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DB.c
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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. Eventually will also
* support compressed quality information.
*
* 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;
void *Malloc(int64 size, char *mesg)
{ void *p;
if ((p = malloc(size)) == NULL)
{ if (mesg == NULL)
fprintf(stderr,"%s: Out of memory\n",Prog_Name);
else
fprintf(stderr,"%s: Out of memory (%s)\n",Prog_Name,mesg);
}
return (p);
}
void *Realloc(void *p, int64 size, char *mesg)
{ if ((p = realloc(p,size)) == NULL)
{ if (mesg == NULL)
fprintf(stderr,"%s: Out of memory\n",Prog_Name);
else
fprintf(stderr,"%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)
fprintf(stderr,"%s: Out of memory\n",Prog_Name);
else
fprintf(stderr,"%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)
fprintf(stderr,"%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) - 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) + strlen(sep) + strlen(root) + strlen(suffix);
if (len > max)
{ max = 1.2*len + 100;
if ((cat = (char *) realloc(cat,max+1)) == NULL)
{ fprintf(stderr,"%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) + strlen(right) + 40;
if (len > max)
{ max = 1.2*len + 100;
if ((suffix = (char *) realloc(suffix,max+1)) == NULL)
{ fprintf(stderr,"%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)
fprintf(out,"%*lld%c%03lld",width-4,num/1000ll,COMMA,num%1000ll);
else if (num < 1000000000ll)
fprintf(out,"%*lld%c%03lld%c%03lld",width-8,num/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);
}
}
/*******************************************************************************************
*
* 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, 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++ = (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] = ((byte >> 6) & 0x3);
s1[i] = ((byte >> 4) & 0x3);
s2[i] = ((byte >> 2) & 0x3);
s3[i] = (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';
}
// 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;
}
/*******************************************************************************************
*
* DB OPEN, TRIM & CLOSE ROUTINES
*
********************************************************************************************/
// Open the given database "root" into the supplied HITS_DB record "db"
// The index array is allocated and read in, the 'bases' file is open for reading.
int Open_DB(char* path, HITS_DB *db)
{ char *root, *pwd, *bptr, *fptr;
int nreads;
FILE *index, *dbvis;
int status;
int part, cutoff, all;
int ofirst, bfirst, olast;
status = 0;
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;
if (db->cutoff < 0 && part > 0)
{ fprintf(stderr,"%s: DB %s has not yet been partitioned, cannot request a block !\n",
Prog_Name,root);
goto exit;
}
if ((dbvis = Fopen(Catenate(pwd,"/",root,".db"),"r")) == NULL)
{ status = 1;
goto exit;
}
if ((index = Fopen(Catenate(pwd,PATHSEP,root,".idx"),"r")) == NULL)
{ status = 1;
goto exit1;
}
fread(db,sizeof(HITS_DB),1,index);
nreads = db->oreads;
{ int p, nblocks, nfiles, blast;
int64 size;
char buffer[2*MAX_NAME+100];
nblocks = 0;
fscanf(dbvis,DB_NFILE,&nfiles);
for (p = 0; p < nfiles; p++)
fgets(buffer,2*MAX_NAME+100,dbvis);
if (fscanf(dbvis,DB_NBLOCK,&nblocks) != 1 || part > nblocks)
if (part > 0)
{ status = 1;
if (nblocks == 0)
fprintf(stderr,"%s: DB has not been partitioned\n",Prog_Name);
else
fprintf(stderr,"%s: DB has only %d blocks\n",Prog_Name,nblocks);
goto exit2;
}
else
{ cutoff = 0;
all = 1;
}
else
fscanf(dbvis,DB_PARAMS,&size,&cutoff,&all);
if (part > 0)
{ for (p = 1; p <= part; p++)
fscanf(dbvis,DB_BDATA,&ofirst,&bfirst);
fscanf(dbvis,DB_BDATA,&olast,&blast);
}
else
{ ofirst = bfirst = 0;
olast = nreads;
}
}
db->trimmed = 0;
db->tracks = NULL;
db->part = part;
db->cutoff = cutoff;
