CID 1077117 (Medium): Division or modulo by zero (DIVIDE_BY_ZERO)

[mr-c]

from lib/hashbits.cc

1902 //
1903 // consume_fasta: consume a FASTA file of reads
1904 //
1905
1906 void Hashbits::consume_fasta_overlap(const std::string &filename,
1907                              HashIntoType curve[2][100],Hashbits &ht2,
1908                              unsigned int &total_reads,
1909                              unsigned long long &n_consumed,
1910                              CallbackFn callback,
1911                              void * callback_data)
1912 {
        1. assignment: Assigning: "total_reads" = "0U".
1913  total_reads = 0;
1914  n_consumed = 0;
1915  Read read;
1916
1917 //get total number of reads in dataset
1918
1919  IParser* parser = IParser::get_parser(filename.c_str());
        2. Condition "!parser->is_complete()", taking true branch
        5. Condition "!parser->is_complete()", taking false branch
1920  while(!parser->is_complete())  {
1921    read = parser->get_next_read();
        3. incr: Incrementing "total_reads". The value of "total_reads" is now 1.
1922    total_reads++;
        4. Jumping back to the beginning of the loop
1923  }
1924 //block size for curve
        6. assignment: Assigning: "block_size" = "total_reads / 100U". The value of "block_size" is now 0.
1925  int block_size = total_reads/100;
1926  
1927  total_reads = 0;
1928  khmer::HashIntoType start = 0, stop = 0;
1929  
1930  delete parser;
1931  parser = IParser::get_parser(filename.c_str());
1932
1933
1934
1935  string currName = "";
1936  string currSeq = "";
1937
1938  //
1939  // iterate through the FASTA file & consume the reads.
1940  //
1941
        7. Condition "!parser->is_complete()", taking true branch
1942  while(!parser->is_complete())  {
1943    read = parser->get_next_read();
1944    currSeq = read.sequence;
1945    currName = read.name; 
1946
1947      unsigned int this_n_consumed;
1948      bool is_valid;
1949
1950      this_n_consumed = check_and_process_read_overlap(currSeq,
1951                                               is_valid, ht2);
1952
1953        n_consumed += this_n_consumed;
1954               
1955    // reset the sequence info, increment read number
1956
1957    total_reads++;
1958

CID 1077117 (#1 of 1): Division or modulo by zero (DIVIDE_BY_ZERO)
8. divide_by_zero: In expression "total_reads % block_size" modulo by expression "block_size" which may be zero has undefined behavior.
1959    if (total_reads%block_size == 0) {
1960        curve[0][total_reads/block_size-1] = n_overlap_kmers(start,stop);
1961        curve[1][total_reads/block_size-1] = n_kmers(start,stop);
1962    }
1963    // run callback, if specified
1964    if (total_reads % CALLBACK_PERIOD == 0 && callback) {
1965      try {
1966        callback("consume_fasta", callback_data, total_reads, n_consumed);
1967      } catch (...) {
1968        throw;
1969      }
1970    }
1971
1972  } // while
1973  
1974  delete parser;
1975 }

[mr-c]

@luizirber Did you write up a fix for this? If not I will do so.