Extracting filtered sequences from the Solexa/Illumina sig2.txt files

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This program takes as input a solex sig2 file and will generate a collection of filtered sequences based. A short fragment is dropped if within the 12 first bases two or more ambiguos bases appear. An ambiguos base is calculated based on the difference between the highest intensity and the second highest intensity. If this is less than 1/3 of the total range of the 4 signals for that base, then it is an ambiguos base. This approach is based on the explanation of the chastity filter used in the Illumina pipeline. However, since we had to guess to a certain extend how the correct implementation handles the data, we cannot be sure that this is exactly the same implementation.

Usage: sig22seq <s_1_0023_sig2.txt> > s_1_0023_seq.txt;