[R/dEploidTools.R:1:22:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                     ^
```
[R/dEploidTools.R:1:28:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                           ^
```
[R/dEploidTools.R:2:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L2) *style:* **Variable and function names should be all lowercase.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:2:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L2) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:2:48:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L2) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
                                               ^
```
[R/dEploidTools.R:3:15:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L3) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i+1
              ^
```
[R/dEploidTools.R:3:22:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L3) *style:* **Put spaces around all infix operators.**
```r
        arg_i = arg_i+1
                    ~^~
```
[R/dEploidTools.R:6:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L6) *style:* **Variable and function names should be all lowercase.**
```r
    outPrefix = "dataExplore"
    ^~~~~~~~~
```
[R/dEploidTools.R:6:15:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L6) *style:* **Use <-, not =, for assignment.**
```r
    outPrefix = "dataExplore"
              ^
```
[R/dEploidTools.R:7:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L7) *style:* **Variable and function names should be all lowercase.**
```r
    vcfFileName = ""
    ^~~~~~~~~~~
```
[R/dEploidTools.R:7:17:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L7) *style:* **Use <-, not =, for assignment.**
```r
    vcfFileName = ""
                ^
```
[R/dEploidTools.R:8:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L8) *style:* **Variable and function names should be all lowercase.**
```r
    refFileName = ""
    ^~~~~~~~~~~
```
[R/dEploidTools.R:8:17:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L8) *style:* **Use <-, not =, for assignment.**
```r
    refFileName = ""
                ^
```
[R/dEploidTools.R:9:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L9) *style:* **Variable and function names should be all lowercase.**
```r
    altFileName = ""
    ^~~~~~~~~~~
```
[R/dEploidTools.R:9:17:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L9) *style:* **Use <-, not =, for assignment.**
```r
    altFileName = ""
                ^
```
[R/dEploidTools.R:10:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L10) *style:* **Variable and function names should be all lowercase.**
```r
    plafFileName = ""
    ^~~~~~~~~~~~
```
[R/dEploidTools.R:10:18:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L10) *style:* **Use <-, not =, for assignment.**
```r
    plafFileName = ""
                 ^
```
[R/dEploidTools.R:11:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L11) *style:* **Variable and function names should be all lowercase.**
```r
    excludeFileName = ""
    ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:11:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L11) *style:* **Use <-, not =, for assignment.**
```r
    excludeFileName = ""
                    ^
```
[R/dEploidTools.R:12:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L12) *style:* **Variable and function names should be all lowercase.**
```r
    dEploidPrefix = ""
    ^~~~~~~~~~~~~
```
[R/dEploidTools.R:12:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L12) *style:* **Use <-, not =, for assignment.**
```r
    dEploidPrefix = ""
                  ^
```
[R/dEploidTools.R:13:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L13) *style:* **Variable and function names should be all lowercase.**
```r
    excludeBool = FALSE
    ^~~~~~~~~~~
```
[R/dEploidTools.R:13:17:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L13) *style:* **Use <-, not =, for assignment.**
```r
    excludeBool = FALSE
                ^
```
[R/dEploidTools.R:15:11:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L15) *style:* **Use <-, not =, for assignment.**
```r
    arg_i = 1
          ^
```
[R/dEploidTools.R:16:11:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
          ^
```
[R/dEploidTools.R:16:33:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
                                ^
```
[R/dEploidTools.R:17:14:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L17) *style:* **Use <-, not =, for assignment.**
```r
        argv = args[arg_i]
             ^
```
[R/dEploidTools.R:18:12:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
           ^
```
[R/dEploidTools.R:18:28:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
                           ^
```
[R/dEploidTools.R:19:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L19) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:19:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L19) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:19:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L19) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:19:52:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:20:13:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L20) *style:* **Variable and function names should be all lowercase.**
```r
            vcfFileName = args[arg_i]
            ^~~~~~~~~~~
```
[R/dEploidTools.R:20:25:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L20) *style:* **Use <-, not =, for assignment.**
```r
            vcfFileName = args[arg_i]
                        ^
```
[R/dEploidTools.R:21:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                  ^
```
[R/dEploidTools.R:21:36:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                                   ^
```
[R/dEploidTools.R:22:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L22) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:22:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L22) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:22:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L22) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:22:52:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:23:13:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L23) *style:* **Variable and function names should be all lowercase.**
```r
            plafFileName = args[arg_i]
            ^~~~~~~~~~~~
```
[R/dEploidTools.R:23:26:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L23) *style:* **Use <-, not =, for assignment.**
```r
            plafFileName = args[arg_i]
                         ^
```
[R/dEploidTools.R:24:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                  ^
```
[R/dEploidTools.R:24:35:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                                  ^
```
[R/dEploidTools.R:25:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L25) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:25:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L25) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:25:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L25) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:25:52:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:26:13:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L26) *style:* **Variable and function names should be all lowercase.**
```r
            refFileName = args[arg_i]
