options.txt

version:    Reports Ranbow version

hap:	Haplotyping
	-mode index
		Step 1: make index for fasta, VCF, and bam files
	-mode hap
		Step 2: haplotyping 
		Eg:	python ranbow.py hap -mode hap -par params.txt	-processorIndex ?
	-mode collect
		Step 3: collect haplotypes, generate bam files
	-mode modVCF
		Step 4:	Modify the vcf file according to assembled haplotypes

eval:	Evaluate the haplotype assembly 
	-mode index
		Step 1: Generate the index file for Roche 454 fastq, vcf, and fastq files
	-mode run
		Step 2: run evaluation 
	-mode collect
		Step 3: collect result of evaluation 

phylo:	Phylogenetic tree reconstruction from the assembled haplotypes
	-mode index
		Step 1: make index for fasta, VCF, and sam files
	-mode run
		Step 2: haplotyping 
	-mode collect
		Step 3: collect haplotypes, generate bam files
	-mode tree
		Step 4:	Modify the vcf file according to assembled haplotypes