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Catrack.c
View file @ 466611d6
......@@ -66,44 +66,26 @@ int main(int argc, char *argv[])
// Open DB stub and get number of blocks
{ char *pwd, *root;
int i, plen, index, isdam;
FILE *dstub;
char *dstub_name;
int plen;
DAZZ_STUB *stub;
plen = strlen(argv[1]);
if (strcmp(argv[1]+(plen-3),".dam") == 0)
root = Root(argv[1],".dam");
else
root = Root(argv[1],".db");
pwd = PathTo(argv[1]);
prefix = Strdup(Catenate(pwd,PATHSEP,root,"."),"Allocating track name");
dstub = fopen(Catenate(pwd,"/",root,".db"),"r");
isdam = 0;
if (dstub == NULL)
{ dstub = fopen(Catenate(pwd,"/",root,".dam"),"r");
isdam = 1;
if (dstub == NULL)
{ fprintf(stderr,"%s: Cannot find %s either as a .db or a .dam\n",Prog_Name,root);
exit (1);
if (strcmp(argv[1]+(plen-3),".dam") == 0)
{ root = Root(argv[1],".dam");
stub = Read_DB_Stub(Catenate(pwd,"/",root,".dam"),0);
}
else
{ root = Root(argv[1],".db");
stub = Read_DB_Stub(Catenate(pwd,"/",root,".db"),0);
}
dstub_name = Strdup(Catenate(pwd,"/",root,isdam?".dam":".db"),"Allocating db file name");
if (dstub_name == NULL)
exit (1);
FSCANF(dstub,DB_NFILE,&nblocks)
nblocks = stub->nblocks;
for (i = 0; i < nblocks; i++)
{ char prolog[MAX_NAME], fname[MAX_NAME];
Free_DB_Stub(stub);
FSCANF(dstub,DB_FDATA,&index,fname,prolog)
}
FSCANF(dstub,DB_NBLOCK,&nblocks)
prefix = Strdup(Catenate(pwd,PATHSEP,root,"."),"Allocating track name");
fclose(dstub);
free(dstub_name);
free(pwd);
free(root);
}
......@@ -176,13 +158,15 @@ int main(int argc, char *argv[])
if (afile_name == NULL || dfile_name == NULL)
goto error;
afile = fopen(afile_name,"r");
if (afile == NULL)
{ free(afile_name);
free(dfile_name);
break;
dfile = fopen(Numbered_Suffix(prefix,nfiles+1,Catenate(".",argv[c],".","data")),"r");
}
dfile = fopen(dfile_name,"r");
if (dfile == NULL && errno != ENOENT)
{ fprintf(stderr,"%s: The file %s is corrupted\n",Prog_Name,dfile_name);
{ fprintf(stderr,"%s: Cannot find/open data file %s\n",Prog_Name,dfile_name);
goto error;
}
......@@ -325,6 +309,8 @@ int main(int argc, char *argv[])
nfiles += 1;
if (dfile != NULL)
fclose(dfile);
free(dfile_name);
free(afile_name);
}
if (nfiles == 0)
......@@ -363,10 +349,8 @@ int main(int argc, char *argv[])
}
if (nfiles != nblocks)
{ fprintf(stderr,"%s: Did not catenate all tracks of DB (nfiles %d != nblocks %d)\n",
fprintf(stderr,"%s: Warning: Did not catenate all tracks of DB (nfiles %d != nblocks %d)\n",
Prog_Name,nfiles,nblocks);
goto error;
}
FCLOSE(aout);
if (dout != NULL)
......@@ -376,7 +360,7 @@ int main(int argc, char *argv[])
{ int i;
char *name;
for (i = 1; i <= nblocks ;i++)
for (i = 1; i <= nfiles ;i++)
{ name = Numbered_Suffix(prefix,i,Catenate(".",argv[c],".","anno"));
if (unlink(name) != 0)
fprintf(stderr,"%s: [WARNING] Couldn't delete file %s\n",Prog_Name,name);
......
DB.c
View file @ 466611d6
......@@ -465,6 +465,205 @@ void Change_Read(char *s)
}
/*******************************************************************************************
*
* DB STUB HANDLING ROUTINES
*
********************************************************************************************/
// Read the contents of the DB stub file at "path" and return it encoded in a DAZZ_STUB
// structure. This is allocated by the routine. "path" is assumed to be the complete
// name of the file.
