int main(int argc, char *argv[])
{ HITS_DB _db, *db = &_db;
HITS_READ *reads;
int VERBOSE;
int SORTED;
int RANGE;
// Process options
{ int i, j, k;
int flags[128];
ARG_INIT("LAcheck")
RANGE = 0;
reads = NULL;
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("vS")
break;
case 'a':
RANGE = 1;
if (argv[i][2] != ':')
{ fprintf(stderr,"%s: Unrecognizable option %s\n",Prog_Name,argv[i]);
exit (1);
}
if (Open_DB(argv[i]+3,db))
exit (1);
Trim_DB(db);
reads = db->reads;
break;
}
else
argv[j++] = argv[i];
argc = j;
VERBOSE = flags['v'];
SORTED = flags['S'];
if (argc < 2)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
exit (1);
}
}
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);
}
}
Read_All_Sequences(block,0);
return (isdam);
}
static HITS_DB *read_DB(char *name, int dust)
{ static HITS_DB block;
HITS_TRACK *dtrack;
if (Open_DB(name,&block))
exit (1);
if (dust)
dtrack = Load_Track(&block,"dust");
else
dtrack = NULL;
Trim_DB(&block);
if (block.totlen > 0x7fffffffll)
{ fprintf(stderr,"File (%s) is too large\n",name);
exit (1);
}
if (block.nreads > 0xffff)
{ fprintf(stderr,"There are more than %d reads in file (%s)\n",0xffff,name);
exit (1);
}
if (block.maxlen > 0xffff)
{ fprintf(stderr,"Reads are over %d bases long in file (%s)\n",0xffff,name);
exit (1);
}
Read_All_Sequences(&block,0);
if (dtrack != NULL)
{ int *anno = (int *) (dtrack->anno);
int i;
for (i = 0; i <= block.nreads; i++)
anno[i] /= sizeof(int);
}
return (&block);
}
static int read_DB(DAZZ_DB *block, char *name, char **mask, int *mstat, int mtop, int kmer)
{ int i, isdam, status, kind, stop;
isdam = Open_DB(name,block);
if (isdam < 0)
Clean_Exit(1);
for (i = 0; i < mtop; i++)
{ status = Check_Track(block,mask[i],&kind);
if (status >= 0)
if (kind == MASK_TRACK)
mstat[i] = 0;
else
{ if (mstat[i] != 0)
mstat[i] = -3;
}
else
{ if (mstat[i] == -2)
mstat[i] = status;
}
if (status == 0 && kind == MASK_TRACK)
Open_Track(block,mask[i]);
}
Trim_DB(block);
stop = 0;
for (i = 0; i < mtop; i++)
{ DAZZ_TRACK *track;
int64 *anno;
int j;
status = Check_Track(block,mask[i],&kind);
if (status < 0 || kind != MASK_TRACK)
continue;
stop += 1;
track = Open_Track(block,mask[i]);
Load_All_Track_Data(track);
anno = (int64 *) (track->anno);
for (j = 0; j <= block->nreads; j++)
anno[j] /= sizeof(int);
}
if (stop > 1)
{ int64 nsize;
DAZZ_TRACK *track;
nsize = merge_size(block,stop);
track = merge_tracks(block,stop,nsize);
while (block->tracks != NULL)
Close_Track(block,block->tracks);
block->tracks = track;
}
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);
}
char *openModel(char *Alas, char *Adb, char *Bdb, int first, int last,
int nolink, int nolap, int elim, int max_comp, int max_expn)
{ static char buffer[2*MAX_NAME+100];
static DAZZ_DB _db1;
static DAZZ_DB _db2;
FILE *dbfile;
if (FIRSTCALL)
{ FIRSTCALL = 0;
Prog_Name = Strdup("DaViewer","");
}
if ( ! UNDEFINED)
{ Close_DB(MODEL.db1);
if (MODEL.db1 != MODEL.db2)
Close_DB(MODEL.db2);
fclose(MODEL.input);
free(MODEL.local);
free(MODEL.pile+MODEL.first);
free(MODEL.tbuf);
}
UNDEFINED = 1;
{ int i, nfiles, nblocks, cutoff, all, oindx;
int64 size;
int la_first, la_last;
