Misformatted metadata causes incorrect output

[arisp99]

Bug Description

If the metadata in a file in misformatted (i.e., does not contain six lines), read_file() and read() returns the incorrect output. Currently, we lose information and, instead of being treated as rows, samples are treated as columns.

# Metadata contains only four lines
misformatted <- tibble::tribble(
                         ~Gene,            ~atp6,           ~mdr1,
               "Mutation Name", "atp6-Ala623Glu", "mdr1-Asn86Tyr",
                   "AA Change",      "Ala623Glu",      "Asn86Tyr",
                    "Targeted",            "Yes",           "Yes",
                  "D10-JJJ-23",              "0",            "13",
                  "D10-JJJ-43",              "0",             "0",
                  "D10-JJJ-50",             "15",             "0"
               )

path <- tempfile()
readr::write_csv(misformatted, path)
MIPr::read_file(path)
#> # A tibble: 2 × 8
#>   sample     gene  mutation_name  aa_change targeted d10_jjj_23 d10_jjj_43 value
#>   <chr>      <chr> <chr>          <chr>     <chr>    <chr>      <chr>      <chr>
#> 1 D10-JJJ-50 atp6  atp6-Ala623Glu Ala623Glu Yes      0          0          15   
#> 2 D10-JJJ-50 mdr1  mdr1-Asn86Tyr  Asn86Tyr  Yes      13         0          0
unlink(path)

^{Created on 2021-09-14 by the reprex package (v2.0.1)}

Expected Behavior

We would expect to see six rows in our final dataset with all the metadata represented as columns, as shown below:

MIPr::read_file(path)
#> # A tibble: 6 × 8
#>   sample     gene  mutation_name aa_change targeted value
#>   <chr>      <chr> <chr>         <chr>     <chr>    <chr>
#> 1 D10-JJJ-23 atp6  atp6-Ala623G… Ala623Glu Yes      0    
#> 2 D10-JJJ-43 atp6  atp6-Ala623G… Ala623Glu Yes      0    
#> 3 D10-JJJ-50 atp6  atp6-Ala623G… Ala623Glu Yes      15   
#> 4 D10-JJJ-23 mdr1  mdr1-Asn86Tyr Asn86Tyr  Yes      13   
#> 5 D10-JJJ-43 mdr1  mdr1-Asn86Tyr Asn86Tyr  Yes      0    
#> 6 D10-JJJ-50 mdr1  mdr1-Asn86Tyr Asn86Tyr  Yes      0