Peek into a BAM File with Tag Filtering

This function provides a quick look into the contents of a BAM file, filtered by a specific tag. It validates the input parameters, checks for the file's existence, and utilizes a helper function to handle the BAM processing if the file exists. An error is raised if the input conditions are not met.

Usage

peekbam(bam, n = 100, field = c("tag", "name"), TAG = "CB")

Arguments

bam

A character string specifying the path to a single BAM file. Only a single file should be specified.

n

An integer, defaulting to 100, indicating the number of entries to peek. n must be greater than 0.

TAG

A character string specifying the tag to filter by within the BAM file. The default is "CB" (Cell Barcode).

Value

The function itself does not return a value; it operates through side effects such as invoking a Rust helper function or printing messages to the console.

Details

If the file does not exist, a message will be displayed. If n is less than 1 or if more than one BAM file is specified, the function will stop with an error.

References

This documentation was written by ChatGPT v4 - OpenAI, conversation with the author, 5-2-2024.

Examples

# Assuming 'example.bam' is a valid BAM file path:
peekbam("example.bam", n = 10, TAG = "CB")
#> File not found:
#> example.bam