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DB.c
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/*******************************************************************************************
*
* Compressed data base module. Auxiliary routines to open and manipulate a data base for
* which the sequence and read information are separated into two separate files, and the
* sequence is compressed into 2-bits for each base. Support for tracks of additional
* information, and trimming according to the current partition.
*
* Author : Gene Myers
* Date : July 2013
* Revised: April 2014
*
********************************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include <unistd.h>
#include <dirent.h>
#include "DB.h"
#ifdef HIDE_FILES
#define PATHSEP "/."
#else
#define PATHSEP "/"
#endif
/*******************************************************************************************
*
* GENERAL UTILITIES
*
********************************************************************************************/
char *Prog_Name;
#ifdef INTERACTIVE
char Ebuffer[1000];
#endif
void *Malloc(int64 size, char *mesg)
{ void *p;
if ((p = malloc(size)) == NULL)
{ if (mesg == NULL)
EPRINTF(EPLACE,"%s: Out of memory\n",Prog_Name);
else
EPRINTF(EPLACE,"%s: Out of memory (%s)\n",Prog_Name,mesg);
}
return (p);
}
void *Realloc(void *p, int64 size, char *mesg)
{ if (size <= 0)
size = 1;
if ((p = realloc(p,size)) == NULL)
{ if (mesg == NULL)
EPRINTF(EPLACE,"%s: Out of memory\n",Prog_Name);
else
EPRINTF(EPLACE,"%s: Out of memory (%s)\n",Prog_Name,mesg);
}
return (p);
}
char *Strdup(char *name, char *mesg)
{ char *s;
if (name == NULL)
return (NULL);
if ((s = strdup(name)) == NULL)
{ if (mesg == NULL)
EPRINTF(EPLACE,"%s: Out of memory\n",Prog_Name);
else
EPRINTF(EPLACE,"%s: Out of memory (%s)\n",Prog_Name,mesg);
}
return (s);
}
FILE *Fopen(char *name, char *mode)
{ FILE *f;
if (name == NULL || mode == NULL)
return (NULL);
if ((f = fopen(name,mode)) == NULL)
EPRINTF(EPLACE,"%s: Cannot open %s for '%s'\n",Prog_Name,name,mode);
return (f);
}
char *PathTo(char *name)
{ char *path, *find;
if (name == NULL)
return (NULL);
if ((find = rindex(name,'/')) != NULL)
{ *find = '\0';
path = Strdup(name,"Extracting path from");
*find = '/';
}
else
path = Strdup(".","Allocating default path");
return (path);
}
char *Root(char *name, char *suffix)
{ char *path, *find, *dot;
int epos;
if (name == NULL)
return (NULL);
find = rindex(name,'/');
if (find == NULL)
find = name;
else
find += 1;
if (suffix == NULL)
{ dot = strchr(find,'.');
if (dot != NULL)
*dot = '\0';
path = Strdup(find,"Extracting root from");
if (dot != NULL)
*dot = '.';
}
else
{ epos = strlen(find);
epos -= strlen(suffix);
if (epos > 0 && strcasecmp(find+epos,suffix) == 0)
{ find[epos] = '\0';
path = Strdup(find,"Extracting root from");
find[epos] = suffix[0];
}
else
path = Strdup(find,"Allocating root");
}
return (path);
}
char *Catenate(char *path, char *sep, char *root, char *suffix)
{ static char *cat = NULL;
static int max = -1;
int len;
if (path == NULL || root == NULL || sep == NULL || suffix == NULL)
return (NULL);
len = strlen(path);
