Open bschilder opened 2 years ago
Checked and the file it's being written to does indeed already exist:
x <- "IMPACT707/Annotations/IMPACT707_EAS_chr1.annot.gz" file.exists(echotabix::construct_tabix_path(target_path = x)) out < echotabix::convert(target_path = x, chrom_col = "CHR", start_col = "BP", comment_char = "CHR", force_new = FALSE)
and yet file is still being reprocessed:
========= echotabix::convert ========= Converting full summary stats file to tabix format for fast querying. Inferred format: 'table' Determining chrom type from file header. Chromosome format: 1 Detecting column delimiter. Identified column separator: \t Sorting rows by coordinates via bash. Searching for header row with zgrep. ( zgrep ^'CHR' .../IMPACT707_EAS_chr1.annot.gz; zgrep -v ^'CHR' .../IMPACT707_EAS_chr1.annot.gz | sort -k1,1n -k2,2n ) > .../file3ef1cb2ba03_sorted.tsv
Checked and the file it's being written to does indeed already exist:
and yet file is still being reprocessed: