[R/dEploidTools.R:1:22:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L6) *style:* **Use <-, not =, for assignment.**
```r
    outPrefix = "dataExplore"
              ^
```
[R/dEploidTools.R:7:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L7) *style:* **Use <-, not =, for assignment.**
```r
    vcfFileName = ""
                ^
```
[R/dEploidTools.R:8:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L8) *style:* **Use <-, not =, for assignment.**
```r
    refFileName = ""
                ^
```
[R/dEploidTools.R:9:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L9) *style:* **Use <-, not =, for assignment.**
```r
    altFileName = ""
                ^
```
[R/dEploidTools.R:10:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L10) *style:* **Use <-, not =, for assignment.**
```r
    plafFileName = ""
                 ^
```
[R/dEploidTools.R:11:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L11) *style:* **Use <-, not =, for assignment.**
```r
    excludeFileName = ""
                    ^
```
[R/dEploidTools.R:12:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L12) *style:* **Use <-, not =, for assignment.**
```r
    dEploidPrefix = ""
                  ^
```
[R/dEploidTools.R:13:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L13) *style:* **Use <-, not =, for assignment.**
```r
    excludeBool = FALSE
                ^
```
[R/dEploidTools.R:15:11:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L33) *style:* **Use <-, not =, for assignment.**
```r
            excludeBool = TRUE
                        ^
```
[R/dEploidTools.R:34:19:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L82) *style:* **Variable and function names should be all lowercase.**
```r
    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~
```
[R/dEploidTools.R:83:17:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:83:17:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L83) *warning:* **no visible global function definition for ‘extractCoverageFromVcf’**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:83:48:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~
```
[R/dEploidTools.R:85:17:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L125) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool ))
                                      ^~~~~~~~~~~
```
[R/dEploidTools.R:145:6:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L145) *style:* **Commented code should be removed.**
```r
#' # PG0390 = extractCoverageFromVcf(vcfFile)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:147:1:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/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/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                              ^~~~~~~~~~~~
```
[R/dEploidTools.R:149:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L149) *style:* **Variable and function names should be all lowercase.**
```r
    catCmd = "cat"
    ^~~~~~
```
[R/dEploidTools.R:149:12:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L149) *style:* **Use <-, not =, for assignment.**
```r
    catCmd = "cat"
           ^
```
[R/dEploidTools.R:150:1:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L150) *style:* **lines should not be more than 80 characters.**
```r
    if ( grepl("gzip", system(paste("file --mime-type", vcfName), T) ) == TRUE ){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:150:57:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L150) *style:* **Variable and function names should be all lowercase.**
```r
    if ( grepl("gzip", system(paste("file --mime-type", vcfName), T) ) == TRUE ){
                                                        ^~~~~~~
```
[R/dEploidTools.R:151:9:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L151) *style:* **Variable and function names should be all lowercase.**
```r
        catCmd = "zcat <"
        ^~~~~~
```
[R/dEploidTools.R:151:16:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L151) *style:* **Use <-, not =, for assignment.**
```r
        catCmd = "zcat <"
               ^
```
[R/dEploidTools.R:154:1:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:154:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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))
    ^~~~~~~
```
[R/dEploidTools.R:154:13:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L154) *style:* **Use <-, not =, for assignment.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
            ^
```
[R/dEploidTools.R:154:39:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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))
                                      ^~~~~~
```
[R/dEploidTools.R:154:47:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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))
                                              ^~~~~~~
```
[R/dEploidTools.R:154:81:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L154) *style:* **Commented code should be removed.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
                                                                                ^~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:155:1:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:155:10:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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)
         ^
```
[R/dEploidTools.R:155:31:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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)
                              ^~~~~~~
```
[R/dEploidTools.R:155:45:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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)
                                           ~^~
```
[R/dEploidTools.R:155:46:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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)
                                             ^~~~~~~
```
[R/dEploidTools.R:155:61:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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)
                                                           ~^~
```
[R/dEploidTools.R:155:77:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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)
                                                                           ~^~
```
[R/dEploidTools.R:155:119:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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)
