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GDB.c
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/*******************************************************************************************
*
* Genome data base module. Auxiliary routines to open and manipulate a data base for
* which the sequence and genome information are separated into two separate files, and the
* sequence is compressed into 2-bits for each base. Derived from the daligner codes.
*
* Author : Gene Myers
* Date : May 2024
*
********************************************************************************************/
/* Last edited: Jul 25 19:12 2024 (rd109) */
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <strings.h>
#include <ctype.h>
#include <unistd.h>
#include <dirent.h>
#include <limits.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <zlib.h>
#include "gene_core.h"
#include "GDB.h"
/*******************************************************************************************
*
* GENERAL UTILITIES
*
********************************************************************************************/
static char *gdbSchemaText =
"1 3 def 1 0 schema for genome skeleton\n"
".\n"
"P 3 gdb GDB\n"
"D f 4 4 REAL 4 REAL 4 REAL 4 REAL global: base frequency vector\n"
"O S 1 6 STRING id for a scaffold\n"
"D G 1 3 INT gap of given length\n"
"D C 1 3 INT contig of given length\n"
;
static OneSchema *make_GDB_Schema()
{ return (oneSchemaCreateFromText(gdbSchemaText)); }
static char *seqSchemaText =
"1 3 def 1 0 schema for aln and FastGA\n"
".\n"
"P 3 seq SEQUENCE\n"
"O s 2 3 INT 6 STRING length and id for group of sequences = a scaffold\n"
"G S scaffolds (s) group sequence objects (S)\n"
"D n 2 4 CHAR 3 INT non-acgt chars outside (between) sequences within scaffold\n"
"O S 1 3 DNA sequence\n"
"D I 1 6 STRING identifier of sequence\n"
;
OneSchema *make_Seq_Schema()
{ return (oneSchemaCreateFromText(seqSchemaText)); }
static char *ERROR = "error"; // Error return for subroutines returning char *
static char *MyCatenate(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;
cat = (char *) realloc(cat,max+1);
if (cat == NULL)
{ EPRINTF(EPLACE,"%s: Out of memory (Cating 4 strings)\n",Prog_Name);
return (NULL);
}
}
sprintf(cat,"%s%s%s%s",path,sep,root,suffix);
return (cat);
}
/*******************************************************************************************
*
* FILE NAME COMPLETION ROUTINE
*
********************************************************************************************/
static char *find_1seq(char *path, char *root)
{ DIR *dirp;
struct dirent *dp;
FILE *f;
int rlen, one, len;
char *n, *extn, *name, type[4];
dirp = opendir(path);
if (dirp == NULL)
{ EPRINTF(EPLACE,"%s: Cannot open directory %s\n",Prog_Name,path);
return (ERROR);
}
extn = NULL;
rlen = strlen(root);
while ((dp = readdir(dirp)) != NULL)
{ name = dp->d_name;
if (strncmp(root,name,rlen) != 0)
continue;
if (name[rlen] != '.')
continue;
n = MyCatenate(path,"/",name,"");
if (n == NULL)
return (ERROR);
f = fopen(n,"r");
if (f == NULL)
continue;
if (fscanf(f," %d %d",&one,&len) != 2)
goto escape;
if (one != 1 || len != 3)
goto escape;
if (fscanf(f," %s",type) != 1)
goto escape;
if (strcmp(type,"seq") != 0)
goto escape;
fclose(f);
if (extn != NULL)
{ EPRINTF(EPLACE,"%s: Two 1-code sequence files with root %s found\n",Prog_Name,root);
return (ERROR);
}
extn = Strdup(name+rlen,"Allocating extension");
if (extn == NULL)
return (ERROR);
continue;
escape:
fclose(f);
}
return (extn);
}
// Interpret source & target arguments returning complete path + extension names of
// the source and target in spath & tpath. Returns the type of source.
// If target == NULL then tpath has the same path & root as spath
// Else If target is a directory then tpath has the same path as target
// Else tpath has the same path and root as target.