DAZZ_STUB *Read_DB_Stub(char *path, int what)
{ FILE *dbfile;
DAZZ_STUB *stub;
char buf1[MAX_NAME+100];
char buf2[MAX_NAME+100];
int nread;
int i;
int nfiles;
int nblocks;
int64 size;
int all, cutoff;
dbfile = Fopen(path,"r");
if (dbfile == NULL)
EXIT(NULL);
stub = Malloc(sizeof(DAZZ_STUB),"Allocating DB stub record");
if (stub == NULL)
EXIT(NULL);
stub->nreads = NULL;
stub->fname = NULL;
stub->prolog = NULL;
stub->ublocks = NULL;
stub->tblocks = NULL;
if (fscanf(dbfile,DB_NFILE,&nfiles) != 1)
goto stub_trash;
if (what & DB_STUB_NREADS)
{ stub->nreads = (int *) Malloc(sizeof(int)*(nfiles+1),"Allocating DB stub record");
if (stub->nreads == NULL)
goto stub_error;
stub->nreads += 1;
}
if (what & DB_STUB_FILES)
{ stub->fname = (char **) Malloc(sizeof(char *)*(nfiles+1),"Allocating DB stub record");
if (stub->fname == NULL)
goto stub_error;
stub->fname += 1;
stub->nfiles = nfiles;
for (i = 0; i < nfiles; i++)
stub->fname[i] = NULL;
}
if (what & DB_STUB_PROLOGS)
{ stub->prolog = (char **) Malloc(sizeof(char *)*(nfiles+1),"Allocating DB stub record");
if (stub->prolog == NULL)
goto stub_error;
stub->prolog += 1;
for (i = 0; i < nfiles; i++)
stub->prolog[i] = NULL;
}
for (i = 0; i < nfiles; i++)
{ if (fscanf(dbfile,DB_FDATA,&nread,buf1,buf2) != 3)
goto stub_trash;
if (what & DB_STUB_NREADS)
stub->nreads[i] = nread;
if (what & DB_STUB_FILES)
{ stub->fname[i] = Strdup(buf1,"Alloacting DB stub record");
if (stub->fname[i] == NULL)
goto stub_error;
}
if (what & DB_STUB_PROLOGS)
{ stub->prolog[i] = Strdup(buf2,"Alloacting DB stub record");
if (stub->prolog[i] == NULL)
goto stub_error;
}
}
if (fscanf(dbfile,DB_NBLOCK,&nblocks) != 1)
goto stub_trash;
if (fscanf(dbfile,DB_PARAMS,&size,&cutoff,&all) != 3)
goto stub_trash;
if (what & DB_STUB_BLOCKS)
{ stub->ublocks = (int *) Malloc(sizeof(int)*(nblocks+1),"Allocating DB stub record");
stub->tblocks = (int *) Malloc(sizeof(int)*(nblocks+1),"Allocating DB stub record");
if (stub->ublocks == NULL || stub->tblocks == NULL)
goto stub_error;
for (i = 0; i <= nblocks; i++)
if (fscanf(dbfile,DB_BDATA,stub->ublocks+i,stub->tblocks+i) != 2)
goto stub_trash;
}
fclose(dbfile);
stub->nfiles = nfiles;
stub->all = all;
stub->cutoff = cutoff;
stub->bsize = size;
stub->nblocks = nblocks;
return (stub);
stub_trash:
EPRINTF(EPLACE,"%s: Stub file %s is junk\n",Prog_Name,path);
stub_error:
Free_DB_Stub(stub);
EXIT(NULL);
}
// Read the DB stub file "path" and extract the read index range [*first,*last)
// for block n, for the trimmed DB if trim is set, the untrimmed DB otherwise.
