Fix bugs in the GERP step of the pipeline

[verku]

No description provided.

[verku]

Check how many bases have been added to the analysis in the tiny test dataset compared to the previous version

[verku]

Fixed GERP scripts:

gzip -cd GCF_000283155.1_CerSimSim1.0_genomic.Sc9M7eS_2_HRSCAF_41.genome.ancestral.rates.gz | awk '$3 != "N" {print}' | wc -l
3264751

gzip -cd GCF_000283155.1_CerSimSim1.0_genomic.Sc9M7eS_2_HRSCAF_41.genome.ancestral.rates.gz | awk '$4 != "0" {print}' | wc -l
7048181

Version 0.4.1 (code as in manuscript but tree in millions of years):

gzip -cd GCF_000283155.1_CerSimSim1.0_genomic.Sc9M7eS_2_HRSCAF_41.ancestral.rates.gz | awk '$3 != "N" {print}' | w
c -l
3022073

gzip -cd GCF_000283155.1_CerSimSim1.0_genomic.Sc9M7eS_2_HRSCAF_41.ancestral.rates.gz | awk '$4 != "0" {print}' | w
c -l
6518768