            ^~~~~~~~~~~
```
[R/dEploidTools.R:26:25:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L26) *style:* **Use <-, not =, for assignment.**
```r
            refFileName = args[arg_i]
                        ^
```
[R/dEploidTools.R:27:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                  ^
```
[R/dEploidTools.R:27:35:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                                  ^
```
[R/dEploidTools.R:28:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L28) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:28:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L28) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:28:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L28) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:28:52:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L28) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:29:13:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L29) *style:* **Variable and function names should be all lowercase.**
```r
            altFileName = args[arg_i]
            ^~~~~~~~~~~
```
[R/dEploidTools.R:29:25:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L29) *style:* **Use <-, not =, for assignment.**
```r
            altFileName = args[arg_i]
                        ^
```
[R/dEploidTools.R:30:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                  ^
```
[R/dEploidTools.R:30:39:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                                      ^
```
[R/dEploidTools.R:31:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L31) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:31:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L31) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:31:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L31) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:31:52:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L31) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:32:13:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L32) *style:* **Variable and function names should be all lowercase.**
```r
            excludeFileName = args[arg_i]
            ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:32:29:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L32) *style:* **Use <-, not =, for assignment.**
```r
            excludeFileName = args[arg_i]
                            ^
```
[R/dEploidTools.R:33:13:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L33) *style:* **Variable and function names should be all lowercase.**
```r
            excludeBool = TRUE
            ^~~~~~~~~~~
```
[R/dEploidTools.R:33:25:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L33) *style:* **Use <-, not =, for assignment.**
```r
            excludeBool = TRUE
                        ^
```
[R/dEploidTools.R:34:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                  ^
```
[R/dEploidTools.R:34:33:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                                ^
```
[R/dEploidTools.R:35:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L35) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:35:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L35) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:35:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L35) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:35:52:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:36:13:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L36) *style:* **Variable and function names should be all lowercase.**
```r
            outPrefix = args[arg_i]
            ^~~~~~~~~
```
[R/dEploidTools.R:36:23:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L36) *style:* **Use <-, not =, for assignment.**
```r
            outPrefix = args[arg_i]
                      ^
```
[R/dEploidTools.R:37:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                  ^
```
[R/dEploidTools.R:37:40:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                                       ^
```
[R/dEploidTools.R:38:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L38) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:38:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L38) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:38:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L38) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:38:52:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:39:13:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L39) *style:* **Variable and function names should be all lowercase.**
```r
            dEploidPrefix = args[arg_i]
            ^~~~~~~~~~~~~
```
[R/dEploidTools.R:39:27:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L39) *style:* **Use <-, not =, for assignment.**
```r
            dEploidPrefix = args[arg_i]
                          ^
```
[R/dEploidTools.R:44:15:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L44) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i + 1
              ^
```
[R/dEploidTools.R:51:8:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
       ^
```
[R/dEploidTools.R:51:10:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L51) *style:* **Variable and function names should be all lowercase.**
```r
    if ( plafFileName == "" ){
         ^~~~~~~~~~~~
```
[R/dEploidTools.R:51:28:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
                           ^
```
[R/dEploidTools.R:58:12:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
           ^
```
[R/dEploidTools.R:58:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
                  ^
```
[R/dEploidTools.R:58:35:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L58) *style:* **Variable and function names should be all lowercase.**
```r
    return ( list ( vcfFileName = vcfFileName,
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:59:35:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L59) *style:* **Variable and function names should be all lowercase.**
```r
                    refFileName = refFileName,
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:60:35:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L60) *style:* **Variable and function names should be all lowercase.**
```r
                    altFileName = altFileName,
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:61:36:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L61) *style:* **Variable and function names should be all lowercase.**
```r
                    plafFileName = plafFileName,
                                   ^~~~~~~~~~~~
```
[R/dEploidTools.R:62:33:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L62) *style:* **Variable and function names should be all lowercase.**
```r
                    outPrefix = outPrefix,
                                ^~~~~~~~~
```
[R/dEploidTools.R:63:37:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L63) *style:* **Variable and function names should be all lowercase.**
```r
                    dEploidPrefix = dEploidPrefix,
                                    ^~~~~~~~~~~~~
```
[R/dEploidTools.R:64:39:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L64) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeFileName = excludeFileName,