                                                                                ~^~
```
[R/dEploidTools.R:157:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L157) *style:* **Variable and function names should be all lowercase.**
```r
    sampleName = names(vcf)[10]
    ^~~~~~~~~~
```
[R/dEploidTools.R:157:16:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L157) *style:* **Use <-, not =, for assignment.**
```r
    sampleName = names(vcf)[10]
               ^
```
[R/dEploidTools.R:159:9:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L159) *style:* **Use <-, not =, for assignment.**
```r
    tmp = vcf[[sampleName]]
        ^
```
[R/dEploidTools.R:159:16:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L159) *style:* **Variable and function names should be all lowercase.**
```r
    tmp = vcf[[sampleName]]
               ^~~~~~~~~~
```
[R/dEploidTools.R:160:11:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L160) *style:* **Use <-, not =, for assignment.**
```r
    field = strsplit(as.character(tmp),":")
          ^
```
[R/dEploidTools.R:160:40:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L160) *style:* **Commas should always have a space after.**
```r
    field = strsplit(as.character(tmp),":")
                                       ^
```
[R/dEploidTools.R:162:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L162) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/dEploidTools.R:162:15:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L162) *style:* **Use <-, not =, for assignment.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
              ^
```
[R/dEploidTools.R:162:44:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L162) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
                                           ^~~~~~~~~~~~
```
[R/dEploidTools.R:163:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L163) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
    ^~~~~~
```
[R/dEploidTools.R:163:12:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L163) *style:* **Use <-, not =, for assignment.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
           ^
```
[R/dEploidTools.R:163:36:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L163) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                   ^~~~~~~~~
```
[R/dEploidTools.R:163:47:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L163) *style:* **Commas should always have a space after.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                              ^
```
[R/dEploidTools.R:165:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L165) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/dEploidTools.R:165:14:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L165) *style:* **Use <-, not =, for assignment.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
             ^
```
[R/dEploidTools.R:165:41:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L165) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
                                        ^~~~~~
```
[R/dEploidTools.R:166:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L166) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/dEploidTools.R:166:14:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L166) *style:* **Use <-, not =, for assignment.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
             ^
```
[R/dEploidTools.R:166:41:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L166) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
                                        ^~~~~~
```
[R/dEploidTools.R:168:39:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L168) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = vcf[,1],
                                      ^
```
[R/dEploidTools.R:169:37:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L169) *style:* **Commas should always have a space after.**
```r
                         POS = vcf[,2],
                                    ^
```
[R/dEploidTools.R:170:37:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L170) *style:* **Variable and function names should be all lowercase.**
```r
                         refCount = refCount,
                                    ^~~~~~~~
```
[R/dEploidTools.R:171:37:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L171) *style:* **Variable and function names should be all lowercase.**
```r
                         altCount = altCount )
                                    ^~~~~~~~
```
[R/dEploidTools.R:192:1:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L192) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
^~~~~~~~~~~
```
[R/dEploidTools.R:192:12:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L192) *style:* **Put spaces around all infix operators.**
```r
extractPLAF<- function ( plafName ){
          ~^
```
[R/dEploidTools.R:192:26:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L192) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
                         ^~~~~~~~
```
[R/dEploidTools.R:193:25:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L193) *style:* **Variable and function names should be all lowercase.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~
```
[R/dEploidTools.R:193:41:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L193) *style:* **Put spaces around all infix operators.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~
```
[R/dEploidTools.R:198:11:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
         ~^~~
```
[R/dEploidTools.R:198:19:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                 ~^~
```
[R/dEploidTools.R:198:23:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                     ~^~
```
[R/dEploidTools.R:198:24:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
                       ^
```
[R/dEploidTools.R:198:26:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                        ~^~
```
[R/dEploidTools.R:198:28:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                          ~^~
```
[R/dEploidTools.R:199:1:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:199:8:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
      ~^~~
```
[R/dEploidTools.R:199:23:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
                     ~^~
```
[R/dEploidTools.R:199:30:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
                            ~^~
```
[R/dEploidTools.R:199:43:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
