Improve statistics output

[nuno-agostinho]

This PR fixes two issues with statistics output:

1. When running VEP using only FASTA and GTF with stats enabled, VEP will print the following message:

Can't use an undefined value as a HASH reference at /hps/software/users/ensembl/repositories/nuno/ensembl-vep/modules/Bio/EnsEMBL/VEP/Stats.pm line 687.

This PR fixes this message by not printing the data version table when there is no such information.

2. Also, when using --input_data, the statistics will show (for both HTML and TXT files):

Input file	*Bio::EnsEMBL::VEP::Runner::IN

This PR will print --input_data when --input_file is *Bio::EnsEMBL::VEP::Runner::IN.

Testing

For testing, you can use the FASTA and GTF from the t/testdata folder. The following command should not print the message above:

vep --id "21 25587758 rs116645811 G A" \
    --fasta t/testdata/fasta/Homo_sapiens.GRCh38.toplevel.test.fa \
    --gtf t/testdata/custom/test.gtf.gz --stats_html --stats_text

This will output two summary files (in HTML and TXT). The file in TXT should report the following if using --input_file:

[VEP run statistics]
VEP version (API)        112.0 (112)
Annotation sources      Custom: t/testdata/custom/test.gtf.gz (overlap)
Species homo_sapiens
Command line options    --fasta t/testdata/fasta/Homo_sapiens.GRCh38.toplevel.test.fa --force_ove>
Start time      2024-02-21 15:17:28
End time        2024-02-21 15:17:28
Run time        0 seconds
Input file	    i.txt
Output file     variant_effect_output.txt

[Data version]
No data version information available.

[General statistics]
Lines of input read     1
Variants processed      1

And the same TXT file but when using --input_data:

[VEP run statistics]
VEP version (API)	 112.0 (112)
Annotation sources	Custom: t/testdata/custom/test.gtf.gz (overlap)
Species	homo_sapiens
Command line options	--fasta t/testdata/fasta/Homo_sapiens.GRCh38.toplevel.test.fa --force_overwrite --gtf t/testdata/custom/test.gtf.gz --input_data 21 25587758 rs116645811 G A --stats_html --stats_text
Start time	2024-02-21 15:29:01
End time	2024-02-21 15:29:02
Run time	1 seconds
Input data	21 25587758 rs116645811 G A
Output file	variant_effect_output.txt

[Data version]
No data version information available.

[General statistics]
Lines of input read	1
Variants processed	1

The HTML file should look like this if using --input_file:

And the HTML file should look like this if using --input_data:

[dglemos]

The updates look good:

• the stats file displays the input data instead of *Bio::EnsEMBL::VEP::Runner::IN
• the message is clear if no data version is available

All the tests were passing when I ran them locally however, Travis is failing in t/AnnotationSource_File_GTF.t

[dglemos]

Merged into release/112 and main