parseSamReadLines: Parse Sam file read lines
In jefferys/SamSeq: Work with aligned reads from a SAM file

Parse Sam file read lines

1	parseSamReadLines(lines, splitTags = TRUE)

`lines`	A character vector of read lines, in order, from a sam file
`splitTags`	Set `FALSE` to leave optional tags unprocessed as a `tags` column of characters (with embedded tabs). By default will split optional tags out as columns, but this is significantly slower (5x or more).

A data frame of the parsed read lines, with required column names matching the SAM spec. Optional tags, if split out, will each have their own column of values named for the two character tag. Columns will be integer or double if appropriate, all other types are left as character.

jefferys/SamSeq documentation built on Oct. 25, 2019, 8:11 a.m.