Due to an issue with our RTA setup, illumina2srf fails since the QSEQ files do not have the correct machine name which is contained in the folder name (see below). My patch adds a -force-local-machine-name option, which will force illumina2srf to use the folder name, even if it does not match the machine not contained in the qseqs file. This non-default behavior, fixes the issue and allows us to rename the directory to include the proper machine name to be used in the SRF.
Previous error:
/share/apps//sequenceread-2.1.0/bin/illumina2srf -o /scratch0/tmp/jordan/tmp/100301_ILLUMINA-EAS172_61DMU_lane1.srf /data/storage-1-03/solexa/100301_ILLUMINA-EAS172_61DMU/Data/Intensities/BaseCalls/s_1_1_*_qseq.txt
Processing sequence file /data/storage-1-03/solexa/100301_ILLUMINA-EAS172_61DMU/Data/Intensities/BaseCalls/s_1_1_0001_qseq.txt
ERROR: Machine name given in runfolder (ILLUMINA-EAS172) conflicts with that in qseq line: "ILLUMINA-1A5BF1 1 1 1 1160 14114 0 1 ............................................................................ BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
"