davidvi/cleanFastq

Clean corrupted fastq files

fixFastq

Fix broken fastq files with corrupted reads that crash the aligner.

Installation

build with clang++ or g++ parsing the -std=c++0x flag to use c++11:

g++ -std=c++11 fixFastq.cpp -o fixFastq

Run

./fixFastq infile.fastq outfile.fastq

Errors

If there is an error running fixFastq you may need to upgrade your compiler or remove the regular expression from the cpp file:

 regex_match(sequence, regex("[CGATNcgatn]*")) &&