List *xdap_late_read_contig_data(void)
{
List *contig_details;
if (cur_contig_index > io.num_contigs)
contig_details = nil;
else {
bap_rl_file_rec rl_line;
int length;
int index;
int left_end;
int right_end;
index = io.max_gels-cur_contig_index;
bap_read_rl(&io,index,&rl_line);
length = rl_line.clines.length;
left_end = rl_line.clines.left_end;
right_end = rl_line.clines.right_end;
contig_details =
build_list(
atom_str(contig_rec),
build_list(
atom_str(contig_index),
atom_int(index),
nil),
build_list(
atom_str(contig_length),
atom_int(length),
nil),
build_list(
atom_str(contig_left_end),
atom_int(left_end),
nil),
build_list(
atom_str(contig_right_end),
atom_int(right_end),
nil),
nil);
cur_contig_index++;
}
return contig_details;
}
sql_exp *
exp_atom_wrd(sql_allocator *sa, wrd w)
{
sql_subtype it;
sql_find_subtype(&it, "wrd", 19, 0);
return exp_atom(sa, atom_int(sa, &it, (lng)w ));
}
sql_exp *
exp_atom_lng(sql_allocator *sa, lng i)
{
sql_subtype it;
sql_find_subtype(&it, "bigint", 19, 0);
return exp_atom(sa, atom_int(sa, &it, (lng)i ));
}
sql_exp *
exp_atom_int(sql_allocator *sa, int i)
{
sql_subtype it;
sql_find_subtype(&it, "int", 9, 0);
return exp_atom(sa, atom_int(sa, &it, i ));
}
static List *db_details(void)
{
return
build_list(
build_list(
atom_str(db_max_db_size),
atom_int(io.max_db_size),
nil),
build_list(
atom_str(db_max_gels),
atom_int(io.max_gels),
nil),
build_list(
atom_str(db_max_gel_length),
atom_int(io.max_gel_length),
nil),
build_list(
atom_str(db_data_class),
atom_int(io.data_class),
nil),
build_list(
atom_str(db_num_gels),
atom_int(io.num_gels),
nil),
build_list(
atom_str(db_num_contigs),
atom_int(io.num_contigs),
nil),
nil);
}
atom *
atom_dec(sql_allocator *sa, sql_subtype *tpe,
#ifdef HAVE_HGE
hge val,
#else
lng val,
#endif
double dval)
{
atom *a = atom_int(sa, tpe, val);
if (a)
a -> d = dval;
return a;
}
List *xdap_late_read_gel_data(void)
{
List *gel_details;
if (cur_gel_index > io.num_gels)
gel_details = nil;
else {
bap_ar_file_rec ar_line;
bap_rl_file_rec rl_line;
bap_sq_file_rec sq_line;
bap_tg_file_rec tg_line;
int index;
char name[17];
char *seq;
int length;
int comp;
int pos;
int l_nbr;
int r_nbr;
sq_line = (char *) malloc(io.max_gel_length+1);
bap_read_ar(&io,cur_gel_index,&ar_line);
bap_read_rl(&io,cur_gel_index,&rl_line);
bap_read_tg(&io,cur_gel_index,&tg_line);
bap_read_sq(&io,cur_gel_index,sq_line);
index = cur_gel_index;
f2cstr(ar_line.lines.name,BAP_FILE_NAME_LENGTH,name,
(size_t)BAP_FILE_NAME_LENGTH);
length = abs(rl_line.lines.length);
comp = (rl_line.lines.length < 0);
seq = sq_line;
seq[length] = '\0';
pos = rl_line.lines.rel_pos;
l_nbr = rl_line.lines.left_nbr;
r_nbr = rl_line.lines.right_nbr;
gel_details =
build_list(
atom_str(gel_rec),
build_list(
atom_str(gel_index),
atom_int(index),
nil),
build_list(
atom_str(gel_name),
atom_str(name),
nil),
build_list(
atom_str(gel_length),
atom_int(length),
nil),
build_list(
atom_str(gel_comp),
atom_int(comp),
nil),
build_list(
atom_str(gel_seq),
atom_str(seq),
nil),
build_list(
atom_str(gel_pos),
atom_int(pos),
nil),
build_list(