len += strlen(sep);
len += strlen(root);
len += strlen(suffix);
if (len > max)
{ max = ((int) (1.2*len)) + 100;
if ((cat = (char *) realloc(cat,max+1)) == NULL)
{ EPRINTF(EPLACE,"%s: Out of memory (Making path name for %s)\n",Prog_Name,root);
return (NULL);
}
}
sprintf(cat,"%s%s%s%s",path,sep,root,suffix);
return (cat);
}
char *Numbered_Suffix(char *left, int num, char *right)
{ static char *suffix = NULL;
static int max = -1;
int len;
if (left == NULL || right == NULL)
return (NULL);
len = strlen(left);
len += strlen(right) + 40;
if (len > max)
{ max = ((int) (1.2*len)) + 100;
if ((suffix = (char *) realloc(suffix,max+1)) == NULL)
{ EPRINTF(EPLACE,"%s: Out of memory (Making number suffix for %d)\n",Prog_Name,num);
return (NULL);
}
}
sprintf(suffix,"%s%d%s",left,num,right);
return (suffix);
}
#define COMMA ','
// Print big integers with commas/periods for better readability
void Print_Number(int64 num, int width, FILE *out)
{ if (width == 0)
{ if (num < 1000ll)
fprintf(out,"%lld",num);
else if (num < 1000000ll)
fprintf(out,"%lld%c%03lld",num/1000ll,COMMA,num%1000ll);
else if (num < 1000000000ll)
fprintf(out,"%lld%c%03lld%c%03lld",num/1000000ll,
COMMA,(num%1000000ll)/1000ll,COMMA,num%1000ll);
else
fprintf(out,"%lld%c%03lld%c%03lld%c%03lld",num/1000000000ll,
COMMA,(num%1000000000ll)/1000000ll,
COMMA,(num%1000000ll)/1000ll,COMMA,num%1000ll);
}
else
{ if (num < 1000ll)
fprintf(out,"%*lld",width,num);
else if (num < 1000000ll)
{ if (width <= 4)
fprintf(out,"%lld%c%03lld",num/1000ll,COMMA,num%1000ll);
else
fprintf(out,"%*lld%c%03lld",width-4,num/1000ll,COMMA,num%1000ll);
}
else if (num < 1000000000ll)
{ if (width <= 8)
fprintf(out,"%lld%c%03lld%c%03lld",num/1000000ll,COMMA,(num%1000000ll)/1000ll,
COMMA,num%1000ll);
else
fprintf(out,"%*lld%c%03lld%c%03lld",width-8,num/1000000ll,COMMA,(num%1000000ll)/1000ll,
COMMA,num%1000ll);
}
else
{ if (width <= 12)
fprintf(out,"%lld%c%03lld%c%03lld%c%03lld",num/1000000000ll,COMMA,
(num%1000000000ll)/1000000ll,COMMA,
(num%1000000ll)/1000ll,COMMA,num%1000ll);
else
fprintf(out,"%*lld%c%03lld%c%03lld%c%03lld",width-12,num/1000000000ll,COMMA,
(num%1000000000ll)/1000000ll,COMMA,
(num%1000000ll)/1000ll,COMMA,num%1000ll);
}
}
}
// Return the number of digits, base 10, of num
int Number_Digits(int64 num)
{ int digit;
digit = 0;
while (num >= 1)
{ num /= 10;
digit += 1;
}
return (digit);
}
/*******************************************************************************************
*
* READ COMPRESSION/DECOMPRESSION UTILITIES
*
********************************************************************************************/
// Compress read into 2-bits per base (from [0-3] per byte representation
void Compress_Read(int len, char *s)
{ int i;
char c, d;
char *s0, *s1, *s2, *s3;
s0 = s;
s1 = s0+1;
s2 = s1+1;
s3 = s2+1;
c = s1[len];
d = s2[len];
s0[len] = s1[len] = s2[len] = 0;
for (i = 0; i < len; i += 4)
*s++ = (char ) ((s0[i] << 6) | (s1[i] << 4) | (s2[i] << 2) | s3[i]);
s1[len] = c;
s2[len] = d;
}
// Uncompress read form 2-bits per base into [0-3] per byte representation
void Uncompress_Read(int len, char *s)
{ int i, tlen, byte;
char *s0, *s1, *s2, *s3;
char *t;