                                         ~^~
```
[R/dEploidTools.R:199:44:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
                                           ^
```
[R/dEploidTools.R:199:46:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
                                            ~^~
```
[R/dEploidTools.R:199:54:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
                                                    ~^~
```
[R/dEploidTools.R:199:59:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
                                                         ~^~
```
[R/dEploidTools.R:199:72:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
                                                                      ~^~
```
[R/dEploidTools.R:199:77:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
                                                                            ^
```
[R/dEploidTools.R:199:77:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
                                                                            ^
```
[R/dEploidTools.R:199:79:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
                                                                             ~^~
```
[R/dEploidTools.R:199:87:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/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);
                                                                                ~^~
```
[R/dEploidTools.R:200:1:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L200) *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:200:8:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L200) *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:201:25:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L201) *style:* **Put spaces around all infix operators.**
```r
    if (sum(is.nan(llk))>1){
                       ~^~
```
[R/dEploidTools.R:208:1:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L208) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.dic.by.llk.var <- function ( tmpllk ){
^~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:209:1:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L209) *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:209:23:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L209) *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:209:40:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L209) *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:209:48:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L209) *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:213:1:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L213) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.dic.by.theta <- function ( tmpllk, thetallk ){
^~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:214:5:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L214) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    DIC.WSAF.bar = -2 * sum(thetallk)
    ^~~~~~~~~~~~
```
[R/dEploidTools.R:214:18:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L214) *style:* **Use <-, not =, for assignment.**
```r
    DIC.WSAF.bar = -2 * sum(thetallk)
                 ^
```
[R/dEploidTools.R:215:1:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L215) *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:215:22:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L215) *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:215:41:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L215) *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:215:52:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L215) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```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:237:1:](https://github.com/mcveanlab/DEploid-r/blob/5d78f7b7d30c57bcdacf6b62c7b1f660adc5d2fd/R/dEploidTools.R#L237) *style:* **Variable and function names should be all lowercase.**
```r
plotProportions <-function (proportions, title = "Components"){
^~~~~~~~~~~~~~~
```


Thanks for that change. Let me know when it's going live to .25 :).


Nice class name


Sweet, thanks!


This is the commit that breaks the start icon.


Should Simple Graphics Window be updated to match the version elsewhere in the repository?

     Include version 15/161003 of Flexible Windows by Jon Ingold.


1. TBC is missing this line in core SQL INSERT INTO spell_bonus_data VALUES('8026', '0.1', '0', '0', '0', 'Shaman - Flametongue Weapon Proc Rank 1');
(possibly only missing on my end only, need to check)
2.

valid version for wotlk

                    int32 bonusDamage = m_caster->SpellBaseDamageBonusDone(GetSpellSchoolMask(m_spellInfo))
                        + unitTarget->SpellBaseDamageBonusTaken(GetSpellSchoolMask(m_spellInfo)); // Does Amplify Magic/Dampen Magic influence flametongue? If not, this must be removed.
                    float weaponSpeed = (1.0f / IN_MILLISECONDS) * m_CastItem->GetProto()->Delay;
                    int32 totalDamage = int32((damage + 3.85f * bonusDamage) * 0.01 * weaponSpeed);
                    totalDamage = m_caster->SpellBonusWithCoeffs(m_spellInfo, totalDamage, 0, 0, SPELL_DIRECT_DAMAGE, false); // apply flat 10% from Increased Spellpower

for TBC it would be

                    int32 bonusDamage = m_caster->SpellBaseDamageBonusDone(GetSpellSchoolMask(m_spellInfo))
                        + unitTarget->SpellBaseDamageBonusTaken(GetSpellSchoolMask(m_spellInfo)); // Does Amplify Magic/Dampen Magic influence flametongue? If not, this must be removed.
                    float weaponSpeed = (1.0f / IN_MILLISECONDS) * m_CastItem->GetProto()->Delay;
                    int32 totalDamage = (damage * 0.01 * weaponSpeed) + (bonusDamage / 10);
                    totalDamage = m_caster->SpellBonusWithCoeffs(m_spellInfo, totalDamage, 0, 0, SPELL_DIRECT_DAMAGE, false); // apply flat 10% from Increased Spellpower


IMO, it will be a lot simpler to have an attribute (that inherits from TraitAttribute that reduces some of this verbosity, such as [CurrentPlatformTrait]


Sembla que sí funciona


You mean SpellDamageBonusDone like we talked about, right?


@bsclifton I'm curious, why `21px`? This results in a large space beneath the buttons that causes state-confusion for the buttons and mouse:

![buttons](https://cloud.githubusercontent.com/assets/815158/19359471/26001a9e-912f-11e6-8f98-2ddd5791eae1.gif)

I resized to make them the same height has their container; should we make this change permanent?

