rule mapHomologousRegions:
	message: " mapping homologous regions of both references using ISBPs markers as anchors"
	input: 
		#closestMarkers=config['results']+'/2.mergedClosestMarkers.txt',
		marker5prime=config['results']+'/2.closestbedUpstream.txt',
		marker3prime=config['results']+'/2.downstreamClosest.txt',
		refQuery=config['queryFasta'],
		faiQuery=config['queryFasta']+'.fai',
		refTarget=config['targetFasta'],
		faiTarget=config['targetFasta']+'.fai',
		markersOnTarget=config['results']+"/1.filteredISBPs.sorted.bed"
	output: directory(config['results']+'/3.mapping')
	log: config['results']+'/3.mapping.log'
	shell: 
		"""
		echo bin/microMappingPipeline.py {input.marker5prime} {input.marker3prime} {output} {input.refQuery} {input.refTarget} {input.markersOnTarget} &> {log}
		"""

rule gmapRescue:
	message: " Rescue anchoring of failed genes with gmap"
	input: anchoringDir=directory(config['results']+'/3.mapping'),
		blastdb=config['blastdb']
	output: config['results']+'/4.gmapRescue.txt'
	log: config['results']+'/4.gmapRescue.log'
	shell:
		"""
		bin/gmapRescue.sh {input.anchoringDir} {input.blastdb} 1> {output} 2> {log}
		"""