s0 = s;
s1 = s0+1;
s2 = s1+1;
s3 = s2+1;
tlen = (len-1)/4;
t = s+tlen;
for (i = tlen*4; i >= 0; i -= 4)
{ byte = *t--;
s0[i] = (char) ((byte >> 6) & 0x3);
s1[i] = (char) ((byte >> 4) & 0x3);
s2[i] = (char) ((byte >> 2) & 0x3);
s3[i] = (char) (byte & 0x3);
}
s[len] = 4;
}
// Convert read in [0-3] representation to ascii representation (end with '\n')
void Lower_Read(char *s)
{ static char letter[4] = { 'a', 'c', 'g', 't' };
for ( ; *s != 4; s++)
*s = letter[(int) *s];
*s = '\0';
}
void Upper_Read(char *s)
{ static char letter[4] = { 'A', 'C', 'G', 'T' };
for ( ; *s != 4; s++)
*s = letter[(int) *s];
*s = '\0';
}
void Letter_Arrow(char *s)
{ static char letter[4] = { '1', '2', '3', '4' };
for ( ; *s != 4; s++)
*s = letter[(int) *s];
*s = '\0';
}
// Convert read in ascii representation to [0-3] representation (end with 4)
void Number_Read(char *s)
{ static char number[128] =
{ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 2,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 3, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 2,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 3, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
};
for ( ; *s != '\0'; s++)
*s = number[(int) *s];
*s = 4;
}
void Number_Arrow(char *s)
{ static char arrow[128] =
{ 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3,
3, 0, 1, 2, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 2,
3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3,
};
for ( ; *s != '\0'; s++)
*s = arrow[(int) *s];
*s = 4;
}
/*******************************************************************************************
*
* DB OPEN, TRIM & CLOSE ROUTINES
*
********************************************************************************************/
// Open the given database or dam, "path" into the supplied HITS_DB record "db". If the name has
// a part # in it then just the part is opened. The index array is allocated (for all or
// just the part) and read in.
// Return status of routine:
// -1: The DB could not be opened for a reason reported by the routine to EPLACE
// 0: Open of DB proceeded without mishap
// 1: Open of DAM proceeded without mishap
int Open_DB(char* path, HITS_DB *db)
{ HITS_DB dbcopy;
char *root, *pwd, *bptr, *fptr, *cat;
int nreads;
FILE *index, *dbvis;
int status, plen, isdam;
int part, cutoff, all;
int ufirst, tfirst, ulast, tlast;
status = -1;
dbcopy = *db;
plen = strlen(path);
if (strcmp(path+(plen-4),".dam") == 0)
root = Root(path,".dam");
else
root = Root(path,".db");
pwd = PathTo(path);
bptr = rindex(root,'.');
if (bptr != NULL && bptr[1] != '\0' && bptr[1] != '-')
{ part = strtol(bptr+1,&fptr,10);
if (*fptr != '\0' || part == 0)
part = 0;
else
*bptr = '\0';
}
else
part = 0;
isdam = 0;
cat = Catenate(pwd,"/",root,".db");
if (cat == NULL)
return (-1);
if ((dbvis = fopen(cat,"r")) == NULL)
{ cat = Catenate(pwd,"/",root,".dam");
if (cat == NULL)
return (-1);
if ((dbvis = fopen(cat,"r")) == NULL)
{ EPRINTF(EPLACE,"%s: Could not open database %s\n",Prog_Name,path);
goto error;
}
isdam = 1;
}
if ((index = Fopen(Catenate(pwd,PATHSEP,root,".idx"),"r")) == NULL)
goto error1;
