static void
kill_reader (int fd)
{
int i;
LOCK (reader_table_lock);
for (i=0; i < reader_table_size; i++ ) {
if (reader_table[i].used && reader_table[i].fd == fd ) {
destroy_reader (reader_table[i].context);
reader_table[i].context = NULL;
reader_table[i].used = 0;
break;
}
}
UNLOCK (reader_table_lock);
}
static void
apply_plugin_config()
{
Reader *reader, *nreader;
gchar *name;
gint row;
if (!list_modified)
return;
for (reader = readers; reader; reader = readers) {
readers = reader->next;
destroy_reader(reader);
}
for (row = 0; row < GTK_CLIST(reader_clist)->rows; ++row)
{
gint i;
i = 0;
reader = g_new0(Reader, 1);
gtk_clist_get_text(GTK_CLIST(reader_clist), row, i++, &name);
gkrellm_dup_string(&reader->label, name);
gtk_clist_get_text(GTK_CLIST(reader_clist), row, i++, &name);
gkrellm_dup_string(&reader->peer, name);
gtk_clist_get_text(GTK_CLIST(reader_clist), row, i++, &name);
reader->port = atoi(name);
gtk_clist_get_text(GTK_CLIST(reader_clist), row, i++, &name);
gkrellm_dup_string(&reader->community, name);
gtk_clist_get_text(GTK_CLIST(reader_clist), row, i++, &name);
gkrellm_dup_string(&reader->oid_str, name);
reader->objid_length = MAX_OID_LEN;
if (!snmp_parse_oid(reader->oid_str,
reader->objid, &reader->objid_length)) {
//FIXME:
printf("error parsing oid: %s\n", reader->oid_str);
}
gtk_clist_get_text(GTK_CLIST(reader_clist), row, i++, &name);
gkrellm_dup_string(&reader->unit, name);
gtk_clist_get_text(GTK_CLIST(reader_clist), row, i++, &name);
reader->delay = atoi(name);
gtk_clist_get_text(GTK_CLIST(reader_clist), row, i++, &name);
reader->divisor = atoi(name);
gtk_clist_get_text(GTK_CLIST(reader_clist), row, i++, &name);
reader->delta = (strcmp(name, "yes") == 0) ? TRUE : FALSE;
gtk_clist_get_text(GTK_CLIST(reader_clist), row, i++, &name);
reader->scale = (strcmp(name, "yes") == 0) ? TRUE : FALSE;
gtk_clist_get_text(GTK_CLIST(reader_clist), row, i++, &name);
reader->active = (strcmp(name, "yes") == 0) ? TRUE : FALSE;
if (!readers)
readers = reader;
else {
for (nreader = readers; nreader->next ; nreader = nreader->next);
nreader->next = reader;
}
create_reader(main_vbox, reader, 1);
}
list_modified = 0;
}
int
main (int argc, char * argv[])
{
int i, trim_len_fw, trim_len_rev;
//struct reads_info ** ri_left;
//struct reads_info ** ri_right;
// int cnt_reads_left;
// int cnt_reads_right;
int read_size;
char * out[4];
FILE * fd[4];
int ass;
double uncalled_forward, uncalled_reverse;
struct user_args sw;
struct emp_freq * ef;
struct block_t fwd_block;
struct block_t rev_block;
char two_piece;
int elms;
if (!decode_switches (argc, argv, &sw))
{
/* TODO: Validate reads names */
usage ();
return (EXIT_FAILURE);
}
ef = (struct emp_freq *)malloc (sizeof(struct emp_freq));
ef->freqa = ef->freqc = ef->freqg = ef->freqt = ef->total = ef->pa = ef->pc = ef->pg = ef->pt = ef->q = 0.25;
init_scores(sw->phred_base, ef);
/* read the two fastq files containing the left-end and right-end reads */
//ri_left = read_fastq(sw.fastq_left, &cnt_reads_left);
//ri_right = read_fastq(sw.fastq_right, &cnt_reads_right);
//if (!validate_input (cnt_reads_left, cnt_reads_right))
// {
// return (EXIT_FAILURE);
// }
// read_size = strlen (ri_left[0]->data);
/* TODO: THIS IS WRONG!!!! TO GET EMPIRICAL FREQUENCIES WE NEED TO READ THE WHOLE FILE :-( */
//ef = get_emp_freq (cnt_reads_right, read_size, fwd_block.reads, rev_block.reads);
/* reverse the right ends */
/* allocate memory for the assembled results */
/*
ai = (struct asm_info *) malloc (cnt_reads_left * sizeof(struct asm_info));
