Changeset 8292 for trunk

Timestamp:

09/12/11 13:43:29 (6 months ago)

Author:

westram

Message:

• ptserver crashed when designing probes for species with empty data (only gaps) or too few nucs (less than probe len) [fixed and print warnings]

Location:

trunk/PROBE

Files:

• PT_new_design.cxx (modified) (3 diffs)
• probe.h (modified) (1 diff)

trunk/PROBE/PT_new_design.cxx

@@ -907 +907 @@
         int used_idx = 0;
         for (int name = 0; name < psg.data_count; name++) {
-            if (psg.data[name].inside_group()) {
-                group_idx[used_idx++]                  = name; // store marked group indices
-                unsigned long size                     = psg.data[name].get_size();
-                datasize                              += size;
-                if (datasize<size) datasize            = ULONG_MAX; // avoid overflow!
-                if (size > maxseqlength) maxseqlength  = size;
+            const probe_input_data& pid = psg.data[name];
+
+            if (pid.inside_group()) {
+                group_idx[used_idx++] = name;                  // store marked group indices
+
+                unsigned long size  = pid.get_size();
+                datasize           += size;
+
+                if (size<1 || (unsigned long)size<pdc->probelen) {
+                    fprintf(stderr, "Warning: impossible design request for '%s' (contains only %lu bp)\n", pid.get_name(), size);
+                }
+
+                if (datasize<size) datasize           = ULONG_MAX;  // avoid overflow!
+                if (size > maxseqlength) maxseqlength = size;
             }
         }
@@ -946 +954 @@
     char partstring[256];
     PT_init_base_string_counter(partstring, PT_A, partsize);
+
     while (!PT_base_string_counter_eof(partstring)) {
 #if defined(DEBUG)
@@ -962 +971 @@
 
         for (int g = 0; g<group_count; ++g) {
-            int      name             = group_idx[g];
-            long     possible_tprobes = psg.data[name].get_size()-pdc->probelen+1;
+            int  name             = group_idx[g];
+            long possible_tprobes = psg.data[name].get_size()-pdc->probelen+1;
+
+            if (possible_tprobes<1) possible_tprobes = 1; // avoid wrong hash-size if no/not enough data
+
             GB_HASH *hash_one         = GBS_create_hash(possible_tprobes*hash_multiply, GB_MIND_CASE); // count tprobe occurrences for one group/sequence
             ptnd_add_sequence_to_hash(pdc, hash_one, psg.data[name].get_data(), psg.data[name].get_size(), pdc->probelen, partstring, partsize);

trunk/PROBE/probe.h

@@ -105 +105 @@
     char *data;       // sequence
     long  checksum;   // checksum of sequence
-    int   size;
+    int   size; // @@@ misleading (contains 1 if no bases in sequence)
 
     char   *name;