static void debug_memory(struct context* ctx)
{
/* dump memory as user requested */
if (rr_flags->dump_on == ctx->trace.stop_reason
|| rr_flags->dump_on == DUMP_ON_ALL
|| rr_flags->dump_at == ctx->trace.global_time) {
char pid_str[PATH_MAX];
snprintf(pid_str, sizeof(pid_str) - 1, "%s/%d_%d_rep",
get_trace_path(),
ctx->child_tid, ctx->trace.global_time);
print_process_memory(ctx, pid_str);
}
/* check memory checksum */
if (validate
&& ((rr_flags->checksum == CHECKSUM_ALL)
|| (rr_flags->checksum == CHECKSUM_SYSCALL
&& ctx->trace.state == STATE_SYSCALL_EXIT)
|| (rr_flags->checksum <= ctx->trace.global_time))) {
validate_process_memory(ctx);
}
}
/*
* Produce a consensus trace from a specific region of this contig.
*/
Read *cons_trace(EdStruct *xx, int start, int end, int strand,
int match, int exception) {
int *seqList, i, j, count, next;
Read *r;
int max_points = 10000;
char *con = NULL;
diff_cons_seq *rlist = NULL;
char fileName[256];
char t_type[5];
int form;
int offset = 0, w;
/* Get the consensus sequence */
if (NULL == (con = (char *)xmalloc(end - start + 2)))
goto error;
DBcalcConsensus(xx, start, end - start + 1, con, NULL, BOTH_STRANDS);
/* Allocate a list of read pointers and positions */
if (NULL == (rlist = (diff_cons_seq *)xcalloc(DBI_gelCount(xx),
sizeof(*rlist))))
goto error;
/* Allocate a read structure */
if (NULL == (r = read_allocate(max_points, end - start + 1)))
goto error;
/* Derive the initial list of sequences covering the start point */
count = 0;
seqList = DBI_list(xx);
for (i = 1;
i <= DBI_gelCount(xx) && DB_RelPos(xx, DBI_order(xx)[i]) <= start;
i++) {
int seq = DBI_order(xx)[i];
DBgetSeq(DBI(xx), seq);
if (DB_RelPos(xx, seq) + DB_Length(xx, seq) > start &&
strand_matches(xx, seq, strand) &&
seq != exception) {
if (get_trace_path(xx, seq, fileName, t_type) == 0) {
form = trace_type_str2int(t_type);
rlist[count].r = read_reading(fileName, form);
if (rlist[count].r) {
rlist[count].seq = DBgetSeq(DBI(xx), seq);
rlist[count].opos =
get_trace_pos(rlist[count].r, xx, seq, 0,
DB_Start(xx, seq),
DB_Start(xx, seq) + DB_Length(xx, seq),
DB_Seq(xx, seq), 0);
seqList[count++] = seq;
}
}
}
}
if (i <= DBI_gelCount(xx))
next = i;
else
next = 0;
/*
* Loop along the sequence updating seqList as we go.
* At each point we know how many sequences there are so we can
* produce the consensus from these sequences.
*/
for (i = start; i <= end; i++) {
w = do_cons_base(xx, con, i, start, count, seqList, rlist, r, offset,
match, &max_points);
if (w == -1)
goto error;
offset += w;
/* Update seqList for the next position */
if (i < end) {
/* Remove sequences */
for (j = 0; j < count; j++) {
int seq = seqList[j];
if (DB_RelPos(xx, seq) + DB_Length(xx, seq) - 1 <= i) {
read_deallocate(rlist[j].r);
xfree(rlist[j].opos);
memmove(&seqList[j], &seqList[j+1],
(count-1-j) * sizeof(*seqList));
memmove(&rlist[j], &rlist[j+1],
(count-1-j) * sizeof(*rlist));
count--;
j--;
}
}
/* Add sequences */
while (next && DB_RelPos(xx, next) <= i+1) {
/* printf("next=%d %d %d\n",
next, DB_RelPos(xx, next), i+1); */
DBgetSeq(DBI(xx), next);
if (strand_matches(xx, next, strand) &&
get_trace_path(xx, next, fileName, t_type) == 0) {
form = trace_type_str2int(t_type);
rlist[count].r = read_reading(fileName, form);
if (rlist[count].r) {
rlist[count].seq = DBgetSeq(DBI(xx), next);
rlist[count].opos =
get_trace_pos(rlist[count].r, xx, next, 0,
DB_Start(xx, next),
DB_Start(xx,next)+DB_Length(xx,next),
DB_Seq(xx, next), 0);
seqList[count++] = next;
}
}
if (++next > DBI_gelCount(xx))
next = 0;
}
}
}
for (i = 0; i < count; i++) {
read_deallocate(rlist[i].r);
xfree(rlist[i].opos);
}
tidy_up(r, end-start + 1, offset);
xfree(con);
xfree(rlist);
return r;
error:
if (con) xfree(con);
if (rlist) xfree(rlist);
return NULL;
}