                                      ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:65:35:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L65) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeBool = excludeBool) )
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:65:47:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L65) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    excludeBool = excludeBool) )
                                              ^
```
[R/dEploidTools.R:69:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L69) *style:* **Variable and function names should be all lowercase.**
```r
fun.dEploidPrefix <- function ( prefix ){
^~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:81:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L81) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.coverage <- function ( inputs ){
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:82:17:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L82) *style:* **Variable and function names should be all lowercase.**
```r
    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~
```
[R/dEploidTools.R:83:17:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:83:17:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L83) *warning:* **no visible global function definition for ‘extractCoverageFromVcf’**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:83:48:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~
```
[R/dEploidTools.R:85:17:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:85:17:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L85) *warning:* **no visible global function definition for ‘extractCoverageFromTxt’**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:85:48:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                               ^~~~~~~~~~~
```
[R/dEploidTools.R:85:68:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                                                   ^~~~~~~~~~~
```
[R/dEploidTools.R:109:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:109:38:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~
```
[R/dEploidTools.R:109:51:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:110:9:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L110) *style:* **Use <-, not =, for assignment.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
        ^
```
[R/dEploidTools.R:110:22:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L110) *style:* **Variable and function names should be all lowercase.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[R/dEploidTools.R:111:9:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L111) *style:* **Use <-, not =, for assignment.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
        ^
```
[R/dEploidTools.R:111:22:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L111) *style:* **Variable and function names should be all lowercase.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[R/dEploidTools.R:112:39:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L112) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = ref[,1],
                                      ^
```
[R/dEploidTools.R:113:37:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L113) *style:* **Commas should always have a space after.**
```r
                         POS = ref[,2],
                                    ^
```
[R/dEploidTools.R:114:42:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L114) *style:* **Commas should always have a space after.**
```r
                         refCount = ref[,3],
                                         ^
```
[R/dEploidTools.R:115:42:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L115) *style:* **Commas should always have a space after.**
```r
                         altCount = alt[,3] )
                                         ^
```
[R/dEploidTools.R:120:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L120) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
^~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:120:34:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                 ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:120:51:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:121:10:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L121) *style:* **Variable and function names should be all lowercase.**
```r
    if ( excludeBool ) {
         ^~~~~~~~~~~
```
[R/dEploidTools.R:122:39:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L122) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool,
                                      ^~~~~~~~~~~
```
[R/dEploidTools.R:123:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L123) *style:* **lines should not be more than 80 characters.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:123:51:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L123) *style:* **Variable and function names should be all lowercase.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
                                                  ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:125:39:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L125) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool ))
                                      ^~~~~~~~~~~
```
[R/dEploidTools.R:147:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:147:38:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                     ^~~~~~~
```
[R/dEploidTools.R:147:47:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                              ^~~~~~~~~~~~
```
[R/dEploidTools.R:150:12:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L150) *style:* **Place a space before left parenthesis, except in a function call.**
```r
         if( any( grepl( "gzfile connection", w) ) )
           ^
```
[R/dEploidTools.R:154:9:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L154) *style:* **Use <-, not =, for assignment.**
```r
    gzf = gzfile(vcfFile, open = "rb")
        ^
```
[R/dEploidTools.R:154:18:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L154) *style:* **Variable and function names should be all lowercase.**
```r
    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~
```
[R/dEploidTools.R:154:18:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L154) *warning:* **no visible binding for global variable ‘vcfFile’**
```r
    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~
```
[R/dEploidTools.R:155:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L155) *style:* **Variable and function names should be all lowercase.**
```r
    skipNum = 0
    ^~~~~~~
```
[R/dEploidTools.R:155:13:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L155) *style:* **Use <-, not =, for assignment.**
```r
    skipNum = 0
            ^
```
[R/dEploidTools.R:156:10:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L156) *style:* **Use <-, not =, for assignment.**
```r
    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
         ^
```
[R/dEploidTools.R:156:49:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L156) *style:* **Put spaces around all infix operators.**
```r
    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                               ~^~
```
[R/dEploidTools.R:156:61:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L156) *style:* **Put spaces around all infix operators.**
```r
    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                           ~^~
```
