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
|
/********************************************************************************************
*
* Recreate all the .arrow files that have been loaded into a specified database.
*
* Author: Gene Myers
* Date : October 2016
*
********************************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "DB.h"
static char *Usage = "[-v] [-w<int(80)>] <path:db>";
int main(int argc, char *argv[])
{ HITS_DB _db, *db = &_db;
FILE *dbfile;
int VERBOSE, WIDTH;
// Process arguments
{ int i, j, k;
int flags[128];
char *eptr;
ARG_INIT("DB2arrow")
WIDTH = 80;
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("vU")
break;
case 'w':
ARG_NON_NEGATIVE(WIDTH,"Line width")
break;
}
else
argv[j++] = argv[i];
argc = j;
VERBOSE = flags['v'];
if (argc != 2)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
exit (1);
}
}
// Open db, and db stub file
{ int status;
char *pwd, *root;
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->allarr & DB_ARROW) == 0)
{ fprintf(stderr,"%s: There is no Arrow information in the DB: %s\n",Prog_Name,argv[1]);
exit (1);
}
pwd = PathTo(argv[1]);
root = Root(argv[1],".db");
dbfile = Fopen(Catenate(pwd,"/",root,".db"),"r");
free(pwd);
free(root);
if (dbfile == NULL)
exit (1);
}
// For each cell do:
{ HITS_READ *reads;
char lname[MAX_NAME];
FILE *ofile = NULL;
int f, first, last, ofirst, nfiles;
char *read;
if (fscanf(dbfile,DB_NFILE,&nfiles) != 1)
SYSTEM_ERROR
reads = db->reads;
read = New_Read_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 .arrow file for writing
if (fscanf(dbfile,DB_FDATA,&last,fname,prolog) != 3)
SYSTEM_ERROR
if (f == 0 || strcmp(fname,lname) != 0)
{ if (f > 0)
{ if (ofile == stdout)
{ fprintf(stderr," %d reads\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,".arrow"),"w")) == NULL)
exit (1);
if (VERBOSE)
{ fprintf(stderr,"Creating %s.arrow ...\n",fname);
fflush(stdout);
}
}
strcpy(lname,fname);
}
// For the relevant range of reads, write each to the file
// recreating the original headers with the index meta-data about each read
for (i = first; i < last; i++)
{ int j, len;
uint64 big;
float snr[4];
HITS_READ *r;
r = reads + i;
len = r->rlen;
big = *((uint64 *) &(r->coff));
for (j = 0; j < 4; j++)
{ snr[3-j] = (big & 0xffff) / 100.;
big >>= 16;
}
fprintf(ofile,">%s",prolog);
fprintf(ofile," SN=%.2f,%.2f,%.2f,%.2f",snr[0],snr[1],snr[2],snr[3]);
fprintf(ofile,"\n");
Load_Arrow(db,i,read,1);
for (j = 0; j+WIDTH < len; j += WIDTH)
fprintf(ofile,"%.*s\n",WIDTH,read+j);
if (j < len)
fprintf(ofile,"%s\n",read+j);
}
first = last;
}
if (f > 0)
{ if (ofile == stdout)
{ fprintf(stderr," %d reads\n",first-ofirst);
fflush(stderr);
}
else
fclose(ofile);
}
}
fclose(dbfile);
Close_DB(db);
exit (0);
}
|