int Fetch_Block_Range(char *path, int trim, int n, int *first, int *last)
{ FILE *dbfile;
char buffer[2*MAX_NAME+100];
int nfiles;
int nblocks;
int64 size;
int all, cutoff;
int tfirst, tlast;
int ufirst, ulast;
int i;
dbfile = Fopen(path,"r");
if (dbfile == NULL)
EXIT(1);
if (fscanf(dbfile,DB_NFILE,&nfiles) != 1)
goto stub_error;
for (i = 0; i < nfiles; i++)
if (fgets(buffer,2*MAX_NAME+100,dbfile) == NULL)
goto stub_error;
if (fscanf(dbfile,DB_NBLOCK,&nblocks) != 1)
goto stub_error;
if (n < 0 || n >= nblocks)
{ *first = *last = -1;
return (0);
}
if (fscanf(dbfile,DB_PARAMS,&size,&cutoff,&all) != 3)
goto stub_error;
for (i = 1; i <= n; i++)
if (fscanf(dbfile,DB_BDATA,&ufirst,&tfirst) != 2)
goto stub_error;
if (fscanf(dbfile,DB_BDATA,&ulast,&tlast) != 2)
goto stub_error;
fclose(dbfile);
if (trim)
{ *first = tfirst;
*last = tlast;
}
else
{ *first = ufirst;
*last = ulast;
}
return (0);
stub_error:
EPRINTF(EPLACE,"%s: Stub file %s is junk\n",Prog_Name,path);
EXIT(1);
}
// Free a DAZZ_STUB data structure returned by Read_DB_Stub
void Free_DB_Stub(DAZZ_STUB *stub)
{ int i;
if (stub == NULL)
return;
if (stub->fname != NULL)
{ for (i = 0; i < stub->nfiles; i++)
free(stub->fname[i]);
free(stub->fname-1);
}
if (stub->prolog != NULL)
{ for (i = 0; i < stub->nfiles; i++)
free(stub->prolog[i]);
free(stub->prolog-1);
}
if (stub->nreads != NULL)
free(stub->nreads-1);
free(stub->ublocks);
free(stub->tblocks);
free(stub);
}
/*******************************************************************************************
*
* DB OPEN, TRIM, SIZE_OF, LIST_FILES & CLOSE ROUTINES
......@@ -770,6 +969,7 @@ void Trim_DB(DAZZ_DB *db)
{ memmove(anno+j,anno+r,size);
j += size;
}
record->anno = Realloc(record->anno,record->size*j,NULL);
}
else if (size == 4)
{ int *anno4 = (int *) (record->anno);
......@@ -783,6 +983,7 @@ void Trim_DB(DAZZ_DB *db)
j += 1;
}
record->alen = Realloc(record->alen,sizeof(int)*j,NULL);
record->anno = Realloc(record->anno,record->size*(j+1),NULL);
}
else // size == 8
{ int64 *anno8 = (int64 *) (record->anno);
......@@ -796,8 +997,8 @@ void Trim_DB(DAZZ_DB *db)
j += 1;
}
record->alen = Realloc(record->alen,sizeof(int)*j,NULL);
}
record->anno = Realloc(record->anno,record->size*(j+1),NULL);
}
record->nreads = j;
}
......@@ -805,7 +1006,7 @@ void Trim_DB(DAZZ_DB *db)
totlen = maxlen = 0;
for (j = i = 0; i < nreads; i++)
{ f = reads[i].flags;
if ((f & DB_CSS) == 0)
if ((f & DB_CCS) == 0)
css = 0;
r = reads[i].rlen;
if ((f & DB_BEST) >= allflag && r >= cutoff)
......@@ -814,9 +1015,9 @@ void Trim_DB(DAZZ_DB *db)
maxlen = r;
reads[j] = reads[i];
if (css)
reads[j++].flags |= DB_CSS;
reads[j++].flags |= DB_CCS;
else
reads[j++].flags &= ~DB_CSS;
reads[j++].flags &= ~DB_CCS;
css = 1;
}
}
......@@ -1538,7 +1739,7 @@ static int Late_Track_Trim(DAZZ_DB *db, DAZZ_TRACK *track, int ispart)
}
r += size;
}
memmove(anno+j,anno+r,size);
track->anno = Realloc(track->anno,track->size*j,NULL);
}
else if (size == 4)
{ int *anno4 = (int *) (track->anno);
......@@ -1558,6 +1759,8 @@ static int Late_Track_Trim(DAZZ_DB *db, DAZZ_TRACK *track, int ispart)
}
}
track->data = Realloc(track->data,anno4[j],NULL);
track->alen = Realloc(track->alen,sizeof(int)*j,NULL);
track->anno = Realloc(track->anno,track->size*(j+1),NULL);
}
else // size == 8
{ int64 *anno8 = (int64 *) (track->anno);
......@@ -1577,9 +1780,10 @@ static int Late_Track_Trim(DAZZ_DB *db, DAZZ_TRACK *track, int ispart)
}
}
track->data = Realloc(track->data,anno8[j],NULL);
}
track->alen = Realloc(track->alen,sizeof(int)*j,NULL);
track->anno = Realloc(track->anno,track->size*(j+1),NULL);
}
}
fclose(indx);
return (0);
......@@ -2076,6 +2280,7 @@ void Close_Track(DAZZ_DB *db, DAZZ_TRACK *track)
for (record = db->tracks; record != NULL; record = record->next)
{ if (track == record)
{ free(record->anno);
free(record->alen);
if (record->loaded)
free(record->data);
else
......
