[.DEploid/utilities/dEploidTools.r:1:22:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                     ^
```
[.DEploid/utilities/dEploidTools.r:1:28:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                           ^
```
[.DEploid/utilities/dEploidTools.r:2:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L2) *style:* **Variable and function names should be all lowercase.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:2:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L2) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:2:48:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L2) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
                                               ^
```
[.DEploid/utilities/dEploidTools.r:3:15:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L3) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i+1
              ^
```
[.DEploid/utilities/dEploidTools.r:3:22:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L3) *style:* **Put spaces around all infix operators.**
```r
        arg_i = arg_i+1
                    ~^~
```
[.DEploid/utilities/dEploidTools.r:6:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L6) *style:* **Variable and function names should be all lowercase.**
```r
    outPrefix = "dataExplore"
    ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:6:15:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L6) *style:* **Use <-, not =, for assignment.**
```r
    outPrefix = "dataExplore"
              ^
```
[.DEploid/utilities/dEploidTools.r:7:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L7) *style:* **Variable and function names should be all lowercase.**
```r
    vcfFileName = ""
    ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:7:17:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L7) *style:* **Use <-, not =, for assignment.**
```r
    vcfFileName = ""
                ^
```
[.DEploid/utilities/dEploidTools.r:8:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L8) *style:* **Variable and function names should be all lowercase.**
```r
    refFileName = ""
    ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:8:17:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L8) *style:* **Use <-, not =, for assignment.**
```r
    refFileName = ""
                ^
```
[.DEploid/utilities/dEploidTools.r:9:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L9) *style:* **Variable and function names should be all lowercase.**
```r
    altFileName = ""
    ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:9:17:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L9) *style:* **Use <-, not =, for assignment.**
```r
    altFileName = ""
                ^
```
[.DEploid/utilities/dEploidTools.r:10:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L10) *style:* **Variable and function names should be all lowercase.**
```r
    plafFileName = ""
    ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:10:18:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L10) *style:* **Use <-, not =, for assignment.**
```r
    plafFileName = ""
                 ^
```
[.DEploid/utilities/dEploidTools.r:11:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L11) *style:* **Variable and function names should be all lowercase.**
```r
    excludeFileName = ""
    ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:11:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L11) *style:* **Use <-, not =, for assignment.**
```r
    excludeFileName = ""
                    ^
```
[.DEploid/utilities/dEploidTools.r:12:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L12) *style:* **Variable and function names should be all lowercase.**
```r
    dEploidPrefix = ""
    ^~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:12:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L12) *style:* **Use <-, not =, for assignment.**
```r
    dEploidPrefix = ""
                  ^
```
[.DEploid/utilities/dEploidTools.r:13:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L13) *style:* **Variable and function names should be all lowercase.**
```r
    excludeBool = FALSE
    ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:13:17:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L13) *style:* **Use <-, not =, for assignment.**
```r
    excludeBool = FALSE
                ^
```
[.DEploid/utilities/dEploidTools.r:15:11:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L15) *style:* **Use <-, not =, for assignment.**
```r
    arg_i = 1
          ^
```
[.DEploid/utilities/dEploidTools.r:16:11:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
          ^
```
[.DEploid/utilities/dEploidTools.r:16:33:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
                                ^
```
[.DEploid/utilities/dEploidTools.r:17:14:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L17) *style:* **Use <-, not =, for assignment.**
```r
        argv = args[arg_i]
             ^
```
[.DEploid/utilities/dEploidTools.r:18:12:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
           ^
```
[.DEploid/utilities/dEploidTools.r:18:28:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
                           ^
```
[.DEploid/utilities/dEploidTools.r:19:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L19) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:19:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L19) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:19:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L19) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:19:52:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:20:13:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L20) *style:* **Variable and function names should be all lowercase.**
```r
            vcfFileName = args[arg_i]
            ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:20:25:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L20) *style:* **Use <-, not =, for assignment.**
```r
            vcfFileName = args[arg_i]
                        ^
```
[.DEploid/utilities/dEploidTools.r:21:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:21:36:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                                   ^
```
[.DEploid/utilities/dEploidTools.r:22:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L22) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:22:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L22) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:22:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L22) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:22:52:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:23:13:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L23) *style:* **Variable and function names should be all lowercase.**
```r
            plafFileName = args[arg_i]
            ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:23:26:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L23) *style:* **Use <-, not =, for assignment.**
```r
            plafFileName = args[arg_i]
                         ^
```
[.DEploid/utilities/dEploidTools.r:24:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:24:35:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                                  ^
```
[.DEploid/utilities/dEploidTools.r:25:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L25) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:25:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L25) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:25:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L25) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:25:52:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:26:13:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L26) *style:* **Variable and function names should be all lowercase.**
```r
            refFileName = args[arg_i]
            ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:26:25:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L26) *style:* **Use <-, not =, for assignment.**
```r
            refFileName = args[arg_i]
                        ^
```
[.DEploid/utilities/dEploidTools.r:27:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:27:35:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                                  ^
```
[.DEploid/utilities/dEploidTools.r:28:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L28) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:28:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L28) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:28:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L28) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:28:52:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L28) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:29:13:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L29) *style:* **Variable and function names should be all lowercase.**
