Package index • echotabix

Convert

Convert files to tabix-indexed format (sort, compress, index).

convert(): Convert to tabix
convert_and_query(): Convert and query
run_bgzip(): Run bgzip
run_gunzip(): Run gunzip
sort_coordinates(): Sort coordinates
index(): Tabix-index a file
dt_to_vcf(): data.table to VCF

Query

Query tabix-indexed local or remote files.

query(): Query tabix
query_table(): Query a tabix file
query_vcf(): Query VCF file
construct_query(): Construct query
scanTabix_to_dt(): scanTabix to data.table

Read and Parse

Read and parse compressed or VCF files.

read_bgz(): Read bgz
vcf_to_dt(): Variant Call Format (VCF) –> data.table

Path Construction

Construct and validate file paths for tabix and VCF files.

construct_tabix_path(): Construct tabix path
construct_vcf_path(): VCF path

Genomic Utilities

Genome build conversion, coordinate helpers, and column inference.

liftover(): Genome build liftover
granges_to_string(): GRanges to string
infer_chrom_type(): Infer chromosome type
check_delimiter(): Check delimiter

Other

is_vcf(): Is VCF