[R/dEploidTools.R:158:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L158) *style:* **Commented code should be removed.**
```r
        if (grepl("##", line )){
                    ^~~~~~~~~~~~
```
[R/dEploidTools.R:159:13:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L159) *style:* **Variable and function names should be all lowercase.**
```r
            skipNum = skipNum+1
            ^~~~~~~
```
[R/dEploidTools.R:159:21:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L159) *style:* **Use <-, not =, for assignment.**
```r
            skipNum = skipNum+1
                    ^
```
[R/dEploidTools.R:159:23:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L159) *style:* **Variable and function names should be all lowercase.**
```r
            skipNum = skipNum+1
                      ^~~~~~~
```
[R/dEploidTools.R:159:30:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L159) *style:* **Put spaces around all infix operators.**
```r
            skipNum = skipNum+1
                            ~^~
```
[R/dEploidTools.R:163:14:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L163) *style:* **Use <-, not =, for assignment.**
```r
        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
             ^
```
[R/dEploidTools.R:163:53:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L163) *style:* **Put spaces around all infix operators.**
```r
        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                   ~^~
```
[R/dEploidTools.R:163:65:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L163) *style:* **Put spaces around all infix operators.**
```r
        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                               ~^~
```
[R/dEploidTools.R:167:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L167) *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)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:167:10:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L167) *style:* **Use <-, not =, for assignment.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
         ^
```
[R/dEploidTools.R:167:31:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L167) *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)
                              ^~~~~~~
```
[R/dEploidTools.R:167:45:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                           ~^~
```
[R/dEploidTools.R:167:46:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L167) *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)
                                             ^~~~~~~
```
[R/dEploidTools.R:167:61:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                           ~^~
```
[R/dEploidTools.R:167:77:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                           ~^~
```
[R/dEploidTools.R:167:119:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                                ~^~
```
[R/dEploidTools.R:169:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L169) *style:* **Variable and function names should be all lowercase.**
```r
    sampleName = names(vcf)[10]
    ^~~~~~~~~~
```
[R/dEploidTools.R:169:16:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L169) *style:* **Use <-, not =, for assignment.**
```r
    sampleName = names(vcf)[10]
               ^
```
[R/dEploidTools.R:171:9:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L171) *style:* **Use <-, not =, for assignment.**
```r
    tmp = vcf[[sampleName]]
        ^
```
[R/dEploidTools.R:171:16:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L171) *style:* **Variable and function names should be all lowercase.**
```r
    tmp = vcf[[sampleName]]
               ^~~~~~~~~~
```
[R/dEploidTools.R:172:11:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L172) *style:* **Use <-, not =, for assignment.**
```r
    field = strsplit(as.character(tmp),":")
          ^
```
[R/dEploidTools.R:172:40:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L172) *style:* **Commas should always have a space after.**
```r
    field = strsplit(as.character(tmp),":")
                                       ^
```
[R/dEploidTools.R:174:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L174) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/dEploidTools.R:174:15:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L174) *style:* **Use <-, not =, for assignment.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
              ^
```
[R/dEploidTools.R:174:44:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L174) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
                                           ^~~~~~~~~~~~
```
[R/dEploidTools.R:175:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L175) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
    ^~~~~~
```
[R/dEploidTools.R:175:12:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L175) *style:* **Use <-, not =, for assignment.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
           ^
```
[R/dEploidTools.R:175:36:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L175) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                   ^~~~~~~~~
```
[R/dEploidTools.R:175:47:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L175) *style:* **Commas should always have a space after.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                              ^
```
[R/dEploidTools.R:177:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L177) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/dEploidTools.R:177:14:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L177) *style:* **Use <-, not =, for assignment.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
             ^
```
[R/dEploidTools.R:177:41:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L177) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
                                        ^~~~~~
```
[R/dEploidTools.R:178:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L178) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/dEploidTools.R:178:14:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L178) *style:* **Use <-, not =, for assignment.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
             ^
```
[R/dEploidTools.R:178:41:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L178) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
                                        ^~~~~~
```
[R/dEploidTools.R:180:39:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L180) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = vcf[,1],
                                      ^
```
[R/dEploidTools.R:181:37:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L181) *style:* **Commas should always have a space after.**
```r
                         POS = vcf[,2],
                                    ^
```
[R/dEploidTools.R:182:37:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L182) *style:* **Variable and function names should be all lowercase.**
```r
                         refCount = refCount,
                                    ^~~~~~~~
```
[R/dEploidTools.R:183:37:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L183) *style:* **Variable and function names should be all lowercase.**
```r
                         altCount = altCount )
                                    ^~~~~~~~
```
[R/dEploidTools.R:204:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L204) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