// If no_gdb then the source cannot be a gdb.
// In interactive mode returns a negative number if an error occurs.
// The user is responsible for freeing both tpath and spath.
int Get_GDB_Paths(char *source, char *target, char **spath, char **tpath, int no_gdb)
{ char *SROOT, *SPATH;
char *TROOT, *TPATH;
char *SEXTN, *TEXTN;
char *suffix[10] = { "", ".fa", ".fna", ".fasta",
".gz", ".fa.gz", ".fna.gz", ".fasta.gz", ".gdb", ".1gdb" };
int suflen[10] = { 0, 3, 4, 6, 3, 6, 7, 9, 4, 5 };
char *sdir, *tdir, *sdot, *tdot;
OneSchema *schema;
char *p, *e;
int i, tmax;
FILE *input;
struct stat status;
sdir = NULL;
sdot = NULL;
tdir = NULL;
tdot = NULL;
if (no_gdb)
tmax = 7;
else
tmax = 9;
SPATH = source;
p = rindex(SPATH,'/');
if (p == NULL)
{ SROOT = SPATH;
SPATH = ".";
}
else
{ *p = '\0';
sdir = p;
SROOT = p+1;
}
schema = make_Seq_Schema();
if (schema == NULL)
{ EPRINTF(EPLACE,"%s: Failed to create onecode schema\n",Prog_Name);
goto error;
}
for (i = tmax; i >= 0; i--)
{ input = fopen(MyCatenate(SPATH,"/",SROOT,suffix[i]),"r");
if (input != NULL)
break;
}
if (i < 0)
{ SEXTN = find_1seq(SPATH,SROOT);
if (SEXTN == ERROR)
goto error;
else if (SEXTN == NULL)
{ EPRINTF(EPLACE,"%s: Could not find %s or a fasta or 1-code extension there of\n",
Prog_Name,SROOT);
oneSchemaDestroy(schema);
goto error;
}
}
else
{ SEXTN = suffix[i];
fclose(input);
}
if (i == 4)
{ e = SROOT + strlen(SROOT);
for (i = 1; i < 4; i++)
if (strcmp(e-suflen[i],suffix[i]) == 0)
break;
if (i >= 4)
{ EPRINTF(EPLACE,"%s: Could not find valid extension of %s\n",Prog_Name,SROOT);
oneSchemaDestroy(schema);
EXIT(-1);
}
e[-suflen[i]] = '\0';
sdot = e-suflen[i];
i += 4;
SEXTN = suffix[i];
}
else if (i == 0)
{ e = SROOT + strlen(SROOT);
for (i = tmax; i >= 1; i--)
if (strcmp(e-suflen[i],suffix[i]) == 0 && i != 4)
break;
if (i > 0)
{ e[-suflen[i]] = '\0';
sdot = e-suflen[i];
SEXTN = suffix[i];
}
else
{ OneFile *of;
of = oneFileOpenRead(MyCatenate(SPATH,"/",SROOT,""),schema,"seq",1);
if (of == NULL)
{ EPRINTF(EPLACE,"%s: Could not find valid extension of %s\n",Prog_Name,SROOT);
oneSchemaDestroy(schema);
EXIT(-1);
}
oneFileClose(of);
SEXTN = "";
i = -1;
}
}
oneSchemaDestroy(schema);
*spath = Strdup(MyCatenate(SPATH,"/",SROOT,SEXTN),"Allocating source name");
if (*spath == NULL)
goto error;
if (i >= 8)
{ *tpath = Strdup(*spath,"Allocating target name");
if (*tpath == NULL)
{ free(*spath);
goto error;
}
if (sdir != NULL) *sdir = '/';
if (sdot != NULL) *sdot = '.';
if (tdir != NULL) *tdir = '/';
if (tdot != NULL) *tdot = '.';
return (IS_GDB);
}
TEXTN = ".1gdb";
if (target == NULL)
{ TPATH = SPATH;
TROOT = SROOT;
}
else // argc == 3
{ TPATH = target;
if (stat(TPATH,&status) >= 0 && (status.st_mode & S_IFMT) == S_IFDIR)
TROOT = SROOT;
else
{ p = rindex(TPATH,'/');
if (p == NULL)
{ TROOT = TPATH;
TPATH = ".";
}
else
{ *p = '\0';
tdir = p;
TROOT = p+1;
}
p = rindex(TROOT,'.');
