debugging with Luca 2

Author: PaulaAlessio

include/bloom.h

@@ -34,11 +34,6 @@
 #include "defines.h"
 
 
-/**
- * @brief bitMask, ith bit set to 1 in position i
- * */
-static const unsigned char bitMask[0x08] = {0x01, 0x02, 0x04, 0x08,
-                                            0x10, 0x20, 0x40, 0x80};
 /**
 * @brief Bloom filter structure
 *

include/defines.h

@@ -30,6 +30,7 @@
 #define DEFINES_H_
 
 #include <stdint.h>
+#include <inttypes.h>
 
 // General
 #define B_LEN 131072  /**< buffer size */
@@ -48,13 +49,13 @@
 
 #ifndef mem_usageMB
   #define mem_usageMB()  fprintf(stderr, \
-         "- Current allocated memory: %lu MB.\n", \
+         "- Current allocated memory: %" PRIu64 "MB.\n", \
          alloc_mem >> 20)  /**< returns allocated memory in MB */
 #endif
 
 #ifndef mem_usage
   #define mem_usage()  fprintf(stderr, \
-         "- Current allocated memory: %lu Bytes.\n", \
+         "- Current allocated memory: %" PRIu64 "Bytes.\n", \
          alloc_mem)  /**< returns allocated memory in Bytes */
 #endif
 

src/bloom.c

@@ -37,6 +37,12 @@
 static uint8_t fw0[256], fw1[256], fw2[256], fw3[256];
 static uint8_t bw0[256], bw1[256], bw2[256], bw3[256];
 
+/**
+ * @brief bitMask, ith bit set to 1 in position i
+ * */
+static const unsigned char bitMask[0x08] = {0x01, 0x02, 0x04, 0x08,
+                                            0x10, 0x20, 0x40, 0x80};
+
 extern uint64_t alloc_mem; /**< allocated memory */
 
 /**
@@ -503,9 +509,9 @@ Bfilter *create_Bfilter(Fa_data *ptr_fasta, int kmersize, uint64_t bfsizeBits,
   fprintf(stderr, "Creating a bloomfilter.\n");
   fprintf(stderr, "- false positive rate: %f\n", falsePosRate);
   fprintf(stderr, "- kmersize: %d\n", kmersize);
-  fprintf(stderr, "- size of bloom filter (in bits): %ld\n", bfsizeBits);
+  fprintf(stderr, "- size of bloom filter (in bits): %" PRIu64 "\n", bfsizeBits);
   fprintf(stderr, "- number of hash functions used: %d\n", hashNum);
-  fprintf(stderr, "- number of elements that will be inserted: %ld\n", nelem);
+  fprintf(stderr, "- number of elements that will be inserted: %" PRIu64 "\n", nelem);
   for (i=0; i < ptr_fasta -> nentries; i++) {
     maxN = ptr_fasta -> entry[i].N - kmersize + 1;
     for (position = 0; position < maxN; position++) {
@@ -538,7 +544,7 @@ Bfilter *create_Bfilter(Fa_data *ptr_fasta, int kmersize, uint64_t bfsizeBits,
 void save_Bfilter(Bfilter *ptr_bf, char *filterfile, char *paramfile) {
   fprintf(stderr, "Store a bloom filter in: %s (filter), %s (param) \n",
           filterfile, paramfile);
-  fprintf(stderr, "Bloom filter size in bytes, %ld\n", ptr_bf -> bfsizeBytes);
+  fprintf(stderr, "Bloom filter size in bytes, %" PRIu64 "\n", ptr_bf -> bfsizeBytes);
   FILE *fout = fopen(filterfile, "wb");
   if (fout == NULL) {
      free_Bfilter(ptr_bf);
@@ -559,9 +565,9 @@ void save_Bfilter(Bfilter *ptr_bf, char *filterfile, char *paramfile) {
   }
   fprintf(fout, "kmersize = %d\n", ptr_bf -> kmersize);
   fprintf(fout, "hashNum = %d\n", ptr_bf -> hashNum);
-  fprintf(fout, "bfsizeBits = %ld\n", ptr_bf -> bfsizeBits);
+  fprintf(fout, "bfsizeBits = %" PRIu64  "\n", ptr_bf -> bfsizeBits);
   fprintf(fout, "falsePosRate = %lf\n", ptr_bf -> falsePosRate);
-  fprintf(fout, "nelem = %ld\n", ptr_bf -> nelem);
+  fprintf(fout, "nelem = %" PRIu64 "\n", ptr_bf -> nelem);
   fclose(fout);
 }
 
