Add basic summary to callVariant output

[zhuchcn]

Description

Add some basic summary to callVariant output. Looks like this now:

python -m moPepGen.cli callVariant -i test/files/vep/vep_gSNP.gvf test/files/vep/vep_gINDEL.gvf test/files/fusion/star_fusion.gvf --index-dir test/files/index -o test/files/vep/test3.fasta
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] moPepGen callVariant started
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] Reference indices loaded.
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] Using GVF file: test/files/vep/vep_gSNP.gvf
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] Using GVF file: test/files/vep/vep_gINDEL.gvf
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] Using GVF file: test/files/fusion/star_fusion.gvf
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] Variants sorted
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] Start calling variant peptides..
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] callVariant summary:
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] Total transcripts with variants: 5
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] Total transcripts processed: 5
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] Total variant peptides generated (including redundant): 57
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] Total variant peptides saved: 28
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] Variant peptide FASTA file written to disk.
[ 2024-03-01 11:05:00 ] [ moPepGen -  INFO ] rss=79.71 MiB, vms=395.6 MiB, wallclock=0:00:01.330000, system=0:00:00.670000, cpu_usage=100.4%

Closes #412

Checklist

• [X] This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
• [X] This PR does NOT contain molecular files, compressed files, output files such as images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
• [X] I have read the code review guidelines and the code review best practice on GitHub check-list.
• [X] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
• [X] I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.
• [X] All test cases passed locally.