int db_first, db_last;
FILE *input;
input = fopen(Alas,"r");
if (input == NULL)
{ if (rindex(Alas,'/') != NULL)
Alas = rindex(Alas,'/')+1;
EPRINTF(EPLACE,"%s: Cannot open file %s\n",Prog_Name,Alas);
return (Ebuffer);
}
if (scanLAS(input,&la_first,&la_last))
{ if (rindex(Alas,'/') != NULL)
Alas = rindex(Alas,'/')+1;
EPRINTF(EPLACE,"%s: LAS file %s has no overlaps !\n",Prog_Name,Alas);
fclose(input);
return (Ebuffer);
}
fclose(input);
dbfile = Fopen(Adb,"r");
if (dbfile == NULL)
return (Ebuffer);
if (fscanf(dbfile,DB_NFILE,&nfiles) != 1)
goto junk;
for (i = 0; i < nfiles; i++)
if (fgets(buffer,2*MAX_NAME+100,dbfile) == NULL)
goto junk;
if (fscanf(dbfile,DB_NBLOCK,&nblocks) != 1)
{ if (feof(dbfile))
{ EPRINTF(EPLACE,"%s: Database has not been split!",Prog_Name);
goto error;
}
goto junk;
}
if (fscanf(dbfile,DB_PARAMS,&size,&cutoff,&all) != 3)
goto junk;
for (i = 0; i <= nblocks; i++)
{ if (fscanf(dbfile,DB_BDATA,&oindx,&db_last) != 2)
goto junk;
if (la_first >= db_last)
db_first = db_last;
if (la_last < db_last)
break;
}
fclose(dbfile);
if (first >= 0)
{ if (first >= db_last)
{ EPRINTF(EPLACE,"First requested read %d is > last read in las block %d\n",
first+1,db_last);
return (Ebuffer);
}
else if (first > db_first)
db_first = first;
}
if (last >= 0)
{ if (last <= db_first)
{ EPRINTF(EPLACE,"Last requested read %d is < first read in las block %d\n",
last,db_first+1);
return (Ebuffer);
}
else if (last < db_last)
db_last = last;
}
MODEL.first = db_first;
MODEL.last = db_last;
}
MODEL.db1 = &_db1;
if (Open_DB(Adb,MODEL.db1) < 0)
return (Ebuffer);
if (Bdb == NULL)
MODEL.db2 = MODEL.db1;
else
{ MODEL.db2 = &_db2;
if (Open_DB(Bdb,MODEL.db2) < 0)
{ Close_DB(MODEL.db1);
return (Ebuffer);
}
Trim_DB(MODEL.db2);
}
Trim_DB(MODEL.db1);
if (List_DB_Files(Adb,OPEN_MASKS))
return (Ebuffer);
{ int i, n;
DAZZ_READ *read = MODEL.db2->reads;
n = MODEL.db2->nreads;
for (i = 0; i < n; i++)
read[i].flags &= (DB_CSS | DB_BEST);
}
{ int kind;
if (Check_Track(MODEL.db1,"prof",&kind) > -2)
{ MODEL.prf = Load_Track(MODEL.db1,"prof");
if (MODEL.prf == NULL)
{ Close_DB(MODEL.db1);
if (MODEL.db2 != MODEL.db1)
Close_DB(MODEL.db2);
return (Ebuffer);
}
}
else
MODEL.prf = NULL;
if (Check_Track(MODEL.db1,"qual",&kind) > -2)
{ MODEL.qvs = Load_Track(MODEL.db1,"qual");
if (MODEL.qvs == NULL)
{ Close_DB(MODEL.db1);
if (MODEL.db2 != MODEL.db1)
Close_DB(MODEL.db2);
return (Ebuffer);
}
}
else
MODEL.qvs = NULL;
}
MODEL.input = fopen(Alas,"r");
if (buildModel(nolink,nolap,elim,max_comp,max_expn))
{ fclose(MODEL.input);
Close_DB(MODEL.db1);
if (MODEL.db2 != MODEL.db1)
Close_DB(MODEL.db2);
return (Ebuffer);
}
{ DAZZ_TRACK *t, *u, *v;
int j;
int64 *anno;
u = NULL;
for (t = MODEL.db1->tracks; t != NULL; t = v)
{ v = t->next;
t->next = u;
u = t;
}
MODEL.db1->tracks = u;
for (t = MODEL.db1->tracks; t != MODEL.qvs && t != MODEL.prf; t = t->next)
{ anno = (int64 *) (t->anno);
for (j = 0; j <= MODEL.db1->nreads; j++)
anno[j] >>= 2;
}
}
UNDEFINED = 0;
return (NULL);
junk:
if (rindex(Adb,'/') != NULL)
Adb = rindex(Adb,'/')+1;
EPRINTF(EPLACE,"%s: Stub file %s is junk!\n",Prog_Name,Adb);
error:
fclose(dbfile);
return (Ebuffer);
}