Modified the IlluminaToBamTools package to allow for non-redundant, global configuration files and chaining of IlluminaToBam and BamIndexDecoder analyses via project directories.
The First_Base_Report.htm file seems to be a better indicator for the run start date, as runParameters.xml file seems to get updated by the newer HiSeq Control Software version 2.2.38.
Introduced a new IlluminaRunFolderNotComplete Exception sub-class to allow the run method to signal back incompleteness specifically, which can be used to wait for completeness.
Added support for automatic Illumina Run Folder processing after eventual run completion via a loop and an interval option.
In method run_picard_collect_alignment_summary_metrics, change back to the working directory.
Moved from the HTML 4.01 to the XHTML 1.0 document type.
Fixed UCSC Genome Browser custom track links for transcript assembly GTF files generated by the RNASeq.report method and also some XHTML syntax issues in the same method.
Introduced new configuration options to support non-standard 'Intensities' and 'BaseCalls' directories of an Illumina RUn Folder in the IlluminaToBam analysis.
Introduced a new force option to allow processing of an incomplete Illumina Run Folder.
Library files can now be found automatically in the current directory, just based on the project name.
Merge branch 'master' of https://github.com/mkschuster/bsfpython

Conflicts:
	bin/bsf_submit_illumina_to_bam.py
	bin/bsf_submit_irf_processor.py
	lib/Bio/BSF/Analyses/IlluminaToBamTools.py