if (fread(db,sizeof(HITS_DB),1,index) != 1)
{ EPRINTF(EPLACE,"%s: Index file (.idx) of %s is junk\n",Prog_Name,root);
goto error2;
}
{ int p, nblocks, nfiles;
int64 size;
char fname[MAX_NAME], prolog[MAX_NAME];
nblocks = 0;
if (fscanf(dbvis,DB_NFILE,&nfiles) != 1)
{ EPRINTF(EPLACE,"%s: Stub file (.db) of %s is junk\n",Prog_Name,root);
goto error2;
}
for (p = 0; p < nfiles; p++)
if (fscanf(dbvis,DB_FDATA,&tlast,fname,prolog) != 3)
{ EPRINTF(EPLACE,"%s: Stub file (.db) of %s is junk\n",Prog_Name,root);
goto error2;
}
if (fscanf(dbvis,DB_NBLOCK,&nblocks) != 1)
if (part == 0)
{ cutoff = 0;
all = DB_ALL;
}
else
{ EPRINTF(EPLACE,"%s: DB %s has not yet been partitioned, cannot request a block !\n",
Prog_Name,root);
goto error2;
}
else
{ if (fscanf(dbvis,DB_PARAMS,&size,&cutoff,&all) != 3)
{ EPRINTF(EPLACE,"%s: Stub file (.db) of %s is junk\n",Prog_Name,root);
goto error2;
}
if (part > nblocks)
{ EPRINTF(EPLACE,"%s: DB %s has only %d blocks\n",Prog_Name,root,nblocks);
goto error2;
}
}
if (part > 0)
{ for (p = 1; p <= part; p++)
if (fscanf(dbvis,DB_BDATA,&ufirst,&tfirst) != 2)
{ EPRINTF(EPLACE,"%s: Stub file (.db) of %s is junk\n",Prog_Name,root);
goto error2;
}
if (fscanf(dbvis,DB_BDATA,&ulast,&tlast) != 2)
{ EPRINTF(EPLACE,"%s: Stub file (.db) of %s is junk\n",Prog_Name,root);
goto error2;
}
}
else
{ ufirst = tfirst = 0;
ulast = db->ureads;
tlast = db->treads;
}
}
db->trimmed = 0;
db->tracks = NULL;
db->part = part;
db->cutoff = cutoff;
db->allarr |= all;
db->ufirst = ufirst;
db->tfirst = tfirst;
nreads = ulast-ufirst;
if (part <= 0)
{ db->reads = (HITS_READ *) Malloc(sizeof(HITS_READ)*(nreads+2),"Allocating Open_DB index");
if (db->reads == NULL)
goto error2;
db->reads += 1;
if (fread(db->reads,sizeof(HITS_READ),nreads,index) != (size_t) nreads)
{ EPRINTF(EPLACE,"%s: Index file (.idx) of %s is junk\n",Prog_Name,root);
free(db->reads-1);
goto error2;
}
}
else
{ HITS_READ *reads;
int i, r, maxlen;
int64 totlen;
reads = (HITS_READ *) Malloc(sizeof(HITS_READ)*(nreads+2),"Allocating Open_DB index");
if (reads == NULL)
goto error2;
reads += 1;
fseeko(index,sizeof(HITS_READ)*ufirst,SEEK_CUR);
if (fread(reads,sizeof(HITS_READ),nreads,index) != (size_t) nreads)
{ EPRINTF(EPLACE,"%s: Index file (.idx) of %s is junk\n",Prog_Name,root);
free(reads-1);
goto error2;
}
totlen = 0;
maxlen = 0;
for (i = 0; i < nreads; i++)
{ r = reads[i].rlen;
totlen += r;
if (r > maxlen)
maxlen = r;
}
db->maxlen = maxlen;
db->totlen = totlen;
db->reads = reads;
}
((int *) (db->reads))[-1] = ulast - ufirst; // Kludge, need these for DB part
((int *) (db->reads))[-2] = tlast - tfirst;
db->nreads = nreads;
db->path = Strdup(Catenate(pwd,PATHSEP,root,""),"Allocating Open_DB path");
if (db->path == NULL)
goto error2;
db->bases = NULL;
db->loaded = 0;
status = isdam;
error2:
fclose(index);
error1:
fclose(dbvis);
error:
if (bptr != NULL)
*bptr = '.';
free(pwd);
free(root);
if (status < 0)
*db = dbcopy;
return (status);
}
// Trim the DB or part thereof and all loaded tracks according to the cuttof and all settings
// of the current DB partition. Reallocate smaller memory blocks for the information kept
// for the retained reads.
