#389 PSMConvert fatal exception on mac os x

[Alice Cheng]

Obtained FATAL: An exception occurred: Could not convert string '162)' when trying the following command on mac osx. Input file attached below. Seems to work on linux machine though, so not quite sure what is going on.

./crux psm-convert --overwrite T crux-output/tide-search.target.txt sqt

[Alice Cheng]

additional details:

occuring in PeptideSrc.cpp line 354 when trying to convert "162)" into an integer.

Cause seem to originate in line 333:
string peptide_start_index_string = protein_id.substr(left_paren_index+1, protein_id.length() - 1);

user is trying to use syntax substr(start, end) when (correct ?) syntax is substr(start, length of substring). What I'm confused about is why this doesn't error in linux...

Potential Fix (Have not tested effect on linux yet..):
string peptide_start_index_string = protein_id.substr(left_paren_index+1, protein_id.length() - left_paren_index-2);