read_fai | R Documentation |
Read seq_ids and lengths from a samtools/seqkit faidx file or from a fasta directly (requires seqkit in path). Seqkit is preferred because it allows reading the full header including seq description.
read_fai(
file,
col_names = c("seq_id", "seq_desc", "length"),
keep_index = FALSE
)
file |
.fai/.seqkit.fai (plain/pipe), .fa (plain) |
col_names |
custom column names |
keep_index |
do not ignore index columns with length offsets etc. |
Note, only .fai connections can be pipes, .fa have to be plain text files.
tibble
read_fai("foo.fa.fai") # samtools style index, no description
read_fai("foo.fa.seqkit.fai") # seqkit style with description
# custom col_names and keep index info
read_fai("foo.fa.fai", keep_index=T, col_names=c("contig_id", "contig_desc", "len"))
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