find all mapped region in a .sam data.frame

find all mapped region in a .sam data.frame

Arguments

sam	data.frame. see read_sam()

Value

a tibble of 4 variables, chrom, strand, start, end

Examples

sam_file <- system.file('extdata', 'Neat1_1.Aligend_trunc.sam', package = 'paristools')
sam_file %>% read_sam() %>% sam_to_loc_df()
#> # A tibble: 5,859 x 4
#>    chrom strand start   end
#>    <chr> <chr>  <int> <int>
#>  1 neat1 +        170   200
#>  2 neat1 +        774   807
#>  3 neat1 +        294   325
#>  4 neat1 +        311   343
#>  5 neat1 +       1032  1063
#>  6 neat1 +       3158  3177
#>  7 neat1 +       2326  2356
#>  8 neat1 -       2493  2529
#>  9 neat1 -        658   685
#> 10 neat1 -        658   683
#> # … with 5,849 more rows