ilmn_format_converter

Purpose

This program was designed to rapidly interconvert Illumina SCARF and FASTQ formats. There is a substantial speed improvement (important in some of my reprocessing efforts) by moving this to a C++ program over the Perl / Python alternatives. Log messages print to the error stream and the output prints to standard output. See the included license file for terms of use.

VERY IMPORTANT WARNING This interconversion can only safely be performed on files with Illumina quality offset (QUAL+64).

Compilation

Linux

Edit the Makefile to include any necessary changes, such as -m64 and -mtune parameters. It already compiles at -O3 and -Wall warnings.

make
make install

Windows

This software can be compiled with a properly setup Eclipse or other IDE. Otherwise it can be compiled manually.

g++ -o ilmn_format_converter -O3 main.cpp

Running

Viable formats for in and out are only 'scarf' and 'fastq', all lowercase.

ilmn_format_converter --inFormat scarf --outFormat fastq --inFile myScarf.txt 1>output.fq 2>scarf2fq.log

ilmn_format_converter --inFormat fastq --outFormat scarf --inFile output.fq 1>remadeScarf.txt 2>fq2scarf.log