Add '-n' note column in maf and error message into error report

[leexgh]

Fix: https://github.com/genome-nexus/genome-nexus-annotation-pipeline/issues/255

• new parameter -n
• -n will add "genomic_location_explanation" column to output file. Only variants that have altered genomic location will have value in this column
  • example column value: End position changes from 170837525 to 170837526, end position should equal to start position for SNV variants
• Add error message in error report. To create error report, add -e REPORT_PATH in command.
  • Example error message: Reference allele extracted from response (CA) does not match given reference allele (AC).
• Add error message into LOG file.
  • Example log: 2023-09-13 22:45:41 [main] WARN org.cbioportal.annotator.internal.GenomeNexusImpl - Annotation failed for variant 17:g.7578475del;Reference allele extracted from response (TGCCGGGCG) does not match given reference allele (GACGCGGGT)
• Update documentation about -n

[rmadupuri]

This is great! Thanks Xiang!

Should we also set the -n to be default? And is there a character limit to this column?

[leexgh]

@rmadupuri Not sure if we want to add -n by default, for most of the variants this column will be empty, only variants with altered genomic location will have value, so I'm not sure if it makes sense to do it for all variants. Have you ever seen a column reach the limit? Do you know what is the limit?

[rmadupuri]

@leexgh, should we add an extra check - if the value exists atleast for one variant in the maf, then we can prolly include the column? This is to be more transparent that we are updating the coordinates (I wonder how many people would explicitly define the -n and notice the changes otherwise). We can merge this PR and prolly implement this later if agreed.