@@ -594,9 +600,9 @@ Bfilter *read_Bfilter(char *filterfile, char *paramfile) {
   char tmp1[30], tmp2[30];
   fscanf(fin, "%s %s %d", tmp1, tmp2, &kmersize);
   fscanf(fin, "%s %s %d", tmp1, tmp2, &hashNum);
-  fscanf(fin, "%s %s %ld", tmp1, tmp2, &bfsizeBits);
+  fscanf(fin, "%s %s %" SCNu64 , tmp1, tmp2, &bfsizeBits);
   fscanf(fin, "%s %s %lf", tmp1, tmp2, &falsePosRate);
-  fscanf(fin, "%s %s %ld", tmp1, tmp2, &nelem);
+  fscanf(fin, "%s %s %" SCNu64 ,tmp1, tmp2, &nelem);
   fclose(fin);
   Bfilter *ptr_bf = init_Bfilter(kmersize, bfsizeBits, hashNum,
                              falsePosRate, nelem);
@@ -620,7 +626,7 @@ Bfilter *read_Bfilter(char *filterfile, char *paramfile) {
   }
   if (ftell(fin) != ptr_bf -> bfsizeBytes) {
      free_Bfilter(ptr_bf);
-     fprintf(stderr, "Expected bfsizeBytes (%ld) != real bfsizeBytes.(%ld)\n",
+     fprintf(stderr, "Expected bfsizeBytes (%" PRIu64 ") != real bfsizeBytes.(%ld)\n",
              ptr_bf -> bfsizeBytes, ftell(fin));
      fprintf(stderr, "Exiting program.\n");
      fprintf(stderr, "File: %s, line: %d\n", __FILE__, __LINE__);
@@ -639,10 +645,10 @@ Bfilter *read_Bfilter(char *filterfile, char *paramfile) {
           filterfile, paramfile);
   fprintf(stderr, "kmersize = %d\n", ptr_bf -> kmersize);
   fprintf(stderr, "hashNum = %d\n", ptr_bf -> hashNum);
-  fprintf(stderr, "bfsizeBits = %ld\n", ptr_bf -> bfsizeBits);
-  fprintf(stderr, "bfsizeBytes: %ld\n", ptr_bf -> bfsizeBytes);
+  fprintf(stderr, "bfsizeBits = %" PRIu64 "\n", ptr_bf -> bfsizeBits);
+  fprintf(stderr, "bfsizeBytes: %" PRIu64 "\n", ptr_bf -> bfsizeBytes);
   fprintf(stderr, "falsePosRate: %lf\n", ptr_bf -> falsePosRate);
-  fprintf(stderr, "nelem: %ld\n", ptr_bf -> nelem);
+  fprintf(stderr, "nelem: %" PRIu64 "\n", ptr_bf -> nelem);
   fread(ptr_bf -> filter, sizeof(char), ptr_bf -> bfsizeBytes, fin);
   fclose(fin);
   return ptr_bf;

src/fa_read.c

@@ -216,14 +216,14 @@ int read_fasta(char *filename, Fa_data * ptr_fa) {
   fprintf(stderr, "- Allocating memory to store the contents of %s.\n",
           filename);
   mem_usageMB();
-  fprintf(stderr, " * Number of lines: %ld\n", ptr_fa -> nlines);
+  fprintf(stderr, " * Number of lines: %" PRIu64 "\n", ptr_fa -> nlines);
   fprintf(stderr, " * Number of entries: %d\n", ptr_fa -> nentries);
   fprintf(stderr, " * Length of lines: %d\n", ptr_fa -> linelen);
   fprintf(stderr, " * Length of sequences in entries : [  ");
   fflush(stderr);
   int i;
   for (i = 0; i < ptr_fa -> nentries ; i++)
-     fprintf(stderr, "%ld ", ptr_fa -> entrylen[i]);
+     fprintf(stderr, "%" PRIu64, ptr_fa -> entrylen[i]);
   fprintf(stderr, "].\n");
   FILE *fa_in;
   fa_in = fopen_gen(filename, "r");
@@ -233,12 +233,12 @@ int read_fasta(char *filename, Fa_data * ptr_fa) {
      exit(EXIT_FAILURE);
   }
   // Allocate memory to read the file in one step
-  fprintf(stderr, "- Fasta file size: %ld bytes. \n", sz);
-  fprintf(stderr, "- Allocating %ld bytes in the buffer. \n", sz);
+  fprintf(stderr, "- Fasta file size: %" PRIu64 "bytes. \n", sz);
+  fprintf(stderr, "- Allocating %" PRIu64 "bytes in the buffer. \n", sz);
   char*  buffer  =  (char *) malloc(sizeof(char)*sz);
   if (buffer == NULL) {
-    fprintf(stderr, "Error occured. Could not allocate %ld  Bytes.\n",
-          sizeof(char)*sz);
+    fprintf(stderr, "Error occured. Could not allocate %" PRIu64 " Bytes.\n",
+          sz*sizeof(char));
     fprintf(stderr, "File: %s, line: %d\n", __FILE__, __LINE__);
     fprintf(stderr, "Exiting program.\n");
     exit(EXIT_FAILURE);
@@ -322,7 +322,7 @@ void free_fasta(Fa_data *ptr_fa) {
   mem_freed += sizeof(uint64_t) * (ptr_fa -> nentries);
   free(ptr_fa);
   mem_freed += sizeof(Fa_data);
-  fprintf(stderr, " %ld bytes freed\n", mem_freed);
+  fprintf(stderr, " %" PRIu64 "bytes freed\n", mem_freed);
   alloc_mem -= mem_freed;
   mem_usageMB();
 }