db->all = all;
db->ofirst = ofirst;
db->bfirst = bfirst;
if (part <= 0)
{ db->reads = (HITS_READ *) Malloc(sizeof(HITS_READ)*(nreads+1),"Allocating Open_DB index");
fread(db->reads,sizeof(HITS_READ),nreads,index);
}
else
{ HITS_READ *reads;
int i, r, maxlen;
int64 totlen;
nreads = olast-ofirst;
reads = (HITS_READ *) Malloc(sizeof(HITS_READ)*(nreads+1),"Allocating Open_DB index");
fseeko(index,sizeof(HITS_READ)*ofirst,SEEK_CUR);
fread(reads,sizeof(HITS_READ),nreads,index);
for (i = 0; i < nreads; i++)
{ r = reads[i].end - reads[i].beg;
totlen += r;
if (r > maxlen)
maxlen = r;
}
db->maxlen = maxlen;
db->totlen = totlen;
db->reads = reads;
}
db->nreads = nreads;
db->path = Strdup(Catenate(pwd,PATHSEP,root,""),"Allocating Open_DB path");
db->bases = NULL;
db->loaded = 0;
exit2:
fclose(index);
exit1:
fclose(dbvis);
exit:
if (bptr != NULL)
*bptr = '.';
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->all) return;
cutoff = db->cutoff;
if (db->all)
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].end - reads[i].beg >= cutoff)
table[j++] = table[i];
}
else
{ int *anno4, size;
int64 *anno8;
void *anno, *data;
size = record->size;
data = record->data;
if (data == NULL)
{ anno = record->anno;
j = 0;
for (i = r = 0; i < db->nreads; i++, r += size)
if ((reads[i].flags & DB_BEST) >= allflag && reads[i].end - reads[i].beg >= 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].end - reads[i].beg >= 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].end - reads[i].beg >= 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].end - reads[i].beg;
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)
reads = Realloc(reads,sizeof(HITS_READ)*(j+1),NULL);
}
// 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);
free(db->reads);
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);
}
}
/*******************************************************************************************
*
* QV LOAD & CLOSE ROUTINES
*
********************************************************************************************/
HITS_DB *Active_DB = NULL; // Last db/qv used by "Load_QVentry"
HITS_QV *Active_QV; // Becomes invalid after closing
void Load_QVs(HITS_DB *db)
{ FILE *quiva, *istub, *indx;
uint16 *table;
QVcoding *coding;
HITS_QV *qvtrk;
if (db->tracks != NULL && strcmp(db->tracks->name,".@qvs") == 0)
return;
if (db->trimmed)
{ fprintf(stderr,"%s: Cannot load QVs after trimming the DB\n",Prog_Name);
exit (1);
}
if (db->reads[db->nreads-1].coff == 0)
{ fprintf(stderr,"%s: The requested QVs have not been added to the DB!\n",Prog_Name);
exit (1);
}
// Open .qvs, .idx, and .db files
quiva = Fopen(Catenate(db->path,"","",".qvs"),"r");
if (quiva == NULL)
return;
if (db->part > 0)
{ indx = Fopen(Catenate(db->path,"","",".idx"),"r");
if (indx == NULL)
exit (1);
}
{ char *x;
x = rindex(db->path,'/');
*x = '\0';
istub = Fopen(Catenate(db->path,"/",x+2,".db"),"r");
if (istub == NULL)
exit (1);
*x = '/';
}
{ int first, last, nfiles, ncodes;
char prolog[MAX_NAME], fname[MAX_NAME];
int i, j;
table = (uint16 *) Malloc(sizeof(uint16)*db->nreads,"Allocating QV table indices");
fscanf(istub,DB_NFILE,&nfiles);
if (db->part > 0)
{ int pfirst, plast;
int fbeg, fend;
int n, k;
// Determine first how many and which files span the block (fbeg to fend)
pfirst = db->ofirst;
plast = pfirst + db->nreads;
first = 0;
for (fbeg = 0; fbeg < nfiles; fbeg++)
{ fscanf(istub,DB_FDATA,&last,fname,prolog);
if (last > pfirst)
break;
first = last;
}
for (fend = fbeg+1; fend <= nfiles; fend++)
{ if (last >= plast)
break;
fscanf(istub,DB_FDATA,&last,fname,prolog);
first = last;
}
ncodes = fend-fbeg;
coding = (QVcoding *) Malloc(sizeof(QVcoding)*ncodes,"Allocating coding schemes");
// 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);
fscanf(istub,DB_NFILE,&nfiles);
first = 0;
for (n = 0; n < fbeg; n++)