```r
            altFileName = args[arg_i]
            ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:29:25:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L29) *style:* **Use <-, not =, for assignment.**
```r
            altFileName = args[arg_i]
                        ^
```
[.DEploid/utilities/dEploidTools.r:30:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:30:39:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                                      ^
```
[.DEploid/utilities/dEploidTools.r:31:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L31) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:31:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L31) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:31:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L31) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:31:52:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L31) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:32:13:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L32) *style:* **Variable and function names should be all lowercase.**
```r
            excludeFileName = args[arg_i]
            ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:32:29:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L32) *style:* **Use <-, not =, for assignment.**
```r
            excludeFileName = args[arg_i]
                            ^
```
[.DEploid/utilities/dEploidTools.r:33:13:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L33) *style:* **Variable and function names should be all lowercase.**
```r
            excludeBool = TRUE
            ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:33:25:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L33) *style:* **Use <-, not =, for assignment.**
```r
            excludeBool = TRUE
                        ^
```
[.DEploid/utilities/dEploidTools.r:34:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:34:33:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                                ^
```
[.DEploid/utilities/dEploidTools.r:35:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L35) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:35:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L35) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:35:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L35) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:35:52:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:36:13:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L36) *style:* **Variable and function names should be all lowercase.**
```r
            outPrefix = args[arg_i]
            ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:36:23:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L36) *style:* **Use <-, not =, for assignment.**
```r
            outPrefix = args[arg_i]
                      ^
```
[.DEploid/utilities/dEploidTools.r:37:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:37:40:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                                       ^
```
[.DEploid/utilities/dEploidTools.r:38:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L38) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:38:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L38) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:38:21:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L38) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:38:52:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:39:13:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L39) *style:* **Variable and function names should be all lowercase.**
```r
            dEploidPrefix = args[arg_i]
            ^~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:39:27:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L39) *style:* **Use <-, not =, for assignment.**
```r
            dEploidPrefix = args[arg_i]
                          ^
```
[.DEploid/utilities/dEploidTools.r:44:15:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L44) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i + 1
              ^
```
[.DEploid/utilities/dEploidTools.r:51:8:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
       ^
```
[.DEploid/utilities/dEploidTools.r:51:10:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L51) *style:* **Variable and function names should be all lowercase.**
```r
    if ( plafFileName == "" ){
         ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:51:28:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
                           ^
```
[.DEploid/utilities/dEploidTools.r:58:12:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
           ^
```
[.DEploid/utilities/dEploidTools.r:58:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
                  ^
```
[.DEploid/utilities/dEploidTools.r:58:35:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L58) *style:* **Variable and function names should be all lowercase.**
```r
    return ( list ( vcfFileName = vcfFileName,
                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:59:35:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L59) *style:* **Variable and function names should be all lowercase.**
```r
                    refFileName = refFileName,
                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:60:35:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L60) *style:* **Variable and function names should be all lowercase.**
```r
                    altFileName = altFileName,
                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:61:36:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L61) *style:* **Variable and function names should be all lowercase.**
```r
                    plafFileName = plafFileName,
                                   ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:62:33:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L62) *style:* **Variable and function names should be all lowercase.**
```r
                    outPrefix = outPrefix,
                                ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:63:37:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L63) *style:* **Variable and function names should be all lowercase.**
```r
                    dEploidPrefix = dEploidPrefix,
                                    ^~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:64:39:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L64) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeFileName = excludeFileName,
                                      ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:65:35:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L65) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeBool = excludeBool) )
                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:65:47:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L65) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    excludeBool = excludeBool) )
                                              ^
```
[.DEploid/utilities/dEploidTools.r:69:1:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L69) *style:* **Variable and function names should be all lowercase.**
```r
fun.dEploidPrefix <- function ( prefix ){
^~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:81:1:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L81) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.coverage <- function ( inputs ){
^~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:82:17:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L82) *style:* **Variable and function names should be all lowercase.**
```r
    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:17:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:17:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L83) *warning:* **no visible global function definition for ‘extractCoverageFromVcf’**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:48:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:17:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:17:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L85) *warning:* **no visible global function definition for ‘extractCoverageFromTxt’**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:48:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                               ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:68:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                                                   ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:109:1:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:109:38:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:109:51:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:110:9:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L110) *style:* **Use <-, not =, for assignment.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