src/stats_info.c

@@ -245,14 +245,16 @@ void print_info(Info* res, char *infofile) {
              res -> lane_tags[0]);
   fprintf(f, "- Min Quality: %d\n", res -> minQ);
   fprintf(f, "- Number of ACGT in the first tile: \n");
-  fprintf(f, "  A = %ld, C = %ld, G = %ld, T = %ld , N = %ld\n",
+  fprintf(f, "  A = %" PRIu64 ", C = %" PRIu64 ", G = %" PRIu64 
+        ", T = %" PRIu64 " , N = %" PRIu64 "\n",
         res -> ACGT_tile[0],
         res -> ACGT_tile[1],
         res -> ACGT_tile[2],
         res -> ACGT_tile[3],
         res -> ACGT_tile[4]);
   fprintf(f, "\n- Number of ACGT with low Quality in the first tile:\n");
-  fprintf(f, "  A = %ld, C = %ld, G = %ld, T = %ld, N = %ld\n",
+  fprintf(f, "  A = %" PRIu64 ", C = %" PRIu64 ", G = %" PRIu64 
+        ", T = %" PRIu64 " , N = %" PRIu64 "\n",
         res -> lowQ_ACGT_tile[0],
         res -> lowQ_ACGT_tile[1],
         res -> lowQ_ACGT_tile[2],
@@ -266,13 +268,15 @@ void print_info(Info* res, char *infofile) {
   for (i = 0; i < (res -> nQ); i++) {
      fprintf(f, "  Q = %c : ", (char) (res -> qual_tags[i] + ZEROQ));
      for (j = 0 ; j< res -> read_len; j++) {
-        fprintf(f, "%ld ", res -> QPosTile_table[i*(res -> read_len) +j]);
+        fprintf(f, "%" PRIu64, 
+              res -> QPosTile_table[i*(res -> read_len) +j]);
      }
-     fprintf(f, "\n");
+     fprintf(f, " \n");
   }
   fprintf(f, "\n- Number of reads with M low quality nucleotides: \n");
   for (i = 0; i < (res -> read_len +1); i++) {
-     fprintf(f, "  M lowQ = %2d,  Nreads = %ld \n", i, res -> reads_MlowQ[i]);
+     fprintf(f, "  M lowQ = %2d,  Nreads = %" PRIu64 "\n", 
+             i, res -> reads_MlowQ[i]);
      if (res -> reads_MlowQ[i] > max && i >0) max = res -> reads_MlowQ[i];
   }
   fprintf(f, "\n- Histogram with M low quality nucleotides in tile 1: \n\n");
@@ -290,7 +294,8 @@ void print_info(Info* res, char *infofile) {
   fprintf(f, "\n- Number of nucleotides per position: \n\n");
   fprintf(f, "         A       C       G       T       N   \n");
   for (j =  0; j < res -> read_len; j++) {
-     fprintf(f, "%3d: %7ld %7ld %7ld %7ld %7ld \n", j+1,
+     fprintf(f, "%3d: %7" PRIu64 " %7" PRIu64 " %7" PRIu64 
+           " %7" PRIu64 " %7" PRIu64 " \n", j+1,
           res -> ACGT_pos[N_ACGT *j ],
           res -> ACGT_pos[N_ACGT *j+ 1 ],
           res -> ACGT_pos[N_ACGT *j+ 2 ],

src/tree.c

@@ -133,7 +133,7 @@ void free_all_nodes(Tree *tree_ptr) {
   tree_ptr -> pool_available = 0;
   tree_ptr -> nnodes = 0;
   tree_ptr -> L = 0;
-  fprintf(stderr, "%ld Bytes deallocated.\n", dealloc_mem);
+  fprintf(stderr, "%" PRIu64 " Bytes deallocated.\n", dealloc_mem);
   alloc_mem -= dealloc_mem;
   mem_usageMB();
 }
@@ -355,7 +355,7 @@ Tree* read_tree(char *filename) {
      }
      alloc_mem += sizeof(Node)*sz;
   }
-  fprintf(stderr, "- Allocating %ld bytes.\n",
+  fprintf(stderr, "- Allocating %" PRIu64 " bytes.\n",
          (uint64_t)(sizeof(Node)*sz + sizeof(Node*))*(tree_ptr -> pool_count));
   // Reconstructing addresses
   for (i = 0; i < tree_ptr -> pool_count; i++) {