void Trim_DB(HITS_DB *db)
{ int i, j, r;
int allflag, cutoff;
int64 totlen;
int maxlen, nreads;
HITS_TRACK *record;
HITS_READ *reads;
if (db->trimmed) return;
if (db->cutoff <= 0 && (db->allarr & DB_ALL) != 0) return;
cutoff = db->cutoff;
if ((db->allarr & DB_ALL) != 0)
allflag = 0;
else
allflag = DB_BEST;
reads = db->reads;
nreads = db->nreads;
for (record = db->tracks; record != NULL; record = record->next)
if (strcmp(record->name,".@qvs") == 0)
{ uint16 *table = ((HITS_QV *) record)->table;
j = 0;
for (i = 0; i < db->nreads; i++)
if ((reads[i].flags & DB_BEST) >= allflag && reads[i].rlen >= cutoff)
table[j++] = table[i];
}
else
{ int *anno4, size;
int64 *anno8;
char *anno, *data;
size = record->size;
data = (char *) record->data;
if (data == NULL)
{ anno = (char *) record->anno;
j = 0;
for (i = r = 0; i < db->nreads; i++, r += size)
if ((reads[i].flags & DB_BEST) >= allflag && reads[i].rlen >= cutoff)
{ memmove(anno+j,anno+r,size);
j += size;
}
memmove(anno+j,anno+r,size);
}
else if (size == 4)
{ int ai;
anno4 = (int *) (record->anno);
j = anno4[0] = 0;
for (i = 0; i < db->nreads; i++)
if ((reads[i].flags & DB_BEST) >= allflag && reads[i].rlen >= cutoff)
{ ai = anno4[i];
anno4[j+1] = anno4[j] + (anno4[i+1]-ai);
memmove(data+anno4[j],data+ai,anno4[i+1]-ai);
j += 1;
}
record->data = Realloc(record->data,anno4[j],NULL);
}
else // size == 8
{ int64 ai;
anno8 = (int64 *) (record->anno);
j = anno8[0] = 0;
for (i = 0; i < db->nreads; i++)
if ((reads[i].flags & DB_BEST) >= allflag && reads[i].rlen >= cutoff)
{ ai = anno8[i];
anno8[j+1] = anno8[j] + (anno8[i+1]-ai);
memmove(data+anno8[j],data+ai,anno8[i+1]-ai);
j += 1;
}
record->data = Realloc(record->data,anno8[j],NULL);
}
record->anno = Realloc(record->anno,record->size*(j+1),NULL);
}
totlen = maxlen = 0;
for (j = i = 0; i < nreads; i++)
{ r = reads[i].rlen;
if ((reads[i].flags & DB_BEST) >= allflag && r >= cutoff)
{ totlen += r;
if (r > maxlen)
maxlen = r;
reads[j++] = reads[i];
}
}
db->totlen = totlen;
db->maxlen = maxlen;
db->nreads = j;
db->trimmed = 1;
if (j < nreads)
{ db->reads = Realloc(reads-1,sizeof(HITS_READ)*(j+2),NULL);
db->reads += 1;
}
}
// The DB has already been trimmed, but a track over the untrimmed DB needs to be loaded.
// Trim the track by rereading the untrimmed DB index from the file system.
static int Late_Track_Trim(HITS_DB *db, HITS_TRACK *track, int ispart)
{ int i, j, r;
int allflag, cutoff;
int ureads;
char *root;
HITS_READ read;
FILE *indx;
if (!db->trimmed) return (0);
if (db->cutoff <= 0 && (db->allarr & DB_ALL) != 0) return (0);
cutoff = db->cutoff;
if ((db->allarr & DB_ALL) != 0)
allflag = 0;
else
allflag = DB_BEST;
root = rindex(db->path,'/') + 2;
indx = Fopen(Catenate(db->path,"","",".idx"),"r");
fseeko(indx,sizeof(HITS_DB) + sizeof(HITS_READ)*db->ufirst,SEEK_SET);
if (ispart)
ureads = ((int *) (db->reads))[-1];
else
ureads = db->ureads;
if (strcmp(track->name,".@qvs") == 0)
{ EPRINTF(EPLACE,"%s: Cannot load QV track after trimming\n",Prog_Name);
fclose(indx);
EXIT(1);
}
{ int *anno4, size;
int64 *anno8;
char *anno, *data;
size = track->size;
data = (char *) track->data;
if (data == NULL)
{ anno = (char *) track->anno;
j = r = 0;
for (i = r = 0; i < ureads; i++, r += size)
{ if (fread(&read,sizeof(HITS_READ),1,indx) != 1)
{ EPRINTF(EPLACE,"%s: Index file (.idx) of %s is junk\n",Prog_Name,root);
fclose(indx);
EXIT(1);
}
if ((read.flags & DB_BEST) >= allflag && read.rlen >= cutoff)
{ memmove(anno+j,anno+r,size);
j += size;
}
r += size;
}