if (p != NULL)
{ if (strcmp(p+1,"gdb") == 0)
{ *p = '\0';
tdot = p;
TEXTN = ".gdb";
}
else if (strcmp(p+1,"1gdb") == 0)
{ *p = '\0';
tdot = p;
}
}
}
}
*tpath = Strdup(MyCatenate(TPATH,"/",TROOT,TEXTN),"Allocating target name");
if (*tpath == NULL)
{ free(*spath);
goto error;
}
if (sdir != NULL) *sdir = '/';
if (sdot != NULL) *sdot = '.';
if (tdir != NULL) *tdir = '/';
if (tdot != NULL) *tdot = '.';
if (i < 0)
return (IS_ONE);
else if (i < 4)
return (IS_FA);
else
return (IS_FA_GZ);
error:
if (sdir != NULL) *sdir = '/';
if (sdot != NULL) *sdot = '.';
if (tdir != NULL) *tdir = '/';
if (tdot != NULL) *tdot = '.';
EXIT (-1);
}
/*******************************************************************************************
*
* GDB CREATION FROM SOURCE
*
********************************************************************************************/
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, 4, 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, 4, 0,
0, 0, 0, 0, 3, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
};
// Read next line into a buffer and return a pointer to the buffer and set *plen
// the length of the line. NB: replaces '\n' with '\0'.
static char *read_line(void *input, int gzipd, int *plen, int nline, char *spath)
{ static char *buffer;
static int bmax = 0;
int len;
if (bmax == 0)
{ bmax = 500;
buffer = (char *) malloc(bmax);
if (buffer == NULL)
{ EPRINTF(EPLACE,"%s: Out of memory reading %s\n",Prog_Name,spath);
return (ERROR);
}
}
if (gzipd)
{ if (gzgets(input,buffer,bmax) == NULL)
{ if (gzeof(input))
return (NULL);
EPRINTF(EPLACE,"%s: Could not read next line, %d, of file %s\n",Prog_Name,nline,spath);
return (ERROR);
}
}
else
{ if (fgets(buffer,bmax,input) == NULL)
{ if (feof(input))
return (NULL);
EPRINTF(EPLACE,"%s: Could not read next line, %d, of file %s\n",Prog_Name,nline,spath);
return (ERROR);
}
}
len = strlen(buffer);
while (buffer[len-1] != '\n')
{ bmax = ((int) (1.4*bmax)) + 100;
buffer = (char *) realloc(buffer,bmax);
if (buffer == NULL)
{ EPRINTF(EPLACE,"%s: Out of memory reading %s\n",Prog_Name,spath);
return (ERROR);
}
if (gzipd)
{ if (gzgets(input,buffer+len,bmax-len) == NULL)
{ if (gzeof(input))
EPRINTF(EPLACE,"%s: Last line %d of file %s does not end with new-line\n",
Prog_Name,nline,spath);
else
EPRINTF(EPLACE,"%s: Could not read next line, %d, of file %s\n",
Prog_Name,nline,spath);
return (ERROR);
}
}
else
{ if (fgets(buffer+len,bmax-len,input) == NULL)
{ if (feof(input))
EPRINTF(EPLACE,"%s: Last line %d of file %s does not end with new-line\n",
Prog_Name,nline,spath);
else
EPRINTF(EPLACE,"%s: Could not read next line, %d, of file %s\n",
Prog_Name,nline,spath);
return (ERROR);
}
}
len += strlen(buffer+len);
}
buffer[--len] = '\0';
if (plen != NULL)
*plen = len;
return (buffer);
}
FILE **Create_GDB(GDB *gdb, char *spath, int ftype, int bps, char *tpath)
