I have uploaded version 2.1.1 of the sequenceread package. This includes an important change to allow illumina2srf to build against the latest version of the Staden io_lib. It will also still build against io_lib versions 1.12.1 onwards.
Illumina2srf has gained two new options: -force_config_machine_name and -force_qseq_machine_name. These allow it to work if the config.xml and .qseq.txt versions of the machine name do not match. This feature was added for UCLA's SeqWare project.
It is now also possible to run index_decoder with just the -t parameter and no .qseq.txt files. This will cause it to read and check the tags file. It will also build the index that it uses to search for the sequence tags, so you can use it to test new tag sets to see how many sequencing errors can be corrected when searching against the set.