1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
|
/********************************************************************************************
*
* Recreate all the .quiva files that have been loaded into a specified database.
*
* Author: Gene Myers
* Date : May 2014
*
********************************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "DB.h"
#include "QV.h"
#ifdef HIDE_FILES
#define PATHSEP "/."
#else
#define PATHSEP "/"
#endif
static char *Usage = "[-vU] <path:db>";
int main(int argc, char *argv[])
{ DAZZ_DB _db, *db = &_db;
FILE *dbfile, *quiva;
char *dbfile_name;
int VERBOSE, UPPER;
// Process arguments
{ int i, j, k;
int flags[128];
ARG_INIT("DB2quiva")
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
{ ARG_FLAGS("vU") }
else
argv[j++] = argv[i];
argc = j;
VERBOSE = flags['v'];
UPPER = flags['U'];
if (argc != 2)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
fprintf(stderr,"\n");
fprintf(stderr," -U: Use upper case for DNA (default is lower case).\n");
exit (1);
}
}
// Open db, db stub file, and .qvs file
{ char *pwd, *root;
int status;
status = Open_DB(argv[1],db);
if (status < 0)
exit (1);
if (status == 1)
{ fprintf(stderr,"%s: Cannot be called on a .dam index: %s\n",Prog_Name,argv[1]);
exit (1);
}
if (db->part > 0)
{ fprintf(stderr,"%s: Cannot be called on a block: %s\n",Prog_Name,argv[1]);
exit (1);
}
if (db->reads[0].coff < 0 || (db->allarr & DB_ARROW) != 0)
{ fprintf(stderr,"%s: There is no Quiver information in the DB: %s\n",Prog_Name,argv[1]);
exit (1);
}
pwd = PathTo(argv[1]);
root = Root(argv[1],".db");
dbfile_name = Strdup(Catenate(pwd,"/",root,".db"),"Allocating db file name");
dbfile = Fopen(dbfile_name,"r");
quiva = Fopen(Catenate(pwd,PATHSEP,root,".qvs"),"r");
free(pwd);
free(root);
if (dbfile_name == NULL || dbfile == NULL || quiva == NULL)
exit (1);
}
// For each cell do:
{ DAZZ_READ *reads;
char lname[MAX_NAME];
FILE *ofile = NULL;
int f, first, last, ofirst, nfiles;
QVcoding *coding;
char **entry;
FSCANF(dbfile,DB_NFILE,&nfiles)
reads = db->reads;
entry = New_QV_Buffer(db);
first = ofirst = 0;
for (f = 0; f < nfiles; f++)
{ int i;
char prolog[MAX_NAME], fname[MAX_NAME];
// Scan db image file line, create .quiva file for writing
if (reads[first].coff < 0) break;
FSCANF(dbfile,DB_FDATA,&last,fname,prolog)
if (f == 0 || strcmp(fname,lname) != 0)
{ if (f > 0)
{ if (ofile == stdout)
{ fprintf(stderr," %d quivas\n",first-ofirst);
fflush(stderr);
}
else
FCLOSE(ofile)
}
if (strcmp(fname,"stdout") == 0)
{ ofile = stdout;
ofirst = first;
if (VERBOSE)
{ fprintf(stderr,"Sending to stdout ...");
fflush(stdout);
}
}
else
{ if ((ofile = Fopen(Catenate(".","/",fname,".quiva"),"w")) == NULL)
exit (1);
if (VERBOSE)
{ fprintf(stderr,"Creating %s.quiva ...\n",fname);
fflush(stderr);
}
}
strcpy(lname,fname);
}
// For the relevant range of reads, write the header for each to the file
// and then uncompress and write the quiva entry for each
coding = Read_QVcoding(quiva);
for (i = first; i < last; i++)
{ int e, flags, qv, rlen;
DAZZ_READ *r;
r = reads + i;
flags = r->flags;
rlen = r->rlen;
qv = (flags & DB_QV);
FPRINTF(ofile,"@%s/%d/%d_%d",prolog,r->origin,r->fpulse,r->fpulse+rlen)
if (qv > 0)
FPRINTF(ofile," RQ=0.%3d",qv)
FPRINTF(ofile,"\n")
Uncompress_Next_QVentry(quiva,entry,coding,rlen);
if (UPPER)
{ char *deltag = entry[1];
int j;
for (j = 0; j < rlen; j++)
deltag[j] -= 32;
}
for (e = 0; e < 5; e++)
FPRINTF(ofile,"%.*s\n",rlen,entry[e])
}
first = last;
}
if (f > 0)
{ if (ofile == stdout)
{ fprintf(stderr," %d quivas\n",first-ofirst);
fflush(stderr);
}
else
FCLOSE(ofile)
}
}
fclose(quiva);
fclose(dbfile);
Close_DB(db);
exit (0);
}
|
