int test_quick_sort() {
struct dlist* list_to_sort = NULL;
list_to_sort = generate_dlist();
print_dlist(list_to_sort);
//quick_sort(list_to_sort);
struct dlist* tmp = get_element_by_index(list_to_sort, 1);
printf("5 element - %d %p\n", tmp->data, tmp);
print_dlist(list_to_sort);
free_dlist(list_to_sort);
return 0;
}
char *assemble_direct(GapIO *io, int display, double max_mism,
char *inlist, int do_alignments, int enter_all) {
consen_info *ci = NULL;
SeqInfo *si;
int ierr;
char *file;
int name, dir, pos, tol, maxpads = 25;
int contig, rnum;
align_info *ai;
char *rname;
int old_clen, count = 1;
void *dl;
char *res;
dl = alloc_dlist();
if (do_alignments)
/* Calculate consensus */
if (NULL == (ci = all_consensus(io, consensus_cutoff)))
return NULL;
/* Loop around each input file */
if (-1 == set_active_list(inlist))
return NULL;
while (file = get_active_list_item()) {
UpdateTextOutput();
vmessage("Processing number %8d: %s\n", count++, file);
/*
* The last argument controls whether to set the QL/QR based on
* SL/SR. "1" disables SL/SR use, which is what we need when copying
* data in generated by extract_seq. FIXME: this could break things
* for other data sources though, unless explicit QL/QR values have
* been used.
*/
if (NULL == (si = read_sequence_details(file, 1))) {
verror(ERR_WARN, "directed_assembly", "couldn't read '%s'", file);
add_to_dlist(dl, file);
vmessage(" failed\n");
continue;
}
if (si->start < 0)
si->start = 0;
if (si->end > si->length+1)
si->end = si->length+1;
if (si->end - si->start <= 1 || si->length < 1) {
verror(ERR_WARN, "directed assembly", "sequence '%s' too short",
file);
add_to_dlist(dl, file);
freeSeqInfo(si);
vmessage(" failed\n");
continue;
}
if (NULL == (rname = read_sequence_name(si))) {
verror(ERR_WARN, "directed_assembly", "no name found for '%s'",
file);
add_to_dlist(dl, file);
freeSeqInfo(si);
vmessage(" failed\n");
continue;
}
/* FIXME: perform caching of names (also template and vector names) */
if (get_gel_num(io, rname, GGN_NAME) > 0) {
verror(ERR_WARN, "directed_assembly",
"reading '%s' already exists", rname);
add_to_dlist(dl, file);
vmessage(" failed\n");
freeSeqInfo(si);
continue;
}
if (exp_Nentries(si->e, EFLT_AP) == 0) {
verror(ERR_WARN, "directed_assembly", "no AP line in '%s'", file);
add_to_dlist(dl, file);
vmessage(" failed\n");
freeSeqInfo(si);
continue;
}
if (0 != AP_parse(io, rname, exp_get_entry(si->e, EFLT_AP),
&name, &dir, &pos, &contig, &tol)) {
verror(ERR_WARN, "directed_assembly", "invalid AP line in '%s'.",
file);
name = 0;
if (!enter_all) {
verror(ERR_WARN, "directed_assembly",
"invalid AP line in '%s'", file);
add_to_dlist(dl, file);
vmessage(" failed\n");
freeSeqInfo(si);
continue;
}
}
ai = NULL;
if (name != 0) {
if (tol >= 0 && do_alignments) {
/* Align with existing contig */
ai = assemble_align(io, si, ci, contig, &pos, dir, tol,
display, maxpads, max_mism, &ierr);
if (NULL == ai) {
if (ierr == 2) {
vmessage(" Percentage mismatch is too high\n");
name = 0;
} else if (ierr == 3) {
vmessage(" Reading does not overlap\n");
name = 0;
} else if (ierr == 4) {
vmessage(" Reading does not overlap "
"within tolerance\n");
name = 0;
} else {
verror(ERR_WARN, "directed_assembly",
"failed to align reading '%s'", file);
name = 0;
}
if (!enter_all) {
add_to_dlist(dl, file);
freeSeqInfo(si);
continue;
}
}
}
}
if (name == 0) {
/* new contig */
vmessage(" Creating new contig\n");
if (-1 == io_init_contig(io, NumContigs(io)+1))
return NULL;
contig=NumContigs(io);
io_clnbr(io, contig) = 0;
io_crnbr(io, contig) = 0;
io_clength(io, contig) = 0;
pos = 0;
}
old_clen = io_clength(io, contig);
if (-1 == (rnum = enter_reading(io, si, dir, ai, contig, pos)))
return NULL;
if (-1 == link_reading(io, name, rnum, contig, pos))
return NULL;
freeSeqInfo(si);
if (ai) {
xfree(ai->res);
xfree(ai);
}
if (do_alignments) {
if (-1 == recalc_consensus(io, ci, contig, pos,
ABS(io_length(io, rnum)),
old_clen, io_clength(io, contig))) {
verror(ERR_WARN, "directed_assembly",
"failed to recalculate consensus - quitting");
return NULL;
}
}
}
remove_contig_holes_all(io);
flush2t(io);
if (do_alignments)
free_all_consensus(ci);
res = strdup(read_dlist(dl));
free_dlist(dl);
return res;
}
