Program gto_fastq_variation_filter

The gto_fastq_variation_filter filters and segments the regions of singularity from the output of gto_fastq_variation_map.

For help type:


			  			./gto_fastq_variation_filter -h

In the following subsections, we explain the input and output paramters.

Input parameters

The gto_fastq_variation_filter program needs a the output of gto_fastq_variation_map to compute.

The attribution is given according to:


			  			Usage: ./gto_fastq_variation_filter ... [FILE]:<...>
./gto_fastq_variation_filter: a tool to filter maps (gto_fastq_variation_map)

-v                       verbose mode,
-a                       about CHESTER,
-t                threshold [0.0;1.0],
-w                window size,
-u                sub-sampling,

[tFile1]::<...>  target file(s).

The target files may be generated by gto_fastq_variation_map.
Report bugs to <{pratas,raquelsilva,ap,pjf}@ua.pt>.

An example of such an input file is:


			  			1111111111111111111111111111100000000000000000000000000000001111111111111111111
11111111110000000000000000000000000000000000000000000

Output

The output of the gto_fastq_variation_filter program is a text file with the coordenates of the segmented regions.

Using the inputs above, an output example for this is the following:


			  			#132#132
30:60
90:130