== Simulations ==

The set of simulations are:
{One,Many}{Human,Staph}{Error,NoError}Reads{100,250}

'Many' sample simulations are all done with sequencing error

1. Genomes:
hg19 chr1 is used for human (249Mbp)
Strain TW20 circular chromosome is used for Staph (3Mbp)
2. Samples:
Many is 10 for Human 1,000 for Staph
3. Read Length:
Reads are 100 or 250 bp long
4. Insert Size:
insert gap size is Normally distributed with mean 250, stddev 50: N(250,50)
5. Covg:
Covg is 30X for human, 100X for staph
6. Sequencing error:
Error is empirical from PhiX Illumina reads
==
7. Variation:
Pi is 1/1000bp in human, 1/100bp staph
Allele frequency has distribution 1/N

sites=P*sum(1/c(1:(S-1)))*L
  P=pi pairwise
  S=samples
  L=length(bp)

SNPs 90%, indels 10%

* human (Pi=0.001) on chr1 (250Mb)
1 human has:
P=0.001, S=2, L=250,000,000, sites=250,000 (0.1%); 225,000 SNPs; 25,000 indels
10 humans have:
P=0.001, S=20, L=250,000,000, sites=886,935 (0.35%); 798,242 SNPs; 88,694 indels

* staph (Pi=0.01) on genome (3Mb)
2 staph has:
P=0.01, S=2, L=3,000,000, sites=30,000 (1%); 27,000 SNPs; 3,000 indels
1000 staphs have:
P=0.01, S=1000, L=3,000,000, sites=224,534 (7.5%); 202,081 SNPs; 22,453 indels

==
8. Variant Calling
Calling is with k=31
Using released cortex, shades, paths (se,pe,se+pe)

Simulations:
OneHumanErrorReads100
OneHumanErrorReads250
OneHumanNoErrorReads100
OneHumanNoErrorReads250
OneStaphErrorReads100
OneStaphErrorReads250
OneStaphNoErrorReads100
OneStaphNoErrorReads250
ManyHumanErrorReads100
ManyHumanErrorReads250
ManyStaphErrorReads100
ManyStaphErrorReads250

Generate simulation list
echo {One,Many}{Human,Staph}{Error,NoError}Reads{100,250} | tr ' ' '\n' | awk '$1 !~ /Many/ || $1 !~ /NoError/' > sims.txt


readsim -l [100,250] -i 250 -v 0.2 -r [chr1.fa.gz|staph.fa.gz] -d [30,100] [-p ../PhiX.100K.1.fq.gz] <out>