memmove(anno+j,anno+r,size);
}
else if (size == 4)
{ int ai;
anno4 = (int *) (track->anno);
j = anno4[0] = 0;
for (i = 0; i < ureads; i++)
{ if (fread(&read,sizeof(HITS_READ),1,indx) != 1)
{ EPRINTF(EPLACE,"%s: Index file (.idx) of %s is junk\n",Prog_Name,root);
fclose(indx);
EXIT(1);
}
if ((read.flags & DB_BEST) >= allflag && read.rlen >= cutoff)
{ ai = anno4[i];
anno4[j+1] = anno4[j] + (anno4[i+1]-ai);
memmove(data+anno4[j],data+ai,anno4[i+1]-ai);
j += 1;
}
}
track->data = Realloc(track->data,anno4[j],NULL);
}
else // size == 8
{ int64 ai;
anno8 = (int64 *) (track->anno);
j = anno8[0] = 0;
for (i = 0; i < ureads; i++)
{ if (fread(&read,sizeof(HITS_READ),1,indx) != 1)
{ EPRINTF(EPLACE,"%s: Index file (.idx) of %s is junk\n",Prog_Name,root);
fclose(indx);
EXIT(1);
}
if ((read.flags & DB_BEST) >= allflag && read.rlen >= cutoff)
{ ai = anno8[i];
anno8[j+1] = anno8[j] + (anno8[i+1]-ai);
memmove(data+anno8[j],data+ai,anno8[i+1]-ai);
j += 1;
}
}
track->data = Realloc(track->data,anno8[j],NULL);
}
track->anno = Realloc(track->anno,track->size*(j+1),NULL);
}
fclose(indx);
return (0);
}
// Shut down an open 'db' by freeing all associated space, including tracks and QV structures,
// and any open file pointers. The record pointed at by db however remains (the user
// supplied it and so should free it).
void Close_DB(HITS_DB *db)
{ HITS_TRACK *t, *p;
if (db->loaded)
free(((char *) (db->bases)) - 1);
else if (db->bases != NULL)
fclose((FILE *) db->bases);
if (db->reads != NULL)
free(db->reads-1);
free(db->path);
Close_QVs(db);
for (t = db->tracks; t != NULL; t = p)
{ p = t->next;
free(t->anno);
free(t->data);
free(t);
}
}
// Return the size in bytes of the memory occupied by a given DB
int64 sizeof_DB(HITS_DB *db)
{ int64 s;
HITS_TRACK *t;
s = sizeof(HITS_DB)
+ sizeof(HITS_READ)*(db->nreads+2)
+ strlen(db->path)+1
+ (db->totlen+db->nreads+4);
t = db->tracks;
if (t != NULL && strcmp(t->name,".@qvs") == 0)
{ HITS_QV *q = (HITS_QV *) t;
s += sizeof(HITS_QV)
+ sizeof(uint16) * db->nreads
+ q->ncodes * sizeof(QVcoding)
+ 6;
t = t->next;
}
for (; t != NULL; t = t->next)
{ s += sizeof(HITS_TRACK)
+ strlen(t->name)+1
+ t->size * (db->nreads+1);
if (t->data != NULL)
{ if (t->size == 8)
s += sizeof(int)*((int64 *) t->anno)[db->nreads];
else // t->size == 4
s += sizeof(int)*((int *) t->anno)[db->nreads];
}
}
return (s);
}
/*******************************************************************************************
*
* QV LOAD & CLOSE ROUTINES
*
********************************************************************************************/
HITS_DB *Active_DB = NULL; // Last db/qv used by "Load_QVentry"
HITS_QV *Active_QV; // Becomes invalid after closing
int Load_QVs(HITS_DB *db)
{ FILE *quiva, *istub, *indx;
char *root;
uint16 *table;
HITS_QV *qvtrk;
QVcoding *coding, *nx;
int ncodes = 0;
if (db->tracks != NULL && strcmp(db->tracks->name,".@qvs") == 0)
return (0);
if (db->trimmed)
{ EPRINTF(EPLACE,"%s: Cannot load QVs after trimming the DB\n",Prog_Name);
EXIT(1);
}
if (db->reads[db->nreads-1].coff < 0)
{ if (db->part > 0)
{ EPRINTF(EPLACE,"%s: All QVs for this block have not been added to the DB!\n",Prog_Name);
EXIT(1);
}
else
{ EPRINTF(EPLACE,"%s: All QVs for this DB have not been added!\n",Prog_Name);
EXIT(1);
}
}
// Open .qvs, .idx, and .db files
quiva = Fopen(Catenate(db->path,"","",".qvs"),"r");
if (quiva == NULL)
return (-1);
istub = NULL;
indx = NULL;
table = NULL;
coding = NULL;
qvtrk = NULL;
root = rindex(db->path,'/');
if (root[1] == '.')