^~~~~~~~~~~
```
[R/dEploidTools.R:204:12:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L204) *style:* **Put spaces around all infix operators.**
```r
extractPLAF<- function ( plafName ){
          ~^
```
[R/dEploidTools.R:204:26:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L204) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
                         ^~~~~~~~
```
[R/dEploidTools.R:205:25:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L205) *style:* **Variable and function names should be all lowercase.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~
```
[R/dEploidTools.R:205:41:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L205) *style:* **Put spaces around all infix operators.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~
```
[R/dEploidTools.R:210:11:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
         ~^~~
```
[R/dEploidTools.R:210:19:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                 ~^~
```
[R/dEploidTools.R:210:23:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                     ~^~
```
[R/dEploidTools.R:210:24:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L210) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                       ^
```
[R/dEploidTools.R:210:26:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                        ~^~
```
[R/dEploidTools.R:210:28:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                          ~^~
```
[R/dEploidTools.R:211:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:211:8:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
      ~^~~
```
[R/dEploidTools.R:211:23:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
                     ~^~
```
[R/dEploidTools.R:211:30:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
                            ~^~
```
[R/dEploidTools.R:211:43:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
                                         ~^~
```
[R/dEploidTools.R:211:44:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
                                           ^
```
[R/dEploidTools.R:211:46:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
                                            ~^~
```
[R/dEploidTools.R:211:54:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
                                                    ~^~
```
[R/dEploidTools.R:211:59:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
                                                         ~^~
```
[R/dEploidTools.R:211:72:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
                                                                      ~^~
```
[R/dEploidTools.R:211:77:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
                                                                            ^
```
[R/dEploidTools.R:211:77:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
                                                                            ^
```
[R/dEploidTools.R:211:79:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
                                                                             ~^~
```
[R/dEploidTools.R:211:87:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L211) *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);
                                                                                ~^~
```
[R/dEploidTools.R:212:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L212) *style:* **lines should not be more than 80 characters.**
```r
    #  llk<-lgamma(fac*f.samp+cov.alt)+lgamma(fac*(1-f.samp)+cov.ref)-lgamma(fac*f.samp)-lgamma(fac*(1-f.samp));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:212:8:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L212) *style:* **Commented code should be removed.**
```r
    #  llk<-lgamma(fac*f.samp+cov.alt)+lgamma(fac*(1-f.samp)+cov.ref)-lgamma(fac*f.samp)-lgamma(fac*(1-f.samp));
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:213:25:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L213) *style:* **Put spaces around all infix operators.**
```r
    if (sum(is.nan(llk))>1){
                       ~^~
```
[R/dEploidTools.R:220:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L220) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.dic.by.llk.var <- function ( tmpllk ){
^~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:221:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L221) *style:* **lines should not be more than 80 characters.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:221:23:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L221) *style:* **Put spaces around all infix operators.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
                     ~^~
```
[R/dEploidTools.R:221:40:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L221) *style:* **Put spaces around all infix operators.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
                                      ~^~
```
[R/dEploidTools.R:221:48:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L221) *style:* **Put spaces around all infix operators.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
                                              ~^~
```
[R/dEploidTools.R:225:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L225) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.dic.by.theta <- function ( tmpllk, thetallk ){
^~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:226:5:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L226) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    DIC.WSAF.bar = -2 * sum(thetallk)
    ^~~~~~~~~~~~
```
[R/dEploidTools.R:226:18:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L226) *style:* **Use <-, not =, for assignment.**
```r
    DIC.WSAF.bar = -2 * sum(thetallk)
                 ^
```
[R/dEploidTools.R:227:1:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L227) *style:* **lines should not be more than 80 characters.**
```r
    return (  mean(-2*tmpllk) + (mean(-2*tmpllk) - DIC.WSAF.bar) ) # D_bar + pD, where pD = D_bar - D_theta, and D_bar = mean(D_theta)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:227:22:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L227) *style:* **Put spaces around all infix operators.**
```r
    return (  mean(-2*tmpllk) + (mean(-2*tmpllk) - DIC.WSAF.bar) ) # D_bar + pD, where pD = D_bar - D_theta, and D_bar = mean(D_theta)
                    ~^~
```
[R/dEploidTools.R:227:41:](https://github.com/mcveanlab/DEploid-r/blob/93d99627821b7e88585dbde33af3fde7e36db098/R/dEploidTools.R#L227) *style:* **Put spaces around all infix operators.**
```r
    return (  mean(-2*tmpllk) + (mean(-2*tmpllk) - DIC.WSAF.bar) ) # D_bar + pD, where pD = D_bar - D_theta, and D_bar = mean(D_theta)
                                       ~^~
```


My first assignment Its look like a cv.


Yes. We should have two separate tests.


No, these are local references to the ServiceStack projects in the same solution.


Holy crap. Yah, it's like 50/50 on my getting that correct the first time.


URL seems wrong.

Plus "America/New_York_" has an ending "_"


Done, changed all common variable names and class variable names to lowercase with underscores between words.


Students/30221/Giurgi I. Iacob/Tema 222/Polinom.java

what happens if I want to create a polynomial of form `ax + bx^2 + cx^3`?
