/* configuration-dependent initialization */
int main_configure(char *arg1, char *arg2) {
if(options_cmdline(arg1, arg2))
return 1;
options_apply();
str_canary_init(); /* needs prng initialization from options_cmdline */
#if !defined(USE_WIN32) && !defined(__vms)
/* syslog_open() must be called before change_root()
* to be able to access /dev/log socket */
syslog_open();
#endif /* !defined(USE_WIN32) && !defined(__vms) */
if(bind_ports())
return 1;
#ifdef HAVE_CHROOT
/* change_root() must be called before drop_privileges()
* since chroot() needs root privileges */
if(change_root())
return 1;
#endif /* HAVE_CHROOT */
if(drop_privileges(1))
return 1;
/* log_open() must be be called after drop_privileges()
* or logfile rotation won't be possible */
/* log_open() must be be called before daemonize()
* since daemonize() invalidates stderr */
if(log_open())
return 1;
#ifndef USE_FORK
num_clients=0; /* the first valid config */
#endif
return 0;
}
int
main( int argc, char *argv[] )
{
FILE *out_a, *out_b;
char *h1, *h2, *s, *q;
char *id = NULL;
char *outname_a = NULL, *outname_b = NULL, *outdirname = NULL;
int i;
struct options *o = options_new( );
struct tokenset *t = tokenset_new( );
struct fqreader *fq = fqreader_new( NULL );
/* Get the command line options */
options_cmdline( o, argc, argv );
if ( _IS_NULL( o->outname ) || strlen( o->outname ) == 0 ) {
o->outname = realloc( o->outname, 4 * sizeof ( char ) );
strcpy( o->outname, "FQU" );
}
/* Create the output directory if necessary */
outdirname = realloc( outdirname, sizeof ( char ) * ( 2 + strlen( o->outname ) ) );
strcpy( outdirname, o->outname );
if ( strchr( outdirname, '/' ) ) { /* not the current directory */
dirname( outdirname );
mkdirp( outdirname, S_IRWXU | S_IRWXG | S_IRWXO );
}
/* Read the id files */
for ( i = o->optind; i < argc; i++ ) {
char *line;
struct linereader *z = linereader_new( );
linereader_init( z, argv[i] );
if ( _IS_NULL( z ) ) {
fprintf( stderr, "[ERROR] %s: Cannot open input file \"%s\"\n", _I_AM, argv[i] );
exit( 1 );
}
while ( ( line = ( char * ) linereader_next( z ) ) ) {
unsigned len;
stru_trim( line );
if ( line[0] == '#' || stru_is_ws( line ) )
continue;
len = strcspn( line, "\f\n\r\t\v " );
line[len] = '\0';
tokenset_add( t, line );
}
linereader_free( z );
}
outname_a = realloc( outname_a, sizeof ( char ) * ( 6 + strlen( o->outname ) ) );
strcpy( outname_a, o->outname );
strcat( outname_a, "_A.fq" );
out_a = fopen( outname_a, "wb" );
if ( _IS_NULL( out_a ) ) {
fprintf( stderr, "Could not open first output file \"%s\"\n", outname_a );
exit( 1 );
}
outname_b = realloc( outname_b, sizeof ( char ) * ( 6 + strlen( o->outname ) ) );
strcpy( outname_b, o->outname );
strcat( outname_b, "_B.fq" );
out_b = fopen( outname_b, "wb" );
if ( _IS_NULL( out_b ) ) {
fprintf( stderr, "Could not open second output file \"%s\"\n", outname_b );
exit( 1 );
}
while ( fqreader_next( fq, &h1, &h2, &s, &q ) ) {
utils_extract_id( &id, h1 ); /* get the identifier from header 1 */
if ( tokenset_exists( t, id ) )
fprintf( out_a, "@%s\n%s\n+%s\n%s\n", h1, s, h2, q );
else
fprintf( out_b, "@%s\n%s\n+%s\n%s\n", h1, s, h2, q );
}
fclose( out_a );
fclose( out_b );
_FREE( id );
_FREE( outname_a );
_FREE( outname_b );
fqreader_free( fq );
options_free( o );
tokenset_free( t );
return 0;
}
int
main( int argc, char *argv[] )
{
char *h1, *h2, *s, *q;
unsigned i;
unsigned n;
struct options *o = options_new( );
struct fqreader *z;
/* Get the command line options */
options_cmdline( o, argc, argv );
words = tokenset_new( );
word = realloc( word, sizeof ( char ) * ( 1 + o->word_size ) );
if ( o->optind == argc ) { /* read from stdin */
z = fqreader_new( NULL );
while ( fqreader_next( z, &h1, &h2, &s, &q ) ) {
stru_toupper( s );
_update_table( o->word_size, s, o->check_initial );
}
fqreader_free( z );
}
else { /* read from input files */
int k;
for ( k = o->optind; k < argc; k++ ) {
z = fqreader_new( argv[k] );
if ( _IS_NULL( z ) ) {
fprintf( stderr, "[ERROR] %s: Cannot open input file \"%s\"\n", _I_AM, argv[k] );
exit( 1 );
}
while ( fqreader_next( z, &h1, &h2, &s, &q ) ) {
stru_toupper( s );
_update_table( o->word_size, s, o->check_initial );
}
fqreader_free( z );
}
}
/* Print the countlist */
n = tokenset_count( words );
for ( i = 0; i < n; i++ ) {
if ( countlist[i].count < o->min_count )
continue;
printf( "%s\t%d\n", tokenset_get_by_id( words, countlist[i].id ), countlist[i].count );
}
options_free( o );
tokenset_free( words );
_FREE( word );
_FREE( countlist );
return 0;
}
