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Parsable Readme for Github #24

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Parsable Readme for Github #24

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8c4858f
move README
erikbgithub Sep 3, 2021
518bc6f
README: readability enhancements for markdown compiler
erikbgithub Sep 3, 2021
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21 changes: 13 additions & 8 deletions README → README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,9 @@ that comes with the package.
Compilation
===========

```
gcc -g -O2 -Wall -o wgsim wgsim.c -lz -lm
```


History
Expand All @@ -37,30 +39,32 @@ Simulation and evaluation

The command line for simulation:

wgsim -Nxxx -1yyy -d0 -S11 -e0 -rzzz hs37m.fa yyy-zzz.fq /dev/null
wgsim -Nxxx -1yyy -d0 -S11 -e0 -rzzz hs37m.fa yyy-zzz.fq /dev/null

where yyy is the read length, zzz is the error rate and $xxx * $yyy = 10000000.
where `yyy` is the read length, `zzz` is the error rate and
`$xxx * $yyy = 10000000`.
By default, 15% of polymorphisms are INDELs and their lengths are drawn from a
geometric distribution with density 0.7*0.3^{l-1}.
geometric distribution with density `0.7*0.3^{l-1}`.

The command line for evaluation:

wgsim_eval.pl unique aln.sam | wgsim_eval.pl alneval -g 20
wgsim_eval.pl unique aln.sam | wgsim_eval.pl alneval -g 20

The '-g' option may be changed with mappers.
The `-g` option may be changed with mappers.


System
------

GCC: 4.1.2
CPU: AMD Opteron 8350 @ 2.0GHz
Mem: 128GB
* GCC: 4.1.2
* CPU: AMD Opteron 8350 @ 2.0GHz
* Mem: 128GB


Results
-------

```
==================================================================================================================
100bp 200bp 500bp 1000bp 10000bp
------------------ ----------------- ----------------- ----------------- -----------------
Expand All @@ -76,6 +80,7 @@ Results
err% 0.66 0.69 2.31 0.34 0.40 0.70 0.10 0.00 0.20
one% 100 99.4 0 100 100 100 100 100 100
==================================================================================================================
```

1) AGILE throws "Floating point exception" halfway for 100/200bp reads. The
default output is supposed to be PSL, but actually has an additional "score"
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