This constructor handles only the case when I want to create a polynomial of form `ax^b`


I see, thanks and sorry ;)


np :)


The following doc(s) have been deployed to the [terminusma](https://terminusma-static-docs.pantheonsite.io/docs) Multidev environment:
- [docs/guides/terminus](https://terminusma-static-docs.pantheonsite.io/docs/guides/terminus)
- [docs/terminus/commands](https://terminusma-static-docs.pantheonsite.io/docs/terminus/commands)
- [docs/terminus/examples](https://terminusma-static-docs.pantheonsite.io/docs/terminus/examples)
- [docs/terminus/install](https://terminusma-static-docs.pantheonsite.io/docs/terminus/install)


最初のInitial Commitあるの忘れてて同じ名でcommitしてしまった(ﾃﾍﾍﾟﾛ


Superb


This change is incomplete: the same problem happens for other errors. For example try creating a Python file with just the single line `If True:`. That results in error E901 with the same offset issue.


cool


Making a dev branch makes it hard for people to contribute PR, so we decided to start with the easiest and change later if users complain.


Why is it more correct for a ClassResult's duration to be a copy of the SuiteResult's duration rather than a sum of the CaseResults?

The commit message doesn't provide any insight into this and I can't find any real documentation on the JUnit XML format.   What I do know is this causes the time column on page that lists Classes to be pretty pointless.  We are having to manually construct our JUnit XML file.  Maybe I'm not constructing it in the way it is intended but the previous way this worked at least provided us with something meaningful.


No problem and ty :)


it was ok code  could have been better


This is terrible code, needs major work!!!


It would be a nice to have if the versions would also have a date associated with it :bowtie:


I believe, the partis parameter files for V genes always have an "insert_left_N" state so I think the assert must be 2.  but otherwise yes, I should put this assert in case we're dealing with V genes.


TeamCity Chorus :: chorus-precise64-master Continuous [Build 2.6.680.62b9dded771ebd5373f3f8fc9467d368a20c03a5](http://build.palaso.org/viewLog.html?buildId=78433&buildTypeId=bt323) outcome was **SUCCESS**
Summary: Tests passed: 937, ignored: 56 Build time: 00:15:22


test


I'm not sure this should be `posts` - should be `activities` maybe? Just a nitpick, whatever is used throughout.


For some reason, the observable in `history.service` does not work


TeamCity libpalaso :: palaso-precise64-libpalaso-2.6 Continuous [Build 2.6.1123.87397517629f383f824682a758c871941575c383](http://build.palaso.org/viewLog.html?buildId=78438&buildTypeId=PalasoPrecise64v26Cont) outcome was **FAILURE**
Summary: Exit code 1 (new) Build time: 00:02:44


Alt. name: "Not 2sharp4everyone"


You might have to install the "Windows XP runtime" to get this to work (though tbh, we could also probably just not use this)


portrat.set({
  regX: portrat.getBounds().width/2,
  regY: portrat.getBounds().height/2,
});


Hello mumblepins, i have a problem with the installer in the windows 10, by the windows defender antivirus. When the file ParticleCLIinstaller.exe download to computer then cath as a virus and cannot install.
You Know, i turn off, and finaly i can install without problems.

Thanks.


event


TeamCity libpalaso :: palaso-precise64-master Continuous [Build 3.1.24.87397517629f383f824682a758c871941575c383](http://build.palaso.org/viewLog.html?buildId=78441&buildTypeId=bt322) outcome was **FAILURE**
Summary: Exit code 1 (new) Build time: 00:02:35


array size could be figured out using ARRAY_SIZE macro. This would avoid potential inconsistency between actual array size and this var.


no need to specify array size, compiler will figure this out on the basis of data in array.


![001 2](https://cloud.githubusercontent.com/assets/22861842/19487932/a446c5d8-9571-11e6-9d33-f53536cbd2ca.JPG)


Following #57, the README is updated.


dont recent versions of SWIG with py3k do this out of the box?

![image](https://cloud.githubusercontent.com/assets/620988/19487959/2b3288b4-9565-11e6-87a1-755102104c61.png)


joe tried to kiss me


Пытаюсь при обработке косвенных падежей избавиться от предлогов. Если будут ложные срабатывания, откачу.


воно тоді  через strlen неправильний результат давало , не знаю чого


Не умею по-другому синхронизировать... :(


#define ARRAY_SIZE(a) (sizeof(a)/sizeof(a[0]))


you are right. Really better use screen object


This XML Schema looks quite bogus.

```xml
    <xs:element name="location">
    	<xs:complexType>
    		<xs:sequence>
    		   <xs:element name="latitude" type="xs:double" />
    			<xs:element name="longitude" type="xs:double" />
    		</xs:sequence>
    	</xs:complexType>
    </xs:element>
```

btw [minted](https://github.com/gpoore/minted) is awesome to include code into latex documents.


TaskCluster: https://tools.taskcluster.net/task-graph-inspector/#OTCYOV1wSvWrWw4BqIgqyQ/


@slava77 and @cvuosalo: This is the same issue as the last file that if these two variables have no use after this instance, then is there any value keeping them at all?