for (i = 0; i < cnt_reads_left; ++i)
{
ai[i].data = (char *) malloc ((2 * read_size + 1) * sizeof(char));
ai[i].quality_score = (char *) malloc ((2 * read_size + 1) * sizeof(char));
}
*/
init_fastq_reader (sw.fastq_left, sw.fastq_right, sw.memory, &fwd_block, &rev_block);
/* construct output file names */
out[0] = makefilename (sw.outfile, ".assembled.fastq");
out[1] = makefilename (sw.outfile, ".unassembled.forward.fastq");
out[2] = makefilename (sw.outfile, ".unassembled.reverse.fastq");
out[3] = makefilename (sw.outfile, ".discarded.fastq");
fd[0] = fopen (out[0], "w");
fd[1] = fopen (out[1], "w");
fd[2] = fopen (out[2], "w");
fd[3] = fopen (out[3], "w");
while (1)
{
elms = get_next_reads (&fwd_block, &rev_block);
if (!elms) break;
read_size = strlen (fwd_block.reads[0]->data);
// printf ("%d elms (Seq)\n", elms);
//#pragma omp parallel shared(fwd_block.reads, rev_block.reads, ai) private(i, ass, uncalled, kassian_result)
#pragma omp parallel private(i, ass)
{
/* flags[i] = 1 (assembled) 0 (discarded) 2 (unassembled) */
#pragma omp for schedule (guided)
for (i = 0; i < elms; ++ i)
{
mstrrev (rev_block.reads[i]->data);
mstrcpl (rev_block.reads[i]->data);
mstrrev (rev_block.reads[i]->qscore);
if (sw.emp_freqs == 0)
{
ass = assembly (fwd_block.reads[i], rev_block.reads[i], &sw);
*(fwd_block.reads[i]->qscore - 1) = ass;
}
else
{
ass = assembly_ef (fwd_block.reads[i], rev_block.reads[i], ef, &sw);
*(fwd_block.reads[i]->qscore - 1) = ass;
}
}
}
for ( i = 0; i < elms; ++ i)
{
two_piece = *(fwd_block.reads[i]->data - 1);
*(fwd_block.reads[i]->data - 1) = 0;
if (*(fwd_block.reads[i]->qscore - 1) == 1) /* assembled */
{
*(fwd_block.reads[i]->qscore - 1) = 0;
fprintf (fd[0], "%s\n", fwd_block.reads[i]->header);
if (!two_piece)
{
fprintf (fd[0], "%s\n", fwd_block.reads[i]->data);
}
else
{
fprintf (fd[0], "%s", fwd_block.reads[i]->data);
fprintf (fd[0], "%s\n", rev_block.reads[i]->data);
}
fprintf (fd[0], "+\n");
if (!two_piece)
{
fprintf (fd[0], "%s\n", fwd_block.reads[i]->qscore);
}
else
{
fprintf (fd[0], "%s", fwd_block.reads[i]->qscore);
fprintf (fd[0], "%s\n", rev_block.reads[i]->qscore);
}
}
else /* not assembled */
{
*(fwd_block.reads[i]->qscore - 1) = 0;
trim_len_fw = trim (fwd_block.reads[i], &sw, read_size, &uncalled_forward);
trim_len_rev = trim_cpl (rev_block.reads[i], &sw, read_size, &uncalled_reverse);
if (trim_len_fw < sw.min_trim_len || trim_len_rev < sw.min_trim_len || uncalled_forward >= sw.max_uncalled || uncalled_reverse >= sw.max_uncalled)
{ /* discarded reads*/
/* Maybe consider printing the untrimmed sequences */
fprintf (fd[3], "%s\n", fwd_block.reads[i]->header);
fprintf (fd[3], "%s\n+\n%s\n", fwd_block.reads[i]->data, fwd_block.reads[i]->qscore);
fprintf (fd[3], "%s\n", rev_block.reads[i]->header);
fprintf (fd[3], "%s\n+\n%s\n", rev_block.reads[i]->data, rev_block.reads[i]->qscore); /* printing the reverse compliment of the original sequence */
}
else /* unassembled reads*/
{
fprintf (fd[1], "%s\n", fwd_block.reads[i]->header);
fprintf (fd[2], "%s\n", rev_block.reads[i]->header);
fprintf (fd[1], "%s\n+\n%s\n", fwd_block.reads[i]->data, fwd_block.reads[i]->qscore);
fprintf (fd[2], "%s\n+\n%s\n", rev_block.reads[i]->data, rev_block.reads[i]->qscore); /* printing the reverse compliment of the original sequence */
}
}
}
}
free (ef);
free (out[0]);
free (out[1]);
free (out[2]);
free (out[3]);
destroy_reader ();
/* TODO: Fix those file closings */
fclose (fd[0]);
fclose (fd[1]);
fclose (fd[2]);
fclose (fd[3]);
return (0);
}