DB.h
View file @ 466611d6
......@@ -249,7 +249,7 @@ char *Numbered_Suffix(char *left, int num, char *right);
// DB-related utilities
void Print_Number(int64 num, int width, FILE *out); // Print readable big integer
void Print_Number(int64 num, int width, FILE *out); // Print big integer with commas
int Number_Digits(int64 num); // Return # of digits in printed number
#define COMPRESSED_LEN(len) (((len)+3) >> 2)
......@@ -274,7 +274,7 @@ void Number_Arrow(char *s); // Convert arrow pw string from letters to number
********************************************************************************************/
#define DB_QV 0x03ff // Mask for 3-digit quality value
#define DB_CSS 0x0400 // This is the second or later of a group of subreads from a given insert
#define DB_CCS 0x0400 // This is the second or later of a group of subreads from a given insert
#define DB_BEST 0x0800 // This is the "best" subread of a given insert (may be the only 1)
#define DB_ARROW 0x2 // DB is an arrow DB
......@@ -300,7 +300,7 @@ typedef struct
// contains the variable length data
// data != NULL && size == 8: anno is an array of nreads+1 int64's and data[anno[i]..anno[i+1])
// contains the variable length data
// if open is set then the data is not loaded if present, rather data is an open file pointer
// if loaded is set then the data is not loaded if present, rather data is an open file pointer
// set for reading.
typedef struct _track
......@@ -365,6 +365,24 @@ typedef struct
int loaded; // Are arrow vectors loaded in memory?
} DAZZ_ARROW;
// Every DB is referred to by an ASCII stub file with extension .db or .dam. This file
// contains the information about the SMRT cells in the DB and the current division of
// the DB into blocks for HPC processing. This file can be read into the following
// data structure:
typedef struct
{ int nfiles; // Number of files/SMRT cells in DB
int *nreads; // [0..nfiles) = # of reads from cell
char **fname; // [0..nfiles) = file name of cell
char **prolog; // [0..nfiles) = fasta header prolog for cell
int all; // Keep only best read from each well?
int cutoff; // Trim reads less than cutoff
int64 bsize; // Target size for blocks
int nblocks; // Number of blocks for DB
int *ublocks; // [0..nblcoks] = index of 1st read in block in untrimmed DB
int *tblocks; // [0..nblcoks] = index of 1st read in block in trimmed DB
} DAZZ_STUB;
// The DB record holds all information about the current state of an active DB including an
// array of DAZZ_READS, one per read, and a linked list of DAZZ_TRACKs the first of which
// is always a DAZZ_QV pseudo-track (if the QVs have been loaded).
