Files in RajLabMSSM/echotabix

echoverse module: automated creation and querying of tabix files

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md NEWS.md R/DF_to_dt.R R/check_convert_methods.R R/check_delimiter.R R/check_outputs.R R/construct_outputs.R R/construct_query.R R/construct_subset_vcf_name.R R/construct_tabix_path.R R/construct_vcf_path.R R/convert.R R/convert_and_query.R R/dt_to_vcf.R R/fill_NA.R R/filter_table_snps.R R/filter_vcf_samples.R R/filter_vcf_snps.R R/fix_query_style.R R/get_bgzip.R R/get_chain_file.R R/get_column_indices.R R/get_gunzip.R R/get_locus_vcf_folder.R R/get_os.R R/get_vcf_suffixes.R R/granges_style.R R/granges_to_dt.R R/granges_to_string.R R/index.R R/index_conda.R R/index_rsamtools.R R/index_seqminer.R R/index_variantannotation.R R/infer_chrom_column.R R/infer_chrom_type.R R/infer_comment_char.R R/infer_tabix_format.R R/is_tab_delimited.R R/is_tabix.R R/is_vcf.R R/liftover.R R/messager.R R/query.R R/query_table.R R/query_table_conda.R R/query_table_genomicfiles.R R/query_table_rsamtools.R R/query_table_seqminer.R R/query_vcf.R R/query_vcf_conda.R R/query_vcf_rtracklayer.R R/query_vcf_seqminer.R R/query_vcf_variantannotation.R R/read_bgz.R R/read_bgz_datatable.R R/read_bgz_utils.R R/remove_empty_tabix.R R/report_table.R R/report_time.R R/report_vcf.R R/rhtslib_warning.R R/rm_tbi.R R/run_bgzip.R R/run_bgzip_conda.R R/run_bgzip_rsamtools.R R/run_gunzip.R R/run_gunzip_conda.R R/run_gunzip_rutils.R R/save_table.R R/save_vcf.R R/scanTabix_to_dt.R R/select_method.R R/select_zgrep.R R/sort_coordinates.R R/sort_coordinates_bash.R R/sort_coordinates_check_method.R R/sort_coordinates_datatable.R R/suffixes.R R/vcf_to_dt.R R/zzz.R README.Rmd README.md inst/echotabix_0.99.0.pdf inst/hex/hexSticker.Rmd man/DF_to_dt.Rd man/check_delimiter.Rd man/construct_outputs.Rd man/construct_query.Rd man/construct_subset_vcf_name.Rd man/construct_tabix_path.Rd man/construct_vcf_path.Rd man/convert.Rd man/convert_and_query.Rd man/dt_to_vcf.Rd man/fill_NA.Rd man/filter_vcf_query_samples.Rd man/get_chain_file.Rd man/get_locus_vcf_folder.Rd man/granges_to_dt.Rd man/granges_to_string.Rd man/index.Rd man/index_conda.Rd man/index_rsamtools.Rd man/index_seqminer.Rd man/index_variantannotation.Rd man/infer_chrom_type.Rd man/is_tabix.Rd man/is_vcf.Rd man/liftover.Rd man/query.Rd man/query_table.Rd man/query_table_conda.Rd man/query_table_genomicfiles.Rd man/query_table_rsamtools.Rd man/query_table_seqminer.Rd man/query_vcf.Rd man/query_vcf_conda.Rd man/query_vcf_rtracklayer.Rd man/query_vcf_seqminer.Rd man/query_vcf_variantannotation.Rd man/read_bgz.Rd man/report_time.Rd man/rhtslib_warning.Rd man/rm_tbi.Rd man/run_bgzip.Rd man/run_bgzip_conda.Rd man/run_bgzip_rsamtools.Rd man/run_gunzip.Rd man/run_gunzip_conda.Rd man/run_gunzip_rutils.Rd man/save_vcf.Rd man/scanTabix_to_dt.Rd man/select_method.Rd man/sort_coordinates.Rd man/sort_coordinates_bash.Rd man/sort_coordinates_datatable.Rd man/suffixes.Rd man/vcf_to_dt.Rd tests/testthat.R tests/testthat/test-check_convert_method.R tests/testthat/test-construct_query.R tests/testthat/test-construct_tabix_path.R tests/testthat/test-construct_vcf_path.R tests/testthat/test-convert.R tests/testthat/test-convert_and_query.R tests/testthat/test-dt_to_vcf.R tests/testthat/test-infer_chrom_type.R tests/testthat/test-liftover.R tests/testthat/test-query.R tests/testthat/test-query_table_rsamtools.R tests/testthat/test-query_tabular.R tests/testthat/test-query_vcf.R tests/testthat/test-query_vcf_variantannotation.R tests/testthat/test-read_bgz.R tests/testthat/test-rsamtools.R tests/testthat/test-run_bgzip.R tests/testthat/test-run_gunzip.R tests/testthat/test-scanTabix_to_dt.R tests/testthat/test-sort_coordinates.R tests/testthat/test-vcf_to_dt.R vignettes/echotabix.Rmd