{ GDB_SCAFFOLD *scaffs;
GDB_CONTIG *contigs;
OneProvenance *prov;
char *headers, *seqpath;
int ctgtop, scftop;
int64 hdrtop;
int64 count[4];
FILE *bases;
int64 hdrtot, maxctg, seqtot, boff;
int ncontig, nscaff, nprov;
int len, clen;
int64 spos;
int gzipd, nline;
void *input;
OneSchema *schema;
OneFile *of;
prov = NULL;
input = NULL;
schema = NULL;
of = NULL;
// Establish .bps file if needed
bases = NULL;
if (bps != 0)
{ if (tpath == NULL)
seqpath = Numbered_Suffix("._gdb.",getpid(),".bps");
else
{ char *path = PathTo(tpath);
char *root = Root(tpath,".1gdb");
if (root == NULL || path == NULL)
{ free(path);
free(root);
EXIT (NULL);
}
seqpath = MyCatenate(path,"/.",root,".bps");
free(root);
free(path);
}
if (seqpath == NULL)
EXIT (NULL);
seqpath = strdup(seqpath);
if (seqpath == NULL)
EXIT(NULL);
bases = Fopen(seqpath,"w+");
if (bases == NULL)
{ free(seqpath);
EXIT(NULL);
}
}
else
seqpath = NULL;
// Setup expanding arrays for headers, scaffolds, & contigs
hdrtot = 0;
maxctg = 0;
ncontig = 0;
nscaff = 0;
seqtot = 0;
boff = 0;
count[0] = 0;
count[1] = 0;
count[2] = 0;
count[3] = 0;
hdrtop = 100000;
ctgtop = 5000;
scftop = 1000;
contigs = malloc(ctgtop*sizeof(GDB_CONTIG));
scaffs = malloc(scftop*sizeof(GDB_CONTIG));
headers = malloc(hdrtop);
if (*spath != '/')
gdb->srcpath = strdup(MyCatenate(getcwd(NULL,0),"/",spath,""));
else
gdb->srcpath = strdup(spath);
if (contigs == NULL || scaffs == NULL || headers == NULL || gdb->srcpath == NULL)
{ EPRINTF(EPLACE,"%s: Out of memory creating GDB for %s\n",Prog_Name,spath);
goto error;
}
// Read either 1-file or fasta and accumulate skeleton
if (ftype == IS_ONE)
{ int i, isScaffold;
int byte_cnt[256]; // times byte occurs in compressed sequence
int psize;
char *pstr;
schema = make_Seq_Schema();
if (schema == NULL)
{ EPRINTF(EPLACE,"%s: Failed to create onecode schema (Create_GDB)\n",Prog_Name);
goto error;
}
of = oneFileOpenRead (spath, schema, "seq", 1) ;
if (of == NULL)
{ EPRINTF(EPLACE,"%s: Cannot open %s as a 1-code sequence file (Create_GDB)\n",
Prog_Name,spath);
goto error;
}
for (i = 0; i < 256; i++)
byte_cnt[i] = 0;
nprov = of->info['!']->accum.count;
psize = nprov * sizeof(OneProvenance);
for (i = 0; i < nprov; i++)
psize += strlen(of->provenance[i].program)
+ strlen(of->provenance[i].version)
+ strlen(of->provenance[i].command)
+ strlen(of->provenance[i].date) + 4;
if (psize > 0)
{ prov = malloc(psize);
if (prov == NULL)
goto error;
pstr = (char *) (prov + nprov);
for (i = 0; i < nprov; i++)
{ prov[i].program = pstr;
pstr = stpcpy(pstr,of->provenance[i].program) + 1;
prov[i].version = pstr;
pstr = stpcpy(pstr,of->provenance[i].version) + 1;
prov[i].command = pstr;
pstr = stpcpy(pstr,of->provenance[i].command) + 1;
prov[i].date = pstr;
pstr = stpcpy(pstr,of->provenance[i].date) + 1;
}
}
else
prov = NULL;
// line sequence must be either (I!S)+, or (s(n!(Sn)*Sn!)+, e.g.
