(MASK,MMAX*sizeof(char *),"Reallocating mask track array");
MSTAT = (int *) Realloc(MSTAT,MMAX*sizeof(int),"Reallocating mask status array");
if (MASK == NULL || MSTAT == NULL)
exit (1);
}
MASK[MTOP++] = argv[i]+2;
break;
}
else
argv[j++] = argv[i];
argc = j;
VERBOSE = flags['v']; // Globally declared in filter.h
BIASED = flags['b']; // Globally declared in filter.h
SYMMETRIC = 1-flags['A'];
IDENTITY = flags['I'];
if (argc <= 2)
{ 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]);
exit (1);
}
}
