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ctSkennerton / crass

The CRISPR assembler
http://ctskennerton.github.io/crass
GNU General Public License v3.0
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Smith-Waterman alignments going past end of sequence #34

Closed ctSkennerton closed 12 years ago

ctSkennerton commented 12 years ago

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

a_ret = seqA.substr(current_i+ aStartSearch, i_max - current_i + aStartSearch);
ctSkennerton commented 12 years ago

This bug seems reproducible on the file

~/metagenomic_datasets/GOS/JCVI_SMPL_1103283000039.fa runs through quickly too

ctSkennerton commented 12 years ago

version 0.2.2 solves this