// - scaffold files with s (scaffold id) and n (inter-contig N's) and no I lines, or
// - straight sequence files with no s and n lines, and only S lines, allowing I lines
// Ignore N characters in sequences (non-acgt chars within contigs)
if (of->info['s']->given.count > 0 && of->info['I']->given.count == 0)
isScaffold = true;
else if (of->info['s']->given.count == 0 && of->info['n']->given.count == 0)
isScaffold = false;
else
{ EPRINTF(EPLACE,"%s: 1seq file %s has incomplete scaffold properties - can't use it\n",
Prog_Name,spath);
EPRINTF(EPLACE," I.E. #'s' = %lld #'I' = %lld #'n' = %lld\n",
of->info['s']->given.count, of->info['I']->given.count,
of->info['n']->given.count) ;
goto error;
}
spos = 0;
while (oneReadLine(of))
switch (of->lineType)
{ case 's': // scaffold name
if (boff != 0)
{ scaffs[nscaff].ectg = ncontig;
scaffs[nscaff].slen = spos;
nscaff += 1;
}
if (nscaff >= scftop)
{ scftop = 1.2*nscaff + 500;
scaffs = realloc(scaffs,scftop*sizeof(GDB_SCAFFOLD));
if (scaffs == NULL)
{ EPRINTF(EPLACE,"%s: Out of memory creating GDB for %s\n",Prog_Name,spath);
goto error;
}
}
scaffs[nscaff].hoff = hdrtot;
scaffs[nscaff].fctg = ncontig;
spos = 0;
len = oneLen(of);
memcpy(headers+hdrtot,oneString(of),len);
hdrtot += len;
headers[hdrtot++] = '\0';
break;
case 'n': // non-acgt chars outside sequences
spos += oneInt(of,1);
break;
case 'S': // sequence object
len = oneLen(of);
if (ncontig >= ctgtop)
{ ctgtop = 1.2*ncontig + 1000;
contigs = realloc(contigs,ctgtop*sizeof(GDB_CONTIG));
if (contigs == NULL)
{ EPRINTF(EPLACE,"%s: Out of memory creating GDB for %s\n",Prog_Name,spath);
goto error;
}
}
contigs[ncontig].boff = boff;
contigs[ncontig].clen = len;
contigs[ncontig].sbeg = spos;
contigs[ncontig].scaf = nscaff;
ncontig += 1;
clen = COMPRESSED_LEN(len);
uint8* bytes = oneDNA2bit(of);
seqtot += len;
if (len > maxctg)
maxctg = len;
for (i = 0 ; i < clen; i++)
byte_cnt[bytes[i]] += 1;
if (len & 0x3)
count[0] -= (4-(len&0x3));
if (bps)
{ if (fwrite (bytes, clen, 1, bases) != 1)
goto error;
}
boff += clen;
if (isScaffold)
spos += len;
break;
case 'I': // identifier of sequence
if (boff != 0)
{ scaffs[nscaff].ectg = ncontig;
scaffs[nscaff].slen = spos;
nscaff += 1;
}
scaffs[nscaff].hoff = hdrtot;
scaffs[nscaff].fctg = ncontig;
spos = 0;
len = oneLen(of);
memcpy(headers+hdrtot,oneString(of),len);
hdrtot += len;
headers[hdrtot++] = '\0';
break;
}
if (boff != 0)
{ scaffs[nscaff].ectg = ncontig;
scaffs[nscaff].slen = spos;
nscaff += 1;
}
oneFileClose(of);
oneSchemaDestroy(schema);
for (i = 0; i < 256; i++)
{ count[i & 0x3] += byte_cnt[i];
count[(i>>2) & 0x3] += byte_cnt[i];
count[(i>>4) & 0x3] += byte_cnt[i];
count[(i>>6) & 0x3] += byte_cnt[i];
}
}
else // Fasta reader
{ char bpsbuf[1024];
int bpscur;
char *line;
int i, x, m, in;
uint8 byte;
byte = 0;
bpscur = 0;
gzipd = (ftype == IS_FA_GZ);
if (gzipd)
input = gzopen(spath,"r");
else
input = fopen(spath,"r");
if (input == NULL)
{ EPRINTF(EPLACE,"%s: Cannot open %s for reading\n",Prog_Name,spath);
goto error;
}
nprov = 0;
prov = NULL;
// Get the header of the first line. If the file is empty skip.