![buttons2](https://cloud.githubusercontent.com/assets/815158/19359488/406beeda-912f-11e6-9600-03dfc530090c.gif)

**Note: Animations are clipped**


The declaration of `farming.registered_plants` should just move to above the comments here. This can be done on merge by @paramat, really.


Ah, didn't see it was already merged.


also what about the coefficient? makes the comments a bit confusing and also... shouldn't it have a purpose? I am slightly confused tbh.


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How does this test test falling back to the root `ng2.injector`? 😕


It's not just `irb`, it's every repl that uses readline, which is 99% of them (e.g. `psql`). macOS Sierra must be using a new version of readline.


Hi Valentin, do we actually need to disable these modules when removing our package?  What if they are used by some other web application not installed by ourselves?


Sketch from phone call:

```
{ flatness-v; sd-from-val } = get-flatness-and-env(val, existing-env)
if val is a lambda:
  update sd-from-val
end
{ flatness-b; sd-from-body} = get-flatness-and-env(body, updated-sd-from-val)
{ flat-max(flatness-v, flatness-b); sd-from-body }
```


TeamCity Code :: 1. Development :: CMS :: Features [Build 50](http://mp-ci.centralus.cloudapp.azure.com/viewLog.html?buildId=9678&buildTypeId=Code_Development_Cms_Features&guest=1) is now running


Reproduced, thanks for bringing this to attention.


Can we increase number of threads to 10 or something?


Hi @danielo515

> So because the list widget that performs the search is not rendered, then the search is not performed, right?

That's correct, yes.

> I'm trying to find where the search operator is used, but I can't

The search operator is used with the `<$count>` widget in a number of places that you can see in this commit, and the searching itself is done in `$:/core/ui/DefaultSearchResultList`:

https://github.com/Jermolene/TiddlyWiki5/blob/master/core/ui/DefaultSearchResultList.tid#L8


TeamCity Code :: 1. Development :: CMS :: Features [Build 50](http://mp-ci.centralus.cloudapp.azure.com/viewLog.html?buildId=9678&buildTypeId=Code_Development_Cms_Features&guest=1) outcome was **SUCCESS**
Summary: Running Build time: 00:00:38


TeamCity Code :: 1. Development :: CMS :: Features [Build 51](http://mp-ci.centralus.cloudapp.azure.com/viewLog.html?buildId=9679&buildTypeId=Code_Development_Cms_Features&guest=1) is now running


this is new wotlk version probably

                    int32 bonusDamage = m_caster->SpellBaseDamageBonusDone(GetSpellSchoolMask(m_spellInfo))
                        + unitTarget->SpellBaseDamageBonusTaken(GetSpellSchoolMask(m_spellInfo)); // Does Amplify Magic/Dampen Magic influence flametongue? If not, this must be removed.
                    float weaponSpeed = (1.0f / IN_MILLISECONDS) * m_CastItem->GetProto()->Delay;
                    int32 spellPowerDamage = m_caster->SpellBonusWithCoeffs(m_spellInfo, 0, 0, 0, SPELL_DIRECT_DAMAGE, false); // flat 10% from Increased Spellpower
                    int32 totalDamage = int32(((damage + bonusDamage) + 3.85f * spellPowerDamage) * 0.01 * weaponSpeed);

Explanation in next comment, so u can look at it first.


TeamCity Code :: 1. Development :: CMS :: Features [Build 51](http://mp-ci.centralus.cloudapp.azure.com/viewLog.html?buildId=9679&buildTypeId=Code_Development_Cms_Features&guest=1) outcome was **SUCCESS**
Summary: Running Build time: 00:00:16


Why do you need a separate API? Can you reuse the existing `log()` method?


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What are we testing here? It seems to me that we are only testing that the timeout fired.


use single quotes instead of double


Hi, great (and fast !) work.

I added the on/off switch for the boiler in Domoticz, but it doesn't switch the boiler on/of in the Nefit app. Is there something I can help you with or am I doing something wrong ?


just `create(:user)`


I am getting many timedout errors in GMail.
	info@gateknockout.com was rejected due to domain error in thread 2 because All nameservers failed to answer the query gateknockout.com. IN MX: Server 172.31.0.2 UDP port 53 answered SERVFAIL
	epathshalasolutions@smartschoolonline.in was accepted in thread 2
	inpsclasses@gmail.com was accepted in thread 1
	icaiagra@gmail.com was accepted in thread 2
	info@stepps.in was rejected due to domain error in thread 2 because None of DNS query names exist: stepps.in., stepps.in.ec2.internal.
