Add Genes statistics file to snpeff output

[paulzierep]

As per snpeff docs there is a Genes statistics file:

The "Genes statistics" file path is by default the directory where SnpEff is executed and called snpEff_genes.txt. If you change the summary file name / path by either using -stats or csvStats command line, the "Genes statistics" file path will be the same directory as the summary file and the file name is the same "base name" plus a ".genes.txt".

Which gives stats per gene:

$ head snpEff_genes.txt
# The following table is formatted as tab separated values.
#GeneName   GeneId  TranscriptId    BioType variants_impact_HIGH    variants_impact_LOW variants_impact_MODERATE    variants_impact_MODIFIER    variants_effect_3_prime_UTR_variant variants_effect_5_prime_UTR_premature_start_codon_gain_variant  variants_effect_5_prime_UTR_variant variants_effect_downstream_gene_variant variants_effect_intron_variant  variants_effect_missense_variant    variants_effect_non_coding_exon_variant variants_effect_splice_acceptor_variant variants_effect_splice_donor_variant    variants_effect_splice_region_variant   variants_effect_start_lost  variants_effect_stop_gained variants_effect_stop_lost   variants_effect_synonymous_variant  variants_effect_upstream_gene_variant   bases_affected_DOWNSTREAM   total_score_DOWNSTREAM  length_DOWNSTREAM   bases_affected_EXON total_score_EXON    length_EXON bases_affected_INTRON   total_score_INTRON  length_INTRON   bases_affected_SPLICE_SITE_ACCEPTOR total_score_SPLICE_SITE_ACCEPTOR    length_SPLICE_SITE_ACCEPTOR bases_affected_SPLICE_SITE_DONOR    total_score_SPLICE_SITE_DONOR   length_SPLICE_SITE_DONOR    bases_affected_SPLICE_SITE_REGION   total_score_SPLICE_SITE_REGION  length_SPLICE_SITE_REGION   bases_affected_TRANSCRIPT   total_score_TRANSCRIPT  length_TRANSCRIPT   bases_affected_UPSTREAM total_score_UPSTREAM    length_UPSTREAM bases_affected_UTR_3_PRIME  total_score_UTR_3_PRIME length_UTR_3_PRIME  bases_affected_UTR_5_PRIME  total_score_UTR_5_PRIME length_UTR_5_PRIME
AC000029.1  ENSG00000221069 ENST00000408142 miRNA   0   0   0   2   0   0   0   2   0   0   0   0   0   0   0   0   5000    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
AC000068.5  ENSG00000185065 ENST00000431090 antisense   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   5000    0   0   0   0   0   0
AC000081.2  ENSG00000230194 ENST00000433141 processed_pseudogene    0   0   0   8   0   0   0   3   0   0   0   0   0   0   5000    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   5   0   5000    0   0
AC000089.3  ENSG00000235776 ENST00000424559 processed_pseudogene    0   0   0   1   0   0   0   0   0   0   0   0   0   0   5000    0   0   0   0   0   0
AC002472.1  ENSG00000269103 ENST00000547793 protein_coding  0   0   0   6   0   0   0   5   0   0   0   0   0   0   0   5000    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   5000    0   0
AC002472.11 ENSG00000226872 ENST00000450652 antisense   0   0   0   13  0   0   0   5   2   0   0   0   0   0   0   5000    0   0   0   2   0   11199   0   0   0   0   0   0   0   0   0   0   0   0   6   0   5000    0   0
AC002472.13 ENSG00000187905 ENST00000342608 protein_coding  0   1   6   1   0   0   0   0   1   6   0   0   0   1   0   116 1   0   934 0   0   0   0   0   0   1   0   3   0   0   0   0   0   0   0   0   0   0   0
AC002472.13 ENSG00000187905 ENST00000442047 protein_coding  0   1   6   1   0   0   0   0   1   6   0   0   0   1   0   116 1   0   934 0   0   0   0   0   0   1   0   3   0   0   0   0   0   0   0   0   0   0   0

This file could be rather useful for correlation analysis we are planning in a project.
Currently, only the html summary stats are caught by the output. Need to add the option to fetch this output as well.