{ fscanf(istub,DB_FDATA,&last,fname,prolog);
first = last;
}
for (n = fbeg; n < fend; n++)
{ 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);
fread(&read,sizeof(HITS_READ),1,indx);
fseeko(quiva,read.coff,SEEK_SET);
coding[i] = *Read_QVcoding(quiva);
}
else
{ fseeko(quiva,db->reads[first-pfirst].coff,SEEK_SET);
coding[i] = *Read_QVcoding(quiva);
db->reads[first-pfirst].coff = ftello(quiva);
}
j = first-pfirst;
if (j < 0)
j = 0;
k = last-pfirst;
if (k > db->nreads)
k = db->nreads;
while (j < k)
table[j++] = i;
first = last;
}
fclose(indx);
}
else
{ // Load in coding scheme for each file, adjust .coff of first read in the file, and
// record which table each read uses
ncodes = nfiles;
coding = (QVcoding *) Malloc(sizeof(QVcoding)*nfiles,"Allocating coding schemes");
first = 0;
for (i = 0; i < nfiles; i++)
{ fscanf(istub,DB_FDATA,&last,fname,prolog);
fseeko(quiva,db->reads[first].coff,SEEK_SET);
coding[i] = *Read_QVcoding(quiva);
db->reads[first].coff = ftello(quiva);
for (j = first; j < last; j++)
table[j] = i;
first = last;
}
}
// Allocate and fill in the HITS_QV record and add it to the front of the
// track list
qvtrk = (HITS_QV *) Malloc(sizeof(HITS_QV),"Allocating QV pseudo-track");
qvtrk->next = db->tracks;
db->tracks = (HITS_TRACK *) qvtrk;
qvtrk->name = Strdup(".@qvs","Allocating QV pseudo-track name");
qvtrk->ncodes = ncodes;
qvtrk->table = table;
qvtrk->coding = coding;
qvtrk->quiva = quiva;
}
fclose(istub);
fclose(indx);
}
// Close the QV stream, free the QV pseudo track and all associated memory
void Close_QVs(HITS_DB *db)
{ HITS_TRACK *track;
HITS_QV *qvtrk;
int i;
Active_DB = NULL;
track = db->tracks;
if (track != NULL && strcmp(track->name,".@qvs") == 0)
{ qvtrk = (HITS_QV *) track;
for (i = 0; i < qvtrk->ncodes; i++)
Free_QVcoding(qvtrk->coding+i);
free(qvtrk->coding);
free(qvtrk->table);
fclose(qvtrk->quiva);
db->tracks = track->next;
free(track);
}
return;
}
/*******************************************************************************************
*
* TRACK LOAD & CLOSE ROUTINES
*
********************************************************************************************/
// If track is not already in the db's track list, then allocate all the storage for it,
// read it in from the appropriate file, add it to the track list, and return a pointer
// to the newly created HITS_TRACK record. If the track does not exist or cannot be
// opened for some reason, then NULL is returned.
HITS_TRACK *Load_Track(HITS_DB *db, char *track)
{ FILE *afile, *dfile;
int tracklen, size;
int nreads;
void *anno;
void *data;
HITS_TRACK *record;
if (track[0] == '.')
{ fprintf(stderr,"Track names cannot begin with a .\n");
exit (1);
}
for (record = db->tracks; record != NULL; record = record->next)
if (strcmp(record->name,track) == 0)
return (record);
afile = Fopen(Catenate(db->path,".",track,".anno"),"r");
if (afile == NULL)
return (NULL);
dfile = Fopen(Catenate(db->path,".",track,".data"),"r");
fread(&tracklen,sizeof(int),1,afile);
fread(&size,sizeof(int),1,afile);
if (db->trimmed)
{ if (tracklen != db->breads)
{ fprintf(stderr,"%s: Track %s not same size as database !\n",Prog_Name,track);
exit (1);
}
if (db->part > 0)
fseeko(afile,size*db->bfirst,SEEK_CUR);
}
else
{ if (tracklen != db->oreads)
{ fprintf(stderr,"%s: Track %s not same size as database !\n",Prog_Name,track);
exit (1);
}
if (db->part > 0)
fseeko(afile,size*db->ofirst,SEEK_CUR);
}
nreads = db->nreads;
anno = (void *) Malloc(size*(nreads+1),"Allocating Track Anno Vector");
fread(anno,size,nreads+1,afile);
if (dfile != NULL)
{ int64 *anno8, off8, dlen;
int *anno4, off4;
int i;
if (size == 4)
{ anno4 = (int *) anno;
off4 = anno4[0];
if (off4 != 0)
{ for (i = 0; i <= nreads; i++)
anno4[i] -= off4;
fseeko(dfile,off4,SEEK_SET);
}
dlen = anno4[nreads];
data = (void *) Malloc(dlen,"Allocating Track Data Vector");
