indexTabix: Compress and index tabix-compatible files.

In Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

Description

Index (with indexTabix) files that have been sorted into ascending sequence, start and end position ordering.

Usage

indexTabix(file,
           format=c("gff", "bed", "sam", "vcf", "vcf4", "psltbl"),
           seq=integer(), start=integer(), end=integer(),
           skip=0L, comment="#", zeroBased=FALSE, ...)

Arguments

file	A characater(1) path to a sorted, bgzip-compressed file.
format	The format of the data in the compressed file. A characater(1) matching one of the types named in the function signature.
seq	If format is missing, then seq indicates the column in which the ‘sequence’ identifier (e.g., chrq) is to be found.
start	If format is missing, start indicates the column containing the start coordinate of the feature to be indexed.
end	If format is missing, end indicates the column containing the ending coordinate of the feature to be indexed.
skip	The number of lines to be skipped at the beginning of the file.
comment	A single character which, when present as the first character in a line, indicates that the line is to be omitted. from indexing.
zeroBased	A logical(1) indicating whether coordinats in the file are zero-based.
...	Additional arguments.

Value

The return value of indexTabix is an updated instance of file reflecting the newly-created index file.

Author(s)

Martin Morgan <[e-mail]>.

References

http://samtools.sourceforge.net/tabix.shtml

Examples

from <- system.file("extdata", "ex1.sam", package="Rsamtools",
                    mustWork=TRUE)
to <- tempfile()
zipped <- bgzip(from, to)
idx <- indexTabix(zipped, "sam")

tab <- TabixFile(zipped, idx) 

Example output

Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Rsamtools documentation built on Nov. 8, 2020, 8:11 p.m.