        ^
```
[.DEploid/utilities/dEploidTools.r:110:22:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L110) *style:* **Variable and function names should be all lowercase.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:111:9:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L111) *style:* **Use <-, not =, for assignment.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
        ^
```
[.DEploid/utilities/dEploidTools.r:111:22:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L111) *style:* **Variable and function names should be all lowercase.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:112:39:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L112) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = ref[,1],
                                      ^
```
[.DEploid/utilities/dEploidTools.r:113:37:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L113) *style:* **Commas should always have a space after.**
```r
                         POS = ref[,2],
                                    ^
```
[.DEploid/utilities/dEploidTools.r:114:42:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L114) *style:* **Commas should always have a space after.**
```r
                         refCount = ref[,3],
                                         ^
```
[.DEploid/utilities/dEploidTools.r:115:42:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L115) *style:* **Commas should always have a space after.**
```r
                         altCount = alt[,3] )
                                         ^
```
[.DEploid/utilities/dEploidTools.r:120:1:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L120) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
^~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:120:34:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                 ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:120:51:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:121:10:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L121) *style:* **Variable and function names should be all lowercase.**
```r
    if ( excludeBool ) {
         ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:122:39:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L122) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool,
                                      ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:123:1:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L123) *style:* **lines should not be more than 80 characters.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:123:51:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L123) *style:* **Variable and function names should be all lowercase.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
                                                  ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:125:39:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L125) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool ))
                                      ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:147:1:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:147:38:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                     ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:147:47:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                              ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:149:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L149) *style:* **Variable and function names should be all lowercase.**
```r
    catCmd = "cat"
    ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:149:12:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L149) *style:* **Use <-, not =, for assignment.**
```r
    catCmd = "cat"
           ^
```
[.DEploid/utilities/dEploidTools.r:150:1:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L150) *style:* **lines should not be more than 80 characters.**
```r
    if ( grepl("gzip", system(paste("file --mime-type", vcfName), T) ) == TRUE ){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:150:57:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L150) *style:* **Variable and function names should be all lowercase.**
```r
    if ( grepl("gzip", system(paste("file --mime-type", vcfName), T) ) == TRUE ){
                                                        ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:151:9:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L151) *style:* **Variable and function names should be all lowercase.**
```r
        catCmd = "zcat"
        ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:151:16:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L151) *style:* **Use <-, not =, for assignment.**
```r
        catCmd = "zcat"
               ^
```
[.DEploid/utilities/dEploidTools.r:154:1:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L154) *style:* **lines should not be more than 80 characters.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:154:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L154) *style:* **Variable and function names should be all lowercase.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
    ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:154:13:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L154) *style:* **Use <-, not =, for assignment.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
            ^
```
[.DEploid/utilities/dEploidTools.r:154:39:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L154) *style:* **Variable and function names should be all lowercase.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
                                      ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:154:47:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L154) *style:* **Variable and function names should be all lowercase.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
                                              ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:154:81:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L154) *style:* **Commented code should be removed.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
                                                                                ^~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:155:1:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L155) *style:* **lines should not be more than 80 characters.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:155:10:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L155) *style:* **Use <-, not =, for assignment.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
         ^
```
[.DEploid/utilities/dEploidTools.r:155:31:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L155) *style:* **Variable and function names should be all lowercase.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                              ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:155:45:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L155) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                           ~^~
```
[.DEploid/utilities/dEploidTools.r:155:46:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L155) *style:* **Variable and function names should be all lowercase.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                             ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:155:61:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L155) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                           ~^~
```
[.DEploid/utilities/dEploidTools.r:155:77:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L155) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                           ~^~
```
[.DEploid/utilities/dEploidTools.r:155:119:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L155) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                                ~^~
```
[.DEploid/utilities/dEploidTools.r:157:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L157) *style:* **Variable and function names should be all lowercase.**
```r
    sampleName = names(vcf)[10]