......@@ -416,6 +434,30 @@ typedef struct
#define DB_PARAMS "size = %11lld cutoff = %9d all = %1d\n" // block size, len cutoff, all in well
#define DB_BDATA " %9d %9d\n" // First read index (untrimmed), first read index (trimmed)
// Read the specified contents of the DB stub file at "path" and return it encoded in a DAZZ_STUB
// structure. This is allocated by the routine. "path" is assumed to be the complete
// name of the file. If all flags are off, then just the scalar parts of the stub
// are returned (i.e. nfiles, all, cutoff, bsize, nblocks). Returns NULL if an error
// occured in INTERACTIVE mode
#define DB_STUB_NREADS 0x1
#define DB_STUB_FILES 0x2
#define DB_STUB_PROLOGS 0x4
#define DB_STUB_BLOCKS 0x8
DAZZ_STUB *Read_DB_Stub(char *path, int what);
// Read the DB stub file "path" and extract the read index range [*first,*last)
// for block n, for the trimmed DB if trim is set, the untrimmed DB otherwise.
// If n is out of range first and last will be set to -1. Returns 0 unless
// an error occurs in INTERACTIVE mode in which case it returns 1.
int Fetch_Block_Range(char *path, int trim, int n, int *first, int *last);
// Free a DAZZ_STUB data structure returned by Read_DB_Stub
void Free_DB_Stub(DAZZ_STUB *stub);
/*******************************************************************************************
*
......@@ -428,13 +470,13 @@ typedef struct
// (not containing a . !).
// A DAM is basically a DB except that:
// 1. there are no QV's, instead .coff points the '\0' terminated fasta header of the read
// in the file .<dam>.hdr file
// 1. there are no QV's, instead .coff points to the '\0' terminated fasta header of the read
// in an additional file: .DB.hdr
// 2. .origin contains the contig # of the read within a fasta entry (assembly sequences
// contain N-separated contigs), and .fpulse the first base of the contig in the
// fasta entry
// Open the given database or dam, "path" into the supplied DAZZ_DB record "db". If the name has
// Open the given database or dam, "path", into the supplied DAZZ_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:
......
DBdump.c
View file @ 466611d6
......@@ -85,6 +85,7 @@ static int qv_map[51] =
int main(int argc, char *argv[])
{ DAZZ_DB _db, *db = &_db;
DAZZ_STUB *stub;
int Quiva_DB, Arrow_DB;
int FirstRead;
FILE *hdrs = NULL;
......@@ -291,8 +292,6 @@ int main(int argc, char *argv[])
// If get prolog and file names and index ranges from the .db or .dam file
{ char *pwd, *root;
FILE *dstub;
char *dstub_name;
int i;
if (DAM)
......@@ -303,41 +302,22 @@ int main(int argc, char *argv[])
if (db->part > 0)
*rindex(root,'.') = '\0';
if (DAM)
dstub_name = Strdup(Catenate(pwd,"/",root,".dam"),"Allocating dam file name");
stub = Read_DB_Stub(Catenate(pwd,"/",root,".dam"),
DB_STUB_NREADS|DB_STUB_FILES|DB_STUB_PROLOGS);
else
dstub_name = Strdup(Catenate(pwd,"/",root,".db"),"Allocating db file name");
dstub = Fopen(dstub_name,"r");
if (dstub_name == NULL || dstub == NULL)
exit (1);
stub = Read_DB_Stub(Catenate(pwd,"/",root,".db"),
DB_STUB_NREADS|DB_STUB_FILES|DB_STUB_PROLOGS);
free(pwd);
free(root);
FSCANF(dstub,DB_NFILE,&nfiles)
fhead = (char **) Malloc(sizeof(char *)*nfiles,"Allocating file list");
ffile = (char **) Malloc(sizeof(char *)*(nfiles+1),"Allocating file list");
findx = (int *) Malloc(sizeof(int *)*(nfiles+1),"Allocating file index");
if (fhead == NULL || ffile == NULL || findx == NULL)
exit (1);
fhead = stub->prolog;
ffile = stub->fname;
findx = stub->nreads;
nfiles = stub->nfiles;
findx += 1;
findx[-1] = 0;
ffile += 1;
ffile[-1] = empty;
for (i = 0; i < nfiles; i++)
{ char prolog[MAX_NAME], fname[MAX_NAME];
FSCANF(dstub,DB_FDATA,findx+i,fname,prolog)
if ((fhead[i] = Strdup(prolog,"Adding to file list")) == NULL)
exit (1);
if ((ffile[i] = Strdup(fname,"Adding to file list")) == NULL)