	10/13/2016 05:21:05 PM ERROR: Possible problem in Connection, email: sales@tayalinstitute.com was assumed to be correct
	Traceback (most recent call last):
	  File "/home/bitnami/rohit/scrap-preprocessor/validate_email.py", line 27, in validate_email
		server.connect(mxRecord)
	  File "/usr/lib/python2.7/smtplib.py", line 316, in connect
		self.sock = self._get_socket(host, port, self.timeout)
	  File "/usr/lib/python2.7/smtplib.py", line 291, in _get_socket
		return socket.create_connection((host, port), timeout)
	  File "/usr/lib/python2.7/socket.py", line 571, in create_connection
		raise err
	error: [Errno 110] Connection timed out
	sales@tayalinstitute.com was deemed to be accepted in thread 1
	10/13/2016 05:21:06 PM ERROR: Possible problem in Connection, email: icaiagra@gmail.com was assumed to be correct
	Traceback (most recent call last):
	  File "/home/bitnami/rohit/scrap-preprocessor/validate_email.py", line 27, in validate_email
		server.connect(mxRecord)
	  File "/usr/lib/python2.7/smtplib.py", line 316, in connect
		self.sock = self._get_socket(host, port, self.timeout)
	  File "/usr/lib/python2.7/smtplib.py", line 291, in _get_socket
		return socket.create_connection((host, port), timeout)
	  File "/usr/lib/python2.7/socket.py", line 571, in create_connection
		raise err
	error: [Errno 101] Network is unreachable
	icaiagra@gmail.com was deemed to be accepted in thread 2
	bhambrianjuman94@gmail.com was accepted in thread 1
	10/13/2016 05:23:13 PM ERROR: Possible problem in Connection, email: scholarsbritish@gmail.com was assumed to be correct
	Traceback (most recent call last):
	  File "/home/bitnami/rohit/scrap-preprocessor/validate_email.py", line 27, in validate_email
		server.connect(mxRecord)
	  File "/usr/lib/python2.7/smtplib.py", line 316, in connect
		self.sock = self._get_socket(host, port, self.timeout)
	  File "/usr/lib/python2.7/smtplib.py", line 291, in _get_socket
		return socket.create_connection((host, port), timeout)
	  File "/usr/lib/python2.7/socket.py", line 571, in create_connection
		raise err
	error: [Errno 101] Network is unreachable
	scholarsbritish@gmail.com was deemed to be accepted in thread 2
	10/13/2016 05:24:16 PM ERROR: Possible problem in Connection, email: info@niksacademy.com was assumed to be correct
	Traceback (most recent call last):
	  File "/home/bitnami/rohit/scrap-preprocessor/validate_email.py", line 27, in validate_email
		server.connect(mxRecord)
	  File "/usr/lib/python2.7/smtplib.py", line 316, in connect
		self.sock = self._get_socket(host, port, self.timeout)
	  File "/usr/lib/python2.7/smtplib.py", line 291, in _get_socket
		return socket.create_connection((host, port), timeout)
	  File "/usr/lib/python2.7/socket.py", line 571, in create_connection
		raise err
	error: [Errno 110] Connection timed out
	info@niksacademy.com was deemed to be accepted in thread 1

	10/13/2016 05:25:21 PM ERROR: Possible problem in Connection, email: commercearena.agra@gmail.com was assumed to be correct
	Traceback (most recent call last):
	  File "/home/bitnami/rohit/scrap-preprocessor/validate_email.py", line 27, in validate_email
		server.connect(mxRecord)
	  File "/usr/lib/python2.7/smtplib.py", line 316, in connect
		self.sock = self._get_socket(host, port, self.timeout)
	  File "/usr/lib/python2.7/smtplib.py", line 291, in _get_socket
		return socket.create_connection((host, port), timeout)
	  File "/usr/lib/python2.7/socket.py", line 571, in create_connection
		raise err
	error: [Errno 101] Network is unreachable
	commercearena.agra@gmail.com was deemed to be accepted in thread 2
	vallaths.tes@gmail.com was accepted in thread 1
	10/13/2016 05:27:28 PM ERROR: Possible problem in Connection, email: dmandrinagra@gmail.com was assumed to be correct
	Traceback (most recent call last):
	  File "/home/bitnami/rohit/scrap-preprocessor/validate_email.py", line 27, in validate_email
		server.connect(mxRecord)
	  File "/usr/lib/python2.7/smtplib.py", line 316, in connect
		self.sock = self._get_socket(host, port, self.timeout)
	  File "/usr/lib/python2.7/smtplib.py", line 291, in _get_socket
		return socket.create_connection((host, port), timeout)
	  File "/usr/lib/python2.7/socket.py", line 571, in create_connection
		raise err
	error: [Errno 101] Network is unreachable
	dmandrinagra@gmail.com was deemed to be accepted in thread 2


TaskCluster: https://tools.taskcluster.net/task-graph-inspector/#HAgVo_icSCW4DrubZsds_Q/


Thanks for reviewing @tzz!


