readme

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# mutation-call-by-coverage
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Here is provided a set of model tools, with the same configuraration file.

Cheapseq

Cheapseq emulates a sequencing procedure, currently works only with one chromosome (reference sequence). Randonly generates and applies the mutations to all the reads; output the list of the mutations as well as Fasta with all the reads. 

For help: ./cheapseq --help 

Noiser

Take a FastA/FastQ stream, noise randomly some positions, outputs FastA. The main parameter is bases per error (0 is default, means no noise, actually, it is inf). 

For help: ./noiser --help 


DownSAM

Downsamples a SAM file. SAM stream input, SAM stream output. Tha main parameter is reads in input per reads in output. 1 (default) means no downsampling.

For help: ./downSAM --help