Why usb-ledtrig-usbport? And not like other triggers - ledtrig-usbport?


Also `atrribute`, `tikz` is awesome too ;-)


TaskCluster: https://tools.taskcluster.net/task-graph-inspector/#VF9IpDq2TsewHso_jjaZlQ/


PLEASE NOTE , THE PROGRAM MAY NOT RUN AT ALL. THE MAKEFILE MAY NOT EVEN WORK AS INTENDED. THERE MAY BE UNRESOLVED DEPENDENCIES WITHIN THE PROGRAM. MY UBUNTU SYSTEM HAS BEEN OUT OF COMMISSION FOR THE LAST FEW DAYS, SO THE LAST FEW DAYS OF CODING HAVE BEEN PERFORMED ON WINDOWS, WITHOUT TESTING ( DUE TO T2s AND EXTRACURRICULARS) .


I thought it was decided against a 3.6.4 release and we were going to 3.7.0 next?


Let's add a comment here: it's a hack for cross-browser event handling


Done and done.


Yeah, the underline is a bit much here, agreed.

> On Oct 18, 2016, at 6:02 PM, Eric Wendelin <notifications@github.com> wrote:
>
> The boldness and border felt too heavy to me. I'd prefer a "lighter" template.
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub, or mute the thread.
>


I think I just copy-pasted this from the course notes.. We'll find a better example then.. =)

Minted looks interesting.. We'll have a look at it.. =)

I don't know about `atrribute` but I'm a big fan of `tikz`.. =)

Thanks for your comment..


Yes, I have changed the `parse_transitions()` and `parse_emissions` functions to reflect this.


Yes. They accept only IS_VAR operands, and therefore can't define SSA vars.
They also may be removed in zend_ssa.c and zend_dfg.c.


test


@cstockloew I really don't understand why this request does not match the :anonymizeproperty defined profile.
The problem seems to be in PROP_ANONYMIZABLE, If I comment both inputs (in profile and request) they match...


EYTUKAAAAAAN


Comment 1


WHYYYYYYYYYYYYYY


This is the FindBugs fix.


still the plan, but we are going to merge the 3.7.x into staging so till we do it this will stay on 3.6.x to  confuse people not with having two 3.7 labeled branches


Closes #23


Just wondering, how did you come up with the name `fReturn`? I had to think pretty hard to trace through this because the name didn't give me the right indication.


TeamCity Units.NET :: Build and Test [Build 173](http://teamcity.chump.work/viewLog.html?buildId=737&buildTypeId=UnitsNet_BuildTest) is now running


TeamCity Units.NET :: Build and Test [Build 173](http://teamcity.chump.work/viewLog.html?buildId=737&buildTypeId=UnitsNet_BuildTest) outcome was **SUCCESS**
Summary: Tests passed: 820 Build time: 0:0:28


TeamCity Units.NET :: Build and Test [Build 174](http://teamcity.chump.work/viewLog.html?buildId=738&buildTypeId=UnitsNet_BuildTest) is now running


TeamCity Units.NET :: Publish NuGets [Build 173](http://teamcity.chump.work/viewLog.html?buildId=740&buildTypeId=UnitsNet_Publish) is now running


TeamCity Units.NET :: Build and Test [Build 174](http://teamcity.chump.work/viewLog.html?buildId=738&buildTypeId=UnitsNet_BuildTest) outcome was **FAILURE**
Summary: Number of tests is too small: 0; artifacts size (bytes) is too small: 3676440; exit code 1 Build time: 0:0:16


I would like to leave this menu like other menus of the system, the output if assigned only one red button to leave without assigning the same action with exit button.

The cause must involve two buttons with the same action is but we do that is we have two menus unallocated exit, kernel modules and speed EGAMI UP Plugin.


TeamCity Units.NET :: Publish NuGets [Build 173](http://teamcity.chump.work/viewLog.html?buildId=740&buildTypeId=UnitsNet_Publish) outcome was **SUCCESS**
Summary: Running Build time: 0:0:13


good


Явно объект можно не создавать. Лучше просто писать:
```
return SQLite.select()
                .from(StoriesEntity.class)
                .where(StoriesEntity_Table.link.eq(link)).querySingle();
```


Аналогично и в других местах


@codekaka how


Responding to commit comment


@codekaka aa


Вместо link-text лучше оставить привязку к social-links.  К примеру social-links__text
наче если мы пропишем скрытие мы скроем все что с этим классом, А нам важно скрыть именно у этих кнопок


Thanks for the clarification.


