new module: jvarkit vcf2table

[lindenb]

This is a PR for jvarkit/vcf2table https://jvarkit.readthedocs.io/en/latest/VcfToTable/

(...)
 VEP
 +--------------------------+------+----------------+------------+-----------------+--------+------------------+-----------------------------------------------+-------------+---------+-----------------+----------------------+
 | PolyPhen                 | EXON | SIFT           | ALLELE_NUM | Gene            | SYMBOL | Protein_position | Consequence                                   | Amino_acids | Codons  | Feature         | BIOTYPE              |
 +--------------------------+------+----------------+------------+-----------------+--------+------------------+-----------------------------------------------+-------------+---------+-----------------+----------------------+
 | probably_damaging(0.956) | 8/9  | deleterious(0) | 1          | ENSG00000102967 | DHODH  | 346/395          | missense_variant                              | R/W         | Cgg/Tgg | ENST00000219240 | protein_coding       |
 |                          | 3/4  |                | 1          | ENSG00000102967 | DHODH  |                  | non_coding_exon_variant&nc_transcript_variant |             |         | ENST00000571392 | retained_intron      |
 |                          |      |                | 1          | ENSG00000102967 | DHODH  |                  | downstream_gene_variant                       |             |         | ENST00000572003 | retained_intron      |
 |                          |      |                | 1          | ENSG00000102967 | DHODH  |                  | downstream_gene_variant                       |             |         | ENST00000573843 | retained_intron      |
 |                          |      |                | 1          | ENSG00000102967 | DHODH  |                  | downstream_gene_variant                       |             |         | ENST00000573922 | processed_transcript |
 |                          |      |                | 1          | ENSG00000102967 | DHODH  | -/193            | intron_variant                                |             |         | ENST00000574309 | protein_coding       |
 | probably_damaging(0.946) | 8/9  | deleterious(0) | 1          | ENSG00000102967 | DHODH  | 344/393          | missense_variant                              | R/W         | Cgg/Tgg | ENST00000572887 | protein_coding       |
 +--------------------------+------+----------------+------------+-----------------+--------+------------------+-----------------------------------------------+-------------+---------+-----------------+----------------------+
 Genotypes
 +---------+------+-------+----+----+-----+---------+
 | Sample  | Type | AD    | DP | GQ | GT  | PL      |
 +---------+------+-------+----+----+-----+---------+
 | M10475  | HET  | 10,2  | 15 | 10 | 0/1 | 25,0,10 |
 | M10478  | HET  | 10,4  | 16 | 5  | 0/1 | 40,0,5  |
 | M10500  | HET  | 10,10 | 21 | 7  | 0/1 | 111,0,7 |
 | M128215 | HET  | 15,5  | 24 | 0  | 0/1 | 49,0,0  |
 +---------+------+-------+----+----+-----+---------+
 TRIOS
 +-----------+-----------+-----------+-----------+----------+----------+-----------+
 | Father-ID | Father-GT | Mother-ID | Mother-GT | Child-ID | Child-GT | Incompat. |
 +-----------+-----------+-----------+-----------+----------+----------+-----------+
 | M10475    | 0/1       | M10478    | 0/1       | M10500   | 0/1      |           |
 +-----------+-----------+-----------+-----------+----------+----------+-----------+
<<chr1/10001/T n 1

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[SPPearce]

Can we check the contents of the output file in some way, rather than just existence?
Another test to check the other output format and the regions or pedigree would be nice.
Should there also be something in the meta that says which tool gets which args.

[lindenb]

@SPPearce back to you. I added a test to check the content of the output:

{ assert path(process.out.output[0][1]).text.startsWith(">>MT192765.1:197/G (n. 1)")},

[SPPearce]

I'm a bit confused by the regions command.
Would be nice to test the bed file, but otherwise fine