How to get fastq-multx to recognize barcodes that are not at the start of the read

[Manasa Ramakrishna]

Dear Erik, 

Thank you so much for writing fastq-multx as it is fantastic and quick for de-multiplexing my RNAseq data. My question is about whether or not I can get it to recognise barcodes that are not at the start of the read. For example, my *fastq.gz file consisted of 9 samples with barcodes listed below. 7/9 samples decoded perfectly and I have the associated files. However for iCLIP3A and iCLIP3B, I've noticed that the barcode is not at the 5' end of the read so it is something like NNNGGCA.... and NNNTTAA....... 

I've tried giving it a barcode file that has the index as "NNNGGCA" and "NNNTTAA" but this doesn't seem to work. I know you have a "mismatch" option but I'm assuming this means mismatch WITHIN the barcode not leading up to the barcode. 

IgG1 GAT

IgG2 GGC

iCLIP1A AAC

iCLIP2A AGT

iCLIP3A GGCA

IgG3 TTC

iCLIP1B CCC

iCLIP2B TCT

iCLIP3B TTAA

If you have any suggestions as to how I can deal with this, they will be greatly appreciated. 

Cheers, 

Manasa