@codekaka cool


@slava77 and @cvuosalo:  In this file, variables pt, eta, phi are being used and reused but the warning raised by static analyzer points to the instance of 'phi' in this for loop (starting in L165). While pt, eta are used before the loop ends, the 'phi' variable is not used. I think removing this instance of the 'phi' variable should satisfy static analyzer.


Small typo: `asynchronous`


typo


test


Aplikasi mencari kost di daerah Malang "KOST MALANG", yang diisikan (Nama, Asal, No. Telp; Ukuran Kamar, Fasilitas yang akan dipilih, dan Jenis kelamin untuk menentukan Kost)
, Agar mudah mencari kost yang khusu di daerah Malang Kota.

![tugas001](https://cloud.githubusercontent.com/assets/22384224/19488335/9f4db98c-9590-11e6-9c85-b974840127d7.jpg)
![tugas001 2](https://cloud.githubusercontent.com/assets/22384224/19488373/cc493dbc-9590-11e6-810a-f71639d8ee14.jpg)
![tugas001 3](https://cloud.githubusercontent.com/assets/22384224/19488441/1cb4a93a-9591-11e6-96e7-8976fcb71d2f.jpg)


Этот метод лучше полностью переписать. У вас есть возможность откидывать записи, которые уже есть в бд с помощью DBFlow:

@Table(database = StoriesDatabase.class, insertConflict = ConflictAction.ABORT)


Если будете использовать её, то логика этого метода значительно упроститься.


Is `protocolVersion = 1` a good default value or should we separate a real version 1 from an undefined version?


@codekaka c


Company-coq needs annotations anyway (IOW, I'll need to wrap these), but it looks good.  Isn't info_auto mostly deprecated?


I don't quite understand, this whole loop is enclosed in an `if(gstart == nukes.size() + 1)` statement, so we're already asserting it?


Looks like `[NSString adSame:toString]` returns `YES` if both values are `nil` which is undesirable here if it happens.


It seems CitationHunt does not have translation checker that would automatically mark translations having these kind of issues as fuzzy.


@codekaka a


Good point.


**thanks me too**


这个问题曾导致XYWE在Build之后保存的文件无法完成编译，从而无法在游戏中运行。


This doesn't seem to be used anywhere. Ref: https://issues.apache.org/jira/browse/MYNEWT-447.


It was not working in 8.5 but Hugo has just fixed it. Deprecating it was a mistake IMHO (as long as we can make it work).


Этот трюк считается как костыль. В catch лучше писать код, который позволит выйти из исключительной ситуации, а не заносить туда бизнес-логику.


Pedantic: it makes more sense for this commit to just be part of the next one - this commit doesn't actually remove the need for the TODO just yet!


- [  ] Not a big deal, but you're missing a semicolon here.


Ты пробовал fetch и rebase вместо pull?


TeamCity SayMore :: SayMore pull requests [Build *.*.16.888763cb51d651a46a459d677906d9ecf623eed0](http://build.palaso.org/viewLog.html?buildId=78462&buildTypeId=SayMore_SayMorePullRequests) outcome was **SUCCESS**
Summary: Tests passed: 658, ignored: 4 Build time: 00:02:16


- [ ] I would either remove `console.log` statements, or comment them out as good practice to get into. Others on your team will get annoyed 😉


- [ ] Super nitpicky, but spacing is important. Again, this is something others on your (future) team may get annoyed about. 😉


Для базы данных лучше создать отдельный пакет. Идеальная структура примерно такая:

database (или storage) в этом пакете класс StoriesDatabase и пакет entities, в котором уже StoriesEntity.


There are two different things that are getting at the same information: `if(gstart == nukes.size() + 1)` and `std::regex_match(states[j].cbegin(), states[j].cend(), sm, Nrgx)`. We should make sure that they agree, no?


@nllong here is the test to check out

@kbenne @rHorsey FYI


submitted batch submit of 25 files including new Deposit Files (Controllers, DAO, and JSP files) , Home file (along with header and loginbar info). Also, submitted servlet and property files for connecting the database to the local JavaConnectFactory and the AWS internet Database.


Первичным ключом лучше сделать ссылку на шутку.

   @PrimaryKey
    private String id;


👍  That was quick ;)


Are you having success getting macOS to work with the latest VirtualBox (5.1.x)? Some people over [here](https://github.com/timsutton/osx-vm-templates/issues/72) trying to figure out why it doesn't seem to be working. If you have any data to contribute there would be much appreciated!