Ticket #782: dump.patch

SL/PVP/AP_pos_var.cxx

@@ -151 +151 @@
             if (base & (AP_A | AP_G)) char_2_transversion[i] = 1;
             if (base & (AP_C | AP_T)) char_2_transversion[i] |= 2;
         }
+
+#if defined(DEBUG)
+        fprintf(stderr, " index char_2_bitstring char_2_freq\n");
+        for (int i=0; i<256; i++) {
+            fprintf(stderr, " %3i: %3i %3i\n", i, int(char_2_bitstring[i]), int(char_2_freq[i]));
+        }
+#endif
         delete [] char_2_bitstring;
     }
     else {
@@ -158 +165 @@
         const long     *char_2_bitstring = translator->Pro2Bitset();
 
         for (int i=0; i<256; i++) {
-            char_2_transversion[i] = 0;
-            long base = char_2_transition[i] = char_2_bitstring[i];
+            char_2_transversion[i]   = 0;
+            long base                = char_2_transition[i] = char_2_bitstring[i];
             if (base) char_2_freq[i] = toupper(i);
         }
+
+#if defined(DEBUG)
+        fprintf(stderr, " index char_2_bitstring char_2_freq\n");
+        for (int i=0; i<256; i++) {
+            fprintf(stderr, " %3i: %9li %3i\n", i, char_2_bitstring[i], int(char_2_freq[i]));
+        }
+#endif
     }
     treesize = getsize(tree);
     progress = new arb_progress(treesize);
@@ -224 +238 @@
                 }
             }
 
+
+#if defined(DEBUG) && 0
+            // dump non-zero sum[] and frequencies[] for all ali-positions
+            for (int i=0; i<ali_len; i++) {
+                if (sum[i]>0) {
+                    fprintf(stderr, "sum[i=%i]=%i", i, sum[i]);
+                    for (int j=0; j<256 && !error; j++) {
+                        if (frequencies[j]) {
+                            fprintf(stderr, " [j=%i]=%u", j, frequencies[j][i]);
+                        }
+                    }
+                    fputc('\n', stderr);
+                }
+            }
+            fprintf(stderr, "treesize=%li\n", treesize);
+#endif
+
             if (!error) {
                 GBDATA *gb_transi     = GB_search(gb_ali, "FREQUENCIES/TRANSITIONS", GB_INTS);
                 if (!gb_transi) error = GB_await_error();