ctSkennerton/crass — Issue #34: Smith-Waterman alignments going past end of sequence 
Author: ctSkennerton
Created: 2012-02-11 02:11:54+00:00
State: open
Labels: defect, priority-high

In smith-waterman the start site for cutting substrings is past the end of the string. This seems to be a problem with the variable ```current_i``` which has a final value of 1059.

```thrown --> basic_string::substr -> 1022 : 1059 : 35```

```c
a_ret = seqA.substr(current_i+ aStartSearch, i_max - current_i + aStartSearch);
```