Merge branch 'fusionsearch'
Revert "Merge branch 'fusionsearch'"

This reverts commit dbe4d46749ab0a1a76587882de73b17ae575c158, reversing
changes made to fdc9ac201337204a84107ab165956aecf3901fec.
Revert "Fix merge conflict"

This reverts commit fdc9ac201337204a84107ab165956aecf3901fec, reversing
changes made to 3fd2f565311f57067464fea9aef7f01b4203e7de.
Merge remote-tracking branch 'origin/masai_fseq'

Conflicts:
	.gitignore
	bin/trigger.sh
	conf/header.d/FSEQ
	conf/sample_header.sh
	core/prepareJobSubmission.sh
	doc/installation/setup
	mods/countsTable.sh
	mods/fseq.sh
	mods/hicHomer.sh
	mods/reCalAln.sh
	mods/tophatfusion.sh
	mods/wiggler.sh
	sampleConfigs/tophatfusion_config.txt
	tools/circos_tophat_fusion/base.conf
	tools/circos_tophat_fusion/ideogram.conf
	tools/circos_tophat_fusion/ticks.conf
smoketest updated
Merge branch 'master' into masai_fseq