[med-svn] [Git][med-team/dazzdb][upstream] New upstream version 1.0+git20200115.d8adde7
Steffen Möller
gitlab at salsa.debian.org
Wed Jan 22 11:10:10 GMT 2020
Steffen Möller pushed to branch upstream at Debian Med / dazzdb
Commits:
ab403a4d by Steffen Möller at 2020-01-19T17:55:56+01:00
New upstream version 1.0+git20200115.d8adde7
- - - - -
9 changed files:
- Catrack.c
- DB.c
- DB.h
- DBdump.c
- DBshow.c
- DBsplit.c
- DBtrim.c
- README.md
- fasta2DB.c
Changes:
=====================================
Catrack.c
=====================================
@@ -65,45 +65,27 @@ 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;
+ { char *pwd, *root;
+ int plen;
+ DAZZ_STUB *stub;
plen = strlen(argv[1]);
+ pwd = PathTo(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);
- }
+ { root = Root(argv[1],".dam");
+ stub = Read_DB_Stub(Catenate(pwd,"/",root,".dam"),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)
-
- for (i = 0; i < nblocks; i++)
- { char prolog[MAX_NAME], fname[MAX_NAME];
-
- FSCANF(dstub,DB_FDATA,&index,fname,prolog)
+ else
+ { root = Root(argv[1],".db");
+ stub = Read_DB_Stub(Catenate(pwd,"/",root,".db"),0);
}
-
- FSCANF(dstub,DB_NBLOCK,&nblocks)
- fclose(dstub);
- free(dstub_name);
+ nblocks = stub->nblocks;
+
+ Free_DB_Stub(stub);
+
+ prefix = Strdup(Catenate(pwd,PATHSEP,root,"."),"Allocating track name");
+
free(pwd);
free(root);
}
@@ -175,14 +157,16 @@ int main(int argc, char *argv[])
"Allocating .data file name");
if (afile_name == NULL || dfile_name == NULL)
goto error;
-
afile = fopen(afile_name,"r");
if (afile == NULL)
- break;
- dfile = fopen(Numbered_Suffix(prefix,nfiles+1,Catenate(".",argv[c],".","data")),"r");
+ { free(afile_name);
+ free(dfile_name);
+ break;
+ }
+ 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;
}
@@ -194,14 +178,14 @@ int main(int argc, char *argv[])
{ fprintf(stderr," Concatenating %s%d.%s ...\n",prefix,nfiles+1,argv[c]);
fflush(stderr);
}
-
+
FFREAD(&tracklen,sizeof(int),1,afile)
FFREAD(&size,sizeof(int),1,afile)
if (size == 0)
esize = 8;
else
esize = size;
-
+
if (nfiles == 0)
{ tracksiz = size;
if (dfile != NULL)
@@ -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",
- Prog_Name, nfiles, nblocks);
- goto error;
- }
+ fprintf(stderr,"%s: Warning: Did not catenate all tracks of DB (nfiles %d != nblocks %d)\n",
+ Prog_Name,nfiles,nblocks);
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
=====================================
@@ -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->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);
@@ -1577,8 +1780,9 @@ 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);
}
- track->anno = Realloc(track->anno,track->size*(j+1),NULL);
}
fclose(indx);
@@ -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
=====================================
@@ -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
=====================================
@@ -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
=====================================
@@ -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);
-
- 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);
+ stub = Read_DB_Stub(Catenate(pwd,"/",root,".db"),DB_STUB_NREADS|DB_STUB_PROLOGS);
+ 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;
@@ -327,9 +305,10 @@ int main(int argc, char *argv[])
}
}
- else if (db->part > 0)
- { for (i = 0; i < nfiles; i++)
- findx[i] -= db->ufirst;
+ 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
=====================================
@@ -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
=====================================
@@ -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
=====================================
@@ -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:
=====================================
fasta2DB.c
=====================================
@@ -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;
View it on GitLab: https://salsa.debian.org/med-team/dazzdb/commit/ab403a4d3c34fb0591d46528f1ac1e2a6f14e0e8
--
View it on GitLab: https://salsa.debian.org/med-team/dazzdb/commit/ab403a4d3c34fb0591d46528f1ac1e2a6f14e0e8
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