On GitHub, saved changes are called commits. Each commit has an associated commit message, which is a description explaining why a particular change was made. Commit messages capture the history of your changes, so other contributors can understand what you’ve done and why.


Co takhle to přesunout do 4. lekce (Funkce a řetězce)?


My version of git doesn't say WIP if you give a message. It says things like
`stash@{0}: On develop: misc leftovers from merging`

You might want to try something like:
`git stash list --grep-reflog="On ${branch}:"`

That would also fix the possible bug where you have a branch named "branch" and another "branch2" accidentally mixing, e.g. telling me there's a stash present in `branch2` when it was actually from `branch`.


@nagim Done by https://github.com/GitbookIO/gitbook/pull/1543/commits/4c174f916e86ff1202f374c2344d013d3ee47c74


bonus damage variable now contains flat bonuses from spells like amplify magic (mage spell) and similar, this damage is in no way related to "increased spell power" from gear.

Instead "increased spell power" from gear is added in SpellBonusWithCoeffs. Since this spell is Spell_Effect_Dummy, we need to handle it manually. There is no generic behaviour for this. From reading patch notes, blizzard is referring to this "spell power", not the bonus damage from a few measly auras. Therefore with this, spell power on gear will dynamically scale damage based on spell power.

Then there is spellpower coefficient headache incoming. Right now, we dont even use spellpower from gear. In database 10% is taken into account. Therefore we have to do the following in DB:

INSERT INTO spell_bonus_data VALUES('8026', '3.85', '0', '0', '0', 'Shaman - Flametongue Weapon Proc Rank 1');

and remove the 3.85f * from code. This is all still WOTLK. TBC version in next comment.


looks good


Visual Regression Testing found a difference between new version and the baseline.
Check the diffs [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-pr-check/737/).
Accept the new baseline [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-update-baseline/parambuild?branch=ember).


TBC version

                    int32 bonusDamage = m_caster->SpellBaseDamageBonusDone(GetSpellSchoolMask(m_spellInfo))
                        + unitTarget->SpellBaseDamageBonusTaken(GetSpellSchoolMask(m_spellInfo)); // Does Amplify Magic/Dampen Magic influence flametongue? If not, this must be removed.
                    float weaponSpeed = (1.0f / IN_MILLISECONDS) * m_CastItem->GetProto()->Delay;
                    int32 spellPowerDamage = m_caster->SpellBonusWithCoeffs(m_spellInfo, 0, 0, 0, SPELL_DIRECT_DAMAGE, false); // flat 10% from Increased Spellpower
                    int32 totalDamage = int32(((damage + bonusDamage)) * 0.01 * weaponSpeed) + spellPowerDamage;

Again explanation in next comment.


leider das falsche Projekt ;)


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ne falsche branch...


Here we will do this in DB:

INSERT INTO spell_bonus_data VALUES('8026', '0.1', '0', '0', '0', 'Shaman - Flametongue Weapon Proc Rank 1');

To immediately get 10% flat spell damage from gear, as you said you had found on TBC wowwiki in 2007. Flat damage + auras flat damage from spell is still calculated based on weapon attack speed, but spelldamage is added as a flat addition.

Now ask if anything doesnt make sense.


gives syntax error, please see #259


I actually append 'reHLT' or 'withHLT' to directly identify the samples included in the two different campaigns. I think it is even easier like this than having _v14 (for both 'reHLT' and 'withHLT') and _v0 (for standard Spring16).


