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(HITS_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)
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
mstat[i] = -3;
else
mstat[i] = status;
if (status == 0 && kind == MASK_TRACK)
Load_Track(block,mask[i]);
}
Trim_DB(block);
stop = 0;
for (i = 0; i < mtop; i++)
{ HITS_TRACK *track;
int64 *anno;
int j;
status = Check_Track(block,mask[i],&kind);
if (status < 0 || kind != MASK_TRACK)
continue;
stop += 1;
track = Load_Track(block,mask[i]);
anno = (int64 *) (track->anno);
for (j = 0; j <= block->nreads; j++)
anno[j] /= sizeof(int);
}
if (stop > 1)
{ int64 nsize;
HITS_TRACK *track;
nsize = Merge_Size(block,stop);
track = Merge_Tracks(block,stop,nsize);
while (block->tracks != NULL)
Close_Track(block,block->tracks->name);
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);
exit (1);
}
}
Read_All_Sequences(block,0);
return (isdam);
}