exit (1);
}
free(dstub_name);
fclose(dstub);
// If TRIM (the default) then "trim" prolog ranges and the DB
if (TRIM)
......@@ -547,11 +527,11 @@ int main(int argc, char *argv[])
c += 2;
}
if (map > 0 && findx[map-1] <= b+FirstRead && b+FirstRead < findx[map])
if (map > 0 && findx[map-1] <= b && b < findx[map])
;
else
{ map = 0;
while (b + FirstRead >= findx[map])
while (b >= findx[map])
map += 1;
map -= 1;
}
......@@ -566,7 +546,7 @@ int main(int argc, char *argv[])
noreads += 1;
if (DOFLN && i+FirstRead >= findx[map])
if (DOFLN && i >= findx[map])
{ int ten;
if (strcmp(ffile[map+1],ffile[last]) != 0)
......@@ -595,7 +575,7 @@ int main(int argc, char *argv[])
hdrmax = ten;
hdrtot += ten;
}
else if (i+FirstRead >= findx[map])
else if (i >= findx[map])
{ map += 1;
ten = strlen(fhead[map]);
......@@ -713,11 +693,11 @@ int main(int argc, char *argv[])
c += 2;
}
if (map > 0 && findx[map-1] <= b+FirstRead && b+FirstRead < findx[map])
if (map > 0 && findx[map-1] <= b && b < findx[map])
;
else
{ map = 0;
while (b + FirstRead >= findx[map])
while (b >= findx[map])
map += 1;
map -= 1;
}
......@@ -736,7 +716,7 @@ int main(int argc, char *argv[])
flags = r->flags;
qv = (flags & DB_QV);
if (DOFLN && i+FirstRead >= findx[map])
if (DOFLN && i >= findx[map])
{ if (strcmp(ffile[map+1],ffile[last]) != 0)
{ PRINTF("F %ld %s\n",strlen(ffile[map+1]),ffile[map+1])
last = map+1;
......@@ -756,7 +736,7 @@ int main(int argc, char *argv[])
PRINTF("L %d %d %d\n",r->origin,r->fpulse,r->fpulse+len)
}
else
{ if (i+FirstRead >= findx[map])
{ if (i >= findx[map])
{ map += 1;
PRINTF("H %ld %s\n",strlen(fhead[map]),fhead[map])
}
......@@ -854,16 +834,7 @@ int main(int argc, char *argv[])
if (DAM)
fclose(hdrs);
else
{ int i;
for (i = 0; i < nfiles; i++)
{ free(fhead[i]);
free(ffile[i]);
}
free(fhead);
free(ffile-1);
free(findx-1);
}
Free_DB_Stub(stub);
Close_DB(db);
exit (0);
......
DBshow.c
View file @ 466611d6
......@@ -81,12 +81,13 @@ int next_read(File_Iterator *it)
int main(int argc, char *argv[])
{ DAZZ_DB _db, *db = &_db;
DAZZ_STUB *stub;
FILE *hdrs = NULL;
char *hdrs_name = NULL;
int nfiles;
char **flist = NULL;
int *findx = NULL;
char **flist;
int *findx;
int reps, *pts;
int input_pts;
......@@ -264,44 +265,21 @@ int main(int argc, char *argv[])
if (!DAM)
{ char *pwd, *root;
FILE *dstub;
char *dstub_name;
int i;
root = Root(argv[1],".db");
pwd = PathTo(argv[1]);
if (db->part > 0)
*rindex(root,'.') = '\0';
dstub_name = Strdup(Catenate(pwd,"/",root,".db"),"Allocating db file name");
dstub = Fopen(dstub_name,"r");
if (dstub_name == NULL || dstub == NULL)
exit (1);
free(pwd);
free(root);
FSCANF(dstub,DB_NFILE,&nfiles)
flist = (char **) Malloc(sizeof(char *)*nfiles,"Allocating file list");
findx = (int *) Malloc(sizeof(int *)*(nfiles+1),"Allocating file index");
if (flist == NULL || findx == NULL)
exit (1);
stub = Read_DB_Stub(Catenate(pwd,"/",root,".db"),DB_STUB_NREADS|DB_STUB_PROLOGS);
findx += 1;
findx[-1] = 0;
for (i = 0; i < nfiles; i++)
{ char prolog[MAX_NAME], fname[MAX_NAME];
FSCANF(dstub,DB_FDATA,findx+i,fname,prolog)
if ((flist[i] = Strdup(prolog,"Adding to file list")) == NULL)
exit (1);
}
fclose(dstub);
free(dstub_name);
nfiles = stub->nfiles;
flist = stub->prolog;
findx = stub->nreads;
// If TRIM (the default) then "trim" prolog ranges and the DB
findx[-1] = 0;
if (TRIM)
{ int nid, oid, lid;
int cutoff, allflag;
......@@ -327,8 +305,9 @@ int main(int argc, char *argv[])
}
}
else if (db->part > 0)
{ for (i = 0; i < nfiles; i++)
else
{ if (db->part > 0)
for (i = 0; i < nfiles; i++)
findx[i] -= db->ufirst;
}
}
......@@ -660,13 +639,7 @@ int main(int argc, char *argv[])
if (DAM)
fclose(hdrs);
else
{ int i;
for (i = 0; i < nfiles; i++)
free(flist[i]);
free(flist);
free(findx-1);
}
Free_DB_Stub(stub);
Close_DB(db);
exit (0);
......