}
else
{ anno8 = (int64 *) anno;
off8 = anno8[0];
if (off8 != 0)
{ for (i = 0; i <= nreads; i++)
anno8[i] -= off8;
fseeko(dfile,off8,SEEK_SET);
}
dlen = anno8[nreads];
data = (void *) Malloc(dlen,"Allocating Track Data Vector");
}
fread(data,dlen,1,dfile);
fclose(dfile);
}
else
data = NULL;
fclose(afile);
record = (HITS_TRACK *) Malloc(sizeof(HITS_TRACK),"Allocating Track Record");
record->name = Strdup(track,"Allocating Track Name");
record->data = data;
record->anno = anno;
record->size = size;
if (db->tracks != NULL && strcmp(db->tracks->name,".@qvs") == 0)
{ record->next = db->tracks->next;
db->tracks->next = record;
}
else
{ record->next = db->tracks;
db->tracks = record;
}
return (record);
}
void Close_Track(HITS_DB *db, char *track)
{ HITS_TRACK *record, *prev;
prev = NULL;
for (record = db->tracks; record != NULL; record = record->next)
{ if (strcmp(record->name,track) == 0)
{ free(record->anno);
free(record->data);
free(record->name);
if (prev == NULL)
db->tracks = record->next;
else
prev->next = record->next;
free(record);
return;
}
prev = record;
}
return;
}
/*******************************************************************************************
*
* READ BUFFER ALLOCATION AND READ ACCESS
*
********************************************************************************************/
// Allocate and return a buffer big enough for the largest read in 'db', leaving room
// for an initial delimiter character
char *New_Read_Buffer(HITS_DB *db)
{ char *read;
read = (char *) Malloc(db->maxlen+4,"Allocating New Read Buffer");
if (read == NULL)
exit (1);
return (read+1);
}
// Load into 'read' the i'th read in 'db'. As an upper case ASCII string if ascii is 2, as a
// lower-case ASCII string is ascii is 1, and as a numeric string over 0(A), 1(C), 2(G), and
// 3(T) otherwise.
//
// **NB**, the byte before read will be set to a delimiter character!
void Load_Read(HITS_DB *db, int i, char *read, int ascii)
{ FILE *bases = (FILE *) db->bases;
int64 off;
int len;
HITS_READ *r = db->reads;
if (bases == NULL)
{ db->bases = (void *) (bases = Fopen(Catenate(db->path,"","",".bps"),"r"));
if (bases == NULL)
exit (1);
}
if (i >= db->nreads)
{ fprintf(stderr,"%s: Index out of bounds (Load_Read)\n",Prog_Name);
exit (1);
}
off = r[i].boff;
len = r[i].end - r[i].beg;
if (ftello(bases) != off)
fseeko(bases,off,SEEK_SET);
fread(read,1,COMPRESSED_LEN(len),bases);
Uncompress_Read(len,read);
if (ascii == 1)
{ Lower_Read(read);
read[-1] = '\0';
}
else if (ascii == 2)
{ Upper_Read(read);
read[-1] = '\0';
}
else
read[-1] = 4;
}
/*******************************************************************************************
*
* QV BUFFER ALLOCATION QV READ ACCESS
*
********************************************************************************************/
// Allocate and return a buffer of 5 vectors big enough for the largest read in 'db'
char **New_QV_Buffer(HITS_DB *db)
{ char **entry;
char *qvs;
int i;
qvs = (char *) Malloc(db->maxlen*5,"Allocating New QV Buffer");
entry = (char **) Malloc(sizeof(char *)*5,"Allocating New QV Buffer");
if (qvs == NULL || entry == NULL)
exit (1);
for (i = 0; i < 5; i++)
entry[i] = qvs + i*db->maxlen;
return (entry);
}
// Load into entry the QV streams for the i'th read from db. The parameter ascii applies to
// the DELTAG stream as described for Load_Read.
void Load_QVentry(HITS_DB *db, int i, char **entry, int ascii)
{ HITS_READ *reads;
FILE *quiva;
int rlen;
if (db != Active_DB)
{ if (db->tracks == NULL || strcmp(db->tracks->name,".@qvs") != 0)
{ fprintf(stderr,"%s: QV's are not loaded!\n",Prog_Name);
exit (1);
}
Active_QV = (HITS_QV *) db->tracks;
Active_DB = db;
}
if (i >= db->nreads)
{ fprintf(stderr,"%s: Index out of bounds (Load_QVentry)\n",Prog_Name);
exit (1);
}
reads = db->reads;
quiva = Active_QV->quiva;
rlen = reads[i].end-reads[i].beg;