nline = 1;
line = read_line(input,gzipd,&len,nline,spath);
if (line == ERROR)
goto error;
else if (line == NULL)
{ EPRINTF(EPLACE,"%s: Input %s is empty, terminating!\n",Prog_Name,spath);
goto error;
}
if (line[0] != '>')
{ EPRINTF(EPLACE,"%s: First header in fasta file %s is missing\n",
Prog_Name,spath);
goto error;
}
while (line != NULL)
{ for (i = 1; i < len; i++)
if (!isspace(line[i]))
break;
len -= i;
if (nscaff >= scftop)
{ scftop = 1.2*nscaff + 500;
scaffs = realloc(scaffs,scftop*sizeof(GDB_SCAFFOLD));
if (scaffs == NULL)
{ EPRINTF(EPLACE,"%s: Out of memory creating GDB for %s\n",Prog_Name,spath);
goto error;
}
}
scaffs[nscaff].fctg = ncontig;
scaffs[nscaff].hoff = hdrtot;
if (hdrtot + len + 1 > hdrtop)
{ hdrtop = 1.2*(hdrtot+len+1) + 10000;
headers = realloc(headers,hdrtop);
if (headers == NULL)
{ EPRINTF(EPLACE,"%s: Out of memory creating GDB for %s\n",Prog_Name,spath);
goto error;
}
}
memcpy(headers+hdrtot,line+i,len);
hdrtot += len;
headers[hdrtot++] = '\0';
in = 0;
spos = 0;
clen = 0;
while (1)
{ nline += 1;
line = read_line(input,gzipd,&len,nline,spath);
if (line == ERROR)
goto error;
else if (line == NULL || line[0] == '>')
{ if (in)
{ if (bps)
{ if ((clen & 0x7) != 0)
{ if (bpscur >= 1024)
{ fwrite(bpsbuf,1024,1,bases);
bpscur = 0;
}
bpsbuf[bpscur++] = byte;
boff += 1;
}
clen >>= 1;
}
spos += clen;
contigs[ncontig].clen = clen;
seqtot += clen;
if (clen > maxctg)
maxctg = clen;
ncontig += 1;
if (ncontig >= ctgtop)
{ ctgtop = 1.2*ncontig + 1000;
contigs = realloc(contigs,ctgtop*sizeof(GDB_CONTIG));
if (contigs == NULL)
{ EPRINTF(EPLACE,"%s: Out of memory creating GDB for %s\n",
Prog_Name,spath);
goto error;
}
}
}
break;
}
if (bps)
for (i = 0; i < len; i++)
{ x = number[(int) line[i]];
if (x < 4)
{ if (!in)
{ if (ncontig >= ctgtop)
{ ctgtop = 1.2*ncontig + 1000;
contigs = realloc(contigs,ctgtop*sizeof(GDB_CONTIG));
if (contigs == NULL)
{ EPRINTF(EPLACE,"%s: Out of memory creating GDB for %s\n",
Prog_Name,spath);
goto error;
}
}
contigs[ncontig].sbeg = spos;
contigs[ncontig].boff = boff;
contigs[ncontig].scaf = nscaff;
clen = 0;
in = 1;
}
count[x] += 1;
m = (clen & 0x7);
if (m == 0)
byte = x;
else
{ byte |= (x << m);
if (m == 6)
{ if (bpscur >= 1024)
{ fwrite(bpsbuf,1024,1,bases);
bpscur = 0;
}
bpsbuf[bpscur++] = byte;
boff += 1;
}
}
clen += 2;
}
else
{ if (in)
{ if ((clen & 0x7) != 0)
{ if (bpscur >= 1024)
{ fwrite(bpsbuf,1024,1,bases);
bpscur = 0;
}
bpsbuf[bpscur++] = byte;
boff += 1;
}
clen >>= 1;
spos += clen;
contigs[ncontig].clen = clen;
seqtot += clen;
if (clen > maxctg)
