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### Program: gigaBayes Version: 0.4.1 Release date: 2008-12-11
### Bayesian SNP and short-INDEL polymorphism discovery program.
### Copyright: 2007, 2008. Gabor T. Marth, Boston College
### All rights reserved.
###
### Usage: /usr/local/bin/MarthLab/bin/gigaBayes [arguments], where:
### --gig [string, required, no default, single-valued]
###     Description: Input file (GIG binary format assembly file)
### --gff [string, required, no default, single-valued]
###     Description: Output file: GFF3 text format annotation file reporting SNP and INDEL candidates
### --glt [string, optional, default=, single-valued]
###     Description: Output file: individual genotype likelihoods in text format
### --log [string, optional, default=, single-valued]
###     Description: Log file
### --indel [switch, optional, default=false, single-valued]
###     Description: Look for single-base INDELs?
### --cgp [switch, optional, default=true, single-valued]
###     Description: Calculate individual genotype probabilities?
### --region [switch, optional, default=false, single-valued]
###     Description: Analyze a specific region?
### --regionSeq [string, optional, default=, single-valued]
###     Description: Name of reference sequence for region to analyze
### --regionBegin [int, optional, default=1000000000, single-valued]
###     Description: First position of region to analyze
### --regionEnd [int, optional, default=0, single-valued]
###     Description: Last position of region to analyze
### --anchor [switch, optional, default=false, single-valued]
###     Description: Use anchor sequence for polymorphism calling?
### --ploidy [string, optional, default=haploid, single-valued]
###     Permitted values: (haploid|diploid)
###     Description: Sample ploidy
### --sample [string, optional, default=multiple, single-valued]
###     Permitted values: (single|multiple|trio|unknown)
###     Description: Naming scheme for matching reads to samples
### --sampleDel [string, optional, default=-, single-valued]
###     Description: Delimiter string separating sample name and read name
### --CRL [int, optional, default=0, single-valued]
###     Description: Minimum total read coverage for position to be considered
### --CRU [int, optional, default=10000000, single-valued]
###     Description: Maximum total read coverage for position to be considered
### --CAL [int, optional, default=0, single-valued]
###     Description: Minimum read coverage for each allele (any strand)
### --CAL1 [int, optional, default=0, single-valued]
###     Description: Minimum read coverage for major allele (both stands)
### --CAL2 [int, optional, default=0, single-valued]
###     Description: Minimum read coverage for minor allele (both strands)
### --QRL [int, optional, default=10, single-valued]
###     Description: Minimum read base quality value
### --QAL [int, optional, default=40, single-valued]
###     Description: Minimum aggregate allele quality value
### --D [long double, optional, default=10E-3, single-valued]
###     Description: Pairwise nucleotide diversity (theta)
### --M [long double, optional, default=1E-8, single-valued]
###     Description: Per-generation somatic mutation rate (mu)
### --algorithm [string, optional, default=banded, single-valued]
###     Permitted values: (banded|recursive)
###     Description: P(SNP) calculation algorithm
### --PSL [long double, optional, default=0.5, single-valued]
###     Description: P(SNP) lower probability threshold for reporting polymorphism candidate
### --WB [int, optional, default=2, single-valued]
###     Description: Bandwidth for banded P(SNP) calculation algorithm (genotype combination level)
### --TB [int, optional, default=10, single-valued]
###     Description: Number of terms to keep per cycle in banded P(SNP) calculation algorithm (0: keep all)
### --TR [int, optional, default=10, single-valued]
###     Description: Number of terms to keep per cycle of recursive P(SNP) calculation algorithm (0: keep all)
### --O [int, optional, default=1, single-valued]
###     Permitted values: (0|1|2|3|4)
###     Description: Output detail level for candidate polymorphism report
### --R [int, optional, default=10000, single-valued]
###     Description: Batch size for reads to be read from GIG file
### --I [int, optional, default=10000, single-valued]
###     Description: Report interval for debugging printouts
### --debug [switch, optional, default=false, single-valued]
###     Description: Print debugging messages?
### --debug2 [switch, optional, default=false, single-valued]
###     Description: Print very detailed debugging messages?
### --help, -h [switch, optional, default=false, single-valued]
###     Description: Print usage statement?
### --version [switch, optional, default=false, single-valued]
###     Description: Print program version?
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