{ *root = '\0';
istub = Fopen(Catenate(db->path,"/",root+2,".db"),"r");
*root = '/';
}
else
istub = Fopen(Catenate(db->path,"","",".db"),"r");
if (istub == NULL)
goto error;
{ int first, last, nfiles;
char prolog[MAX_NAME], fname[MAX_NAME];
int i, j;
if (fscanf(istub,DB_NFILE,&nfiles) != 1)
{ EPRINTF(EPLACE,"%s: Stub file (.db) of %s is junk\n",Prog_Name,root);
goto error;
}
if (db->part > 0)
{ int pfirst, plast;
int fbeg, fend;
int n, k;
FILE *indx;
// Determine first how many and which files span the block (fbeg to fend)
pfirst = db->ufirst;
plast = pfirst + db->nreads;
first = 0;
for (fbeg = 0; fbeg < nfiles; fbeg++)
{ if (fscanf(istub,DB_FDATA,&last,fname,prolog) != 3)
{ EPRINTF(EPLACE,"%s: Stub file (.db) of %s is junk\n",Prog_Name,root);
goto error;
}
if (last > pfirst)
break;
first = last;
}
for (fend = fbeg+1; fend <= nfiles; fend++)
{ if (last >= plast)
break;
if (fscanf(istub,DB_FDATA,&last,fname,prolog) != 3)
{ EPRINTF(EPLACE,"%s: Stub file (.db) of %s is junk\n",Prog_Name,root);
goto error;
}
first = last;
}
indx = Fopen(Catenate(db->path,"","",".idx"),"r");
ncodes = fend-fbeg;
coding = (QVcoding *) Malloc(sizeof(QVcoding)*ncodes,"Allocating coding schemes");
table = (uint16 *) Malloc(sizeof(uint16)*db->nreads,"Allocating QV table indices");
if (indx == NULL || coding == NULL || table == NULL)
{ ncodes = 0;
goto error;
}
// Carefully get the first coding scheme (its offset is most likely in a HITS_RECORD
// in .idx that is *not* in memory). Get all the other coding schemes normally and
// assign the tables # for each read in the block in "tables".
rewind(istub);
(void) fscanf(istub,DB_NFILE,&nfiles);
first = 0;
for (n = 0; n < fbeg; n++)
{ (void) fscanf(istub,DB_FDATA,&last,fname,prolog);
first = last;
}
for (n = fbeg; n < fend; n++)
{ (void) fscanf(istub,DB_FDATA,&last,fname,prolog);
i = n-fbeg;
if (first < pfirst)
{ HITS_READ read;
fseeko(indx,sizeof(HITS_DB) + sizeof(HITS_READ)*first,SEEK_SET);
if (fread(&read,sizeof(HITS_READ),1,indx) != 1)
{ EPRINTF(EPLACE,"%s: Index file (.idx) of %s is junk\n",Prog_Name,root);
ncodes = i;
goto error;
}
fseeko(quiva,read.coff,SEEK_SET);
nx = Read_QVcoding(quiva);
if (nx == NULL)
{ ncodes = i;
goto error;
}
coding[i] = *nx;
}
else
{ fseeko(quiva,db->reads[first-pfirst].coff,SEEK_SET);
nx = Read_QVcoding(quiva);
if (nx == NULL)
{ ncodes = i;
goto error;
}
coding[i] = *nx;