maxctg = clen;
ncontig += 1;
in = 0;
}
spos += 1;
}
}
else
for (i = 0; i < len; i++)
{ x = number[(int) line[i]];
if (x < 4)
{ if (!in)
{ if (ncontig >= ctgtop)
{ ctgtop = 1.2*ncontig + 1000;
contigs = realloc(contigs,ctgtop*sizeof(GDB_CONTIG));
if (contigs == NULL)
{ EPRINTF(EPLACE,"%s: Out of memory creating GDB for %s\n",
Prog_Name,spath);
goto error;
}
}
contigs[ncontig].sbeg = spos;
contigs[ncontig].boff = boff;
contigs[ncontig].scaf = nscaff;
clen = 0;
in = 1;
}
count[x] += 1;
clen += 1;
}
else
{ if (in)
{ spos += clen;
contigs[ncontig].clen = clen;
seqtot += clen;
if (clen > maxctg)
maxctg = clen;
ncontig += 1;
in = 0;
}
spos += 1;
}
}
}
if (spos == 0)
{ EPRINTF(EPLACE,"%s: Missing sequence entry at line %d in file %s\n",
Prog_Name,nline,spath);
goto error;
}
scaffs[nscaff].slen = spos;
scaffs[nscaff].ectg = ncontig;
nscaff += 1;
}
if (bpscur > 0)
fwrite(bpsbuf,bpscur,1,bases);
if (gzipd)
gzclose(input);
else
fclose(input);
}
if (bps > 0)
rewind(bases);
gdb->nprov = nprov;
gdb->prov = prov;
gdb->nscaff = nscaff;
gdb->ncontig = ncontig;
gdb->maxctg = maxctg;
gdb->hdrtot = hdrtot;
gdb->seqtot = seqtot;
gdb->scaffolds = scaffs;
gdb->contigs = contigs;
gdb->headers = headers;
gdb->seqstate = EXTERNAL;
gdb->seqsrc = ftype;
gdb->seqpath = seqpath;
gdb->seqs = bases;
gdb->freq[0] = (1.*count[0])/seqtot;
gdb->freq[1] = (1.*count[1])/seqtot;
gdb->freq[2] = (1.*count[2])/seqtot;
gdb->freq[3] = (1.*count[3])/seqtot;
if (bps <= 1)
{ if (bps == 1 && tpath == NULL)
unlink(seqpath);
return ((FILE **) &gdb->seqs);
}
else
{ FILE **units;
int i;
units = malloc(sizeof(FILE *)*bps);
if (units == NULL)
goto error;
units[0] = bases;
for (i = 1; i < bps; i++)
units[i] = Fopen(seqpath,"r");
if (tpath == NULL)
unlink(seqpath);
return (units);
}
error:
if (of != NULL)
oneFileClose(of);
if (schema != NULL)
oneSchemaDestroy(schema);
if (input != NULL)
{ if (gzipd)
gzclose(input);
else
fclose(input);
}
free(prov);
free(gdb->srcpath);
free(headers);
free(scaffs);
free(contigs);
if (bases != NULL)
fclose(bases);
if (tpath == NULL)
unlink(seqpath);
free(seqpath);
EXIT (NULL);
}
/*******************************************************************************************
*
* GDB OPEN & CLOSE ROUTINES
*
********************************************************************************************/
// Open the given database "path" into the supplied GDB record "gdb".
// Initially the sequence data, if any, stays in .bps file with a FILE pointer to it.
// Return values in interactive mode:
// 0: Open of GDB proceeded without mishap