SNPTools:	pileline for NGS SNP analysis
author	Yi Wang @ Fuli Yu' Group
Baylor College of Medicine Human Genome Sequencing Center.
All rights reserved.

Workflow summary:

bamqc->pileup->snprob->snpcall
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name	bamqc 0.1
func	show summary information of each bam
author	Yi Wang @ Fuli Yu' Group @ BCM
usage	bamqc [option] <ref_dir> [bam1 bam2...]
	-l <file>	batch BAMs
	-m <mask>	filter read by mask (1796)
	-o <oper>	filter read by  operations rate > orate (0.15)
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name	pileup 0.1
func	multiple BAM pileup compression
author	Yi Wang @ Fuli Yu' Group @ BCM
usage	Pileup <region ref.fa square(1.9)> [bam1 bam2...]
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name	snpcall 0.1
func	genotype calling by artifical evolution
author	Yi Wang @ Fuli Yu' Group @ BCM
usage	SNPCall <data.bin gender.txt> [options]
	-d <density>	relative SNP density to Sanger sequencing (0.33)
	-c <chunk>	specify number of SNPs in the core chunk (256)
	-f <flank>	specify number of SNPs in each side (128)
	-b <burn>	burn-in generations (64)
	-m <mcmc>	sampling generations (192)
	-k <known.txt>	assign known genotypes
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name	snprob 0.1
func	population based SNP detection
author	Yi Wang @ Fuli Yu' Group
usage	SNProb [options] <gender.txt in.gz>
	-n <INT>	bin size for genotype calling (20480)
	-s <FLT>	set significance level (2)
	-m <FLT>	set mapping bias cutoff (1e-6)

	-a <FLT>	set AA prior alt allele rate (0.995)
	-h <FLT>	set AB prior alt allele rate (0.500)
	-b <FLT>	set BB prior alt allele rate (0.010)
	-p <FLT>	set prior alt rate confidence (100)
	-f <FLT>	set Fst of the sample (0.13)
	-o <FLT>	set outlier probability (1e-6)
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Installation
User should install GSL first.
Ubuntu: sudo apt-get install libgsl0-dev
If GSL is not installed in default directory, please modify makefile:
Add -Ixxx/GSL/include after INCLUDE=
Add -Lxxx/GSL/lib after LIBS=

The software is based on samtools's API library: libbam.a
User should enter 'samtools' directory and type the following two commands:
	make clean
	make

Finally go back to 'source' directory and type
	make

Email yw2@bcm.edu if you meet installation problems.
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License
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the 'Software'), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.