`tabix.read.table`: Error: Error: non-character argument

[bschilder]

tabix.read.table fails on Windows. It seems that your GHA checks are also indicating this to you, but those have expired so I can't check.

@zhanxw is seqminer still being maintained or should it be considered deprecated and no longer used? I'm wondering because it's (currently) a dep for several of my packages.

remotes::install_github("RajLabMSSM/echodata")
remotes::install_github("RajLabMSSM/echotabix")
library(echotabix)

BST1 <- echodata::BST1 
    fullSS_path <- echodata::example_fullSS()
    fullSS_tabix <- convert(fullSS_path = fullSS_path,
                            start_col = "BP")
# Wraps seqminer and some other tools
tab1 <- query_tabular(
        fullSS_tabix = fullSS_tabix,
        chrom = BST1$CHR[1],
        start_pos = min(BST1$POS),
        end_pos = max(BST1$POS)
    )

Error report

Found here.

-- Error (test-query_tabular.R:9:5): query_tabular works -----------------------
Error: Error: non-character argument
Backtrace:
    x
 1. \-echotabix::query_tabular(...) test-query_tabular.R:9:4
 2.   \-seqminer::tabix.read.table(tabixFile = fullSS_tabix, tabixRange = coords)
 3.     +-base::do.call(rbind, strsplit(body, "\t"))
 4.     \-base::strsplit(body, "\t")

Seems to be related to this.

Thanks, Brian

[bschilder]

@zhanxw would really appreciate a response on this, particularly on whether seqminer should be used or not.