Not enough row in the data downloaded from http://www.ebi.ac.uk/gwas/api/search/downloads/alternative

[stankiewicz565]

So I got the file alternative before going through readr it has 251402 lines. After I run read_tsv on the file theI get an error message which is seen below. I still get a tibble but with only 33944 rows and even adding the additional rows (1345) that could not be parsed due to the error. It still leaves us with only 35289 rows a far cry from 212000. I ran the Problems() function and have a tibble with the 1345 row that could not be parsed and the individual reasons as to why it could not be processed. The reason were the following :
"no trailing characters"
"a double"
"delimiter or quote"
"closing quote at end of file"
"38 columns"

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ERROR message:

gwascat_2021.03.30 = readr::read_tsv('alternative')

── Column specification ───────────────────────────────────────────────────
cols(
.default = col_character(),
DATE ADDED TO CATALOG = col_date(format = ""),
PUBMEDID = col_double(),
DATE = col_date(format = ""),
CHR_POS = col_double(),
UPSTREAM_GENE_DISTANCE = col_double(),
DOWNSTREAM_GENE_DISTANCE = col_double(),
MERGED = col_double(),
SNP_ID_CURRENT = col_double(),
INTERGENIC = col_double(),
P-VALUE = col_double(),
PVALUE_MLOG = col_double(),
OR or BETA = col_double()
)
Use spec() for the full column specifications.

Warning: 1345 parsing failures.
row col expected actual file
1199 SNP_ID_CURRENT no trailing characters 115231908-C 'alternative'
1200 SNP_ID_CURRENT no trailing characters 114539181-G 'alternative'
1201 SNP_ID_CURRENT no trailing characters 12938-C 'alternative'
1202 SNP_ID_CURRENT no trailing characters 10518889-A 'alternative'
1203 SNP_ID_CURRENT no trailing characters 114747981-C 'alternative'
.... .............. ...................... ........... .............
See problems(...) for more details.

[vjcitn]

i think this was resolved via data.table::fread