    ^~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:157:16:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L157) *style:* **Use <-, not =, for assignment.**
```r
    sampleName = names(vcf)[10]
               ^
```
[.DEploid/utilities/dEploidTools.r:159:9:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L159) *style:* **Use <-, not =, for assignment.**
```r
    tmp = vcf[[sampleName]]
        ^
```
[.DEploid/utilities/dEploidTools.r:159:16:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L159) *style:* **Variable and function names should be all lowercase.**
```r
    tmp = vcf[[sampleName]]
               ^~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:160:11:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L160) *style:* **Use <-, not =, for assignment.**
```r
    field = strsplit(as.character(tmp),":")
          ^
```
[.DEploid/utilities/dEploidTools.r:160:40:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L160) *style:* **Commas should always have a space after.**
```r
    field = strsplit(as.character(tmp),":")
                                       ^
```
[.DEploid/utilities/dEploidTools.r:162:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L162) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:162:15:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L162) *style:* **Use <-, not =, for assignment.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
              ^
```
[.DEploid/utilities/dEploidTools.r:162:44:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L162) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
                                           ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:163:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L163) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
    ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:163:12:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L163) *style:* **Use <-, not =, for assignment.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
           ^
```
[.DEploid/utilities/dEploidTools.r:163:36:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L163) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                   ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:163:47:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L163) *style:* **Commas should always have a space after.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                              ^
```
[.DEploid/utilities/dEploidTools.r:165:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L165) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:165:14:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L165) *style:* **Use <-, not =, for assignment.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
             ^
```
[.DEploid/utilities/dEploidTools.r:165:41:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L165) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
                                        ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:166:5:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L166) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:166:14:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L166) *style:* **Use <-, not =, for assignment.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
             ^
```
[.DEploid/utilities/dEploidTools.r:166:41:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L166) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
                                        ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:168:39:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L168) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = vcf[,1],
                                      ^
```
[.DEploid/utilities/dEploidTools.r:169:37:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L169) *style:* **Commas should always have a space after.**
```r
                         POS = vcf[,2],
                                    ^
```
[.DEploid/utilities/dEploidTools.r:170:37:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L170) *style:* **Variable and function names should be all lowercase.**
```r
                         refCount = refCount,
                                    ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:171:37:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L171) *style:* **Variable and function names should be all lowercase.**
```r
                         altCount = altCount )
                                    ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:192:1:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L192) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:192:12:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L192) *style:* **Put spaces around all infix operators.**
```r
extractPLAF<- function ( plafName ){
          ~^
```
[.DEploid/utilities/dEploidTools.r:192:26:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L192) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
                         ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:193:25:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L193) *style:* **Variable and function names should be all lowercase.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:193:41:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L193) *style:* **Put spaces around all infix operators.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~
```
[.DEploid/utilities/dEploidTools.r:198:11:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
         ~^~~
```
[.DEploid/utilities/dEploidTools.r:198:19:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                 ~^~
```
[.DEploid/utilities/dEploidTools.r:198:23:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                     ~^~
```
[.DEploid/utilities/dEploidTools.r:198:24:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L198) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                       ^
```
[.DEploid/utilities/dEploidTools.r:198:26:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                        ~^~
```
[.DEploid/utilities/dEploidTools.r:198:28:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                          ~^~
```
[.DEploid/utilities/dEploidTools.r:199:1:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L199) *style:* **lines should not be more than 80 characters.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:199:8:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
      ~^~~
```
[.DEploid/utilities/dEploidTools.r:199:23:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                     ~^~
```
[.DEploid/utilities/dEploidTools.r:199:30:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                            ~^~
```
[.DEploid/utilities/dEploidTools.r:199:43:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                         ~^~
```
[.DEploid/utilities/dEploidTools.r:199:44:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L199) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                           ^
```
[.DEploid/utilities/dEploidTools.r:199:46:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                            ~^~
```
[.DEploid/utilities/dEploidTools.r:199:54:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                    ~^~
```
[.DEploid/utilities/dEploidTools.r:199:59:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                         ~^~
```
[.DEploid/utilities/dEploidTools.r:199:72:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                      ~^~
```
[.DEploid/utilities/dEploidTools.r:199:77:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L199) *style:* **Commas should always have a space after.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                            ^
```
[.DEploid/utilities/dEploidTools.r:199:77:](https://github.com/mcveanlab/DEploid-r/blob/c7b2bbeb1491725a52bb55fc687c3ba24517c330/.DEploid/utilities/dEploidTools.r#L199) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                            ^
```


Actually that's what I did... I took your latest updates and added my changes and everything works fine... no conflicts...
As for prefetching ads, I did not change a thing and it works like a charm..
like now I have included 2 NativeExpressAds with a frequency of 10 times to be shown, and the library as it was built is rotating between the 2.
so it is totally fine.


No xD


You're right. Fixed in master.


No need for a PR, I've already fixed Pjotrs affiliation in commit: a1302373bef0e12f60509e97d37a90149f56eae4


this line should be deleted