DBsplit.c
View file @ 466611d6
......@@ -190,7 +190,7 @@ int main(int argc, char *argv[])
for (i = 0; i < nreads; i = j)
{ j = i+1;
reads[i].flags &= off;
while ((reads[j].flags & DB_CSS) != 0)
while ((reads[j].flags & DB_CCS) != 0)
reads[j++].flags &= off;
if (j-i <= 1)
......@@ -236,7 +236,7 @@ int main(int argc, char *argv[])
if (ALL)
for (i = 0; i < nreads; i++)
{ rlen = reads[i].rlen;
if ((reads[i].flags & DB_CSS) == 0)
if ((reads[i].flags & DB_CCS) == 0)
css = 0;
if (rlen >= CUTOFF)
{ if (css == 0 && totlen >= SIZE)
......
DBtrim.c
View file @ 466611d6
......@@ -179,7 +179,7 @@ int main(int argc, char *argv[])
for (i = 0; i < nreads; i = j)
{ j = i+1;
reads[i].flags &= off;
while ((reads[j].flags & DB_CSS) != 0)
while ((reads[j].flags & DB_CCS) != 0)
reads[j++].flags &= off;
if (j-i <= 1)
......
README.md
View file @ 466611d6
......@@ -374,7 +374,7 @@ the reads for testing purposes.
```
Like DBshow, DBdump allows one to display a subset of the reads in the DB and select
which information to show about them including any mask tracks. The difference is
which information to show including any mask tracks. The difference is
that the information is written in a very simple "1-code" ASCII format that makes it
easy for one to read and parse the information for further use. The option flags determine
which items of information are output as follows:
......
debian/changelog
View file @ 466611d6
dazzdb (1.0+git20200115.d8adde7-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.4.1 (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit.
-- Steffen Möller <moeller@big2.fritz.box> Sun, 19 Jan 2020 18:11:41 +0100
dazzdb (1.0+git20190616.034f1ab-1) unstable; urgency=medium
* Afif removed himself from Uploaders
......
debian/control
View file @ 466611d6
......@@ -5,7 +5,7 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
zlib1g-dev
Standards-Version: 4.4.0
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/dazzdb
Vcs-Git: https://salsa.debian.org/med-team/dazzdb.git
Homepage: https://github.com/thegenemyers/DAZZ_DB
......
debian/upstream/metadata
View file @ 466611d6
Bug-Database: https://github.com/thegenemyers/DAZZ_DB/issues
Bug-Submit: https://github.com/thegenemyers/DAZZ_DB/issues/new
Registry:
- Name: conda:bioconda
Entry: dazz_db
fasta2DB.c
View file @ 466611d6
......@@ -560,7 +560,7 @@ int main(int argc, char *argv[])
offset += clen;
if (pwell == well)
{ prec[pcnt].flags |= DB_CSS;
{ prec[pcnt].flags |= DB_CCS;
pcnt += 1;
if (pcnt >= pmax)
{ pmax = ((int) (pcnt*1.2)) + 100;
......