atom_str(gel_l_nbr),
atom_int(l_nbr),
nil),
build_list(
atom_str(gel_r_nbr),
atom_int(r_nbr),
nil),
nil);
/* Get raw data details */
if (tg_line.lines.comment) {
List *raw_data_details;
char *rd;
int rd_length;
int rd_cut;
int rd_ulen;
char rd_type[5];
char rd_file[19];
rd = bap_read_comment(&io, tg_line.lines.comment);
sscanf(rd,"%6d%6d%6d%*s",&rd_length, &rd_cut, &rd_ulen);
f2cstr(&rd[18],4,rd_type,(size_t)4);
f2cstr(&rd[22],18,rd_file,(size_t)18);
raw_data_details =
build_list(
build_list(
atom_str(gel_rd_length),
atom_int(rd_length),
nil),
build_list(
atom_str(gel_rd_cut),
atom_int(rd_cut),
nil),
build_list(
atom_str(gel_rd_ulen),
atom_int(rd_ulen),
nil),
build_list(
atom_str(gel_rd_type),
atom_str(rd_type),
nil),
build_list(
atom_str(gel_rd_file),
atom_str(rd_file),
nil),
nil);
join_list (gel_details, raw_data_details, nil);
}
/*
** Process tags, maintaining separate lists for
** (a) special tags
** (b) annotation
** (c) edits
*/
{
List *specials;
List *notes;
List *edits;
int_4 next;
specials = nil;
notes =
build_list(
atom_str(gel_annotation),
nil);
edits =
build_list(
atom_str(gel_edits),
nil);
while (tg_line.lines.next) {
next = tg_line.lines.next;
bap_read_tg(&io,next,&tg_line);
if (strncmp(tg_line.lines.type.c,"*LC*",4)==0) {
if (tg_line.lines.comment) {
List *lc;
lc = build_list(
atom_str(gel_l_cut_seq),
atom_str(bap_read_comment(&io,tg_line.lines.comment)),
nil);
if (isNil(specials))
specials = build_list(lc,nil);
else
specials = join_list(specials,build_list(lc,nil),nil);
}
} else if (strncmp(tg_line.lines.type.c,"*RC*",4)==0) {
if (tg_line.lines.comment) {
List *rc;
rc = build_list(
atom_str(gel_r_cut_seq),
atom_str(bap_read_comment(&io,tg_line.lines.comment)),
nil);
if (isNil(specials))
specials = build_list(rc,nil);
else
specials = join_list(specials,build_list(rc,nil),nil);
}
} else if (strncmp(tg_line.lines.type.c,"*",1)==0) {
List *ed;
char base[2];
base[0] = tg_line.lines.type.c[3];
base[1] = '\0';
ed = build_list(
build_list(
atom_str(gel_ed_op),
atom_str( (strncmp(tg_line.lines.type.c,"*IN",3))==0
? gel_ed_insert : gel_ed_delete),
nil),
build_list(
atom_str(gel_ed_base),
atom_str(base),
nil),
build_list(
atom_str(gel_ed_base_pos),
atom_int( tg_line.lines.position ),
nil),
nil);
edits = join_list(edits, build_list(ed,nil),nil);
} else {
List *an;
char type[5];
char *com;
strncpy(type,tg_line.lines.type.c,4);
type[4]='\0';
com = bap_read_comment(&io,tg_line.lines.comment);
an = build_list(
build_list(
atom_str(gel_an_pos),
atom_int(tg_line.lines.position),
nil),
build_list(
atom_str(gel_an_len),
atom_int(tg_line.lines.length),
nil),
build_list(
atom_str(gel_an_type),
atom_str(type),
nil),
(com == NULL) ? nil :
build_list(
atom_str(gel_an_comment),
atom_str(com),
nil),
nil);
notes = join_list(notes,build_list(an,nil),nil);
}
}
if (isNil(specials))
gel_details = join_list(gel_details,build_list(edits,nil),build_list(notes,nil),nil);
else
gel_details = join_list(gel_details,specials,build_list(edits,nil),build_list(notes,nil),nil);
}
cur_gel_index++;
free(sq_line);
}
return gel_details;
}
