patch: run cufflinks without gtf if requested
patch bwa fixmates output
check for cufflinks version
Homer chipseq mod added
Empty read indicator for read to default to single stranded libraries
Merge branch 'master' into homer_chipseq
Read handling refactored

Read indicators don't assume underscore implicitly anymore to allow for
more portability.
Bugfixes
Bugfix
summarize fastqc results only when requested
Bugfix bwa in paired mode
Merge branch 'readhandling' into homer_chipseq

Conflicts:
	mods/bowtie.sh
Merge branch 'readhandling'
read indicator handling adjusted
read indicator handling adjusted 2
adjusting default resources
Pair library files required to be different to qualify for paired runs
Merge branch 'readhandling'
Jobnames tagged with NGs
allows to focus on only cis or trans interactions