Memoria de instrucciones


Manual de usuario


Gay


It appears as though Khan Academy has patched this on their server. Now their server verifies the question instead of the client, so the answers aren't being sent anymore. So, unfortunately, I don't think this script will work anymore.


Afegint "conflicte?"


Your gmail password is in plain text.
Figured I'd let you know in case you haven't changed it since this was uploaded.


change


Looks like the commit history of this code was lost, shouldn't the asm be attributed to @vkrasnov?


really sorry for the noise ... i had an install issue as it seems (app didn't update at all and i still had a dev build from me with addons installed). this 9.3.3 jailbreak sucks so much :(


Just curious, what is this for? If you run shfmt on a dir, it will run on all files that either have a shell extension or no extension and a valid shell shebang. So you should be able to replace all of that with `shfmt -i 2 -w .`.


This is me being guilty of some cargo culting.  I don't remember which repo it's from, but I had a reason for wanting to only test `#!/usr/bin/env bash` and *not* `#!/bin/sh`.  In this case, I can clearly switch to `shfmt`'s default behavior :smile_cat:


repo commit


OK! Removed


Visual Regression Testing found a difference between new version and the baseline.
Check the diffs [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-pr-check/739/).
Accept the new baseline [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-update-baseline/parambuild?branch=ember).


OK! Removed too


Fixed


stop errors


Cool - found this and was wondering if it was a bug in the directory walk logic.


idk why my indents get messed up


_internal screaming_


Subtle difference: A mismatch with *tls-version-max* (tls-version-min > tls-version-max) at the other end could cause problems.  (Similar for the tls-version-max text below.)


True, I tried to cleanup at least those used only by this package. Even simpler if you prefer to leave them all enabled :)


Ok


Thanks Tim, that's cool.


_external screaming_


I need to remove the two parameter Spaces or just the first one?


Should be `spatie/string`, yeah? 😄


This version bump broke multi-line support. Particularly with the `--output_wrapper` flag:

```
--output_wrapper=(function() {
%output%;
}).call(this)
```

I'm trying to figure out work arounds.


TaskCluster: https://tools.taskcluster.net/task-graph-inspector/#FZ0yHvj9Q76zUXrIZPVWeQ/


No noticeable performance difference using `git ls-files` and it has the side benefit of automatically ignoring `.gitignore`'d files.


@jonathansampson I just screenshotted Windows and used that size :)

If we go back and do the changes in Electron using Win32 API, you can get the size and position of the buttons via methods like GetSystemMetrics()  If you wanted to take a peek, I had put some code together which shows some of those API calls:
https://github.com/bsclifton/BrowserWindowStyles


Because I was lazy and to me it's obvious what's happening there. Simple as that. :)

Anyway, I replaced this with a more Pythonic way.


## Test
- [ ] Test choice


Excuse the confusion I caused though, I combed back through my tmux buffer
and realized my posting mistake, the docs as they stand are what I entered
in docker as well.

Thank you for the effort.

On Thu, Oct 13, 2016, 5:19 AM xsteadfastx <notifications@github.com> wrote:

> fixed docs to get redis working
>
> thanks to @bobberb for pointing in the right direction.
>
> --
> You are receiving this because you were mentioned.
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> https://github.com/wallabag/docker/commit/af2fb30389d40e38dfc264184abb929a204531e4
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This file only works to the current build. If changes are made and the program is rebuilt this version will not update! Navigate to bin/Release for the rebuilt version.


@mikekavouras tsk tsk


Install the firmware for using Bluetooth on rtl8723bu


@carlossg: Tried to relax the use of `transient` and I ended up with: #73. I also tested it and seems to work with no issues.


To mám zase ostudu... :-D


Why do we need the PSCustomObject here? Can this be removed as well?


The commit message says:

```
This change merges two CLs:
  https://go-review.googlesource.com/#/c/24717
  https://go-review.googlesource.com/#/c/26691
```

and it certainly wasn't the intention not to credit anyone. If you would like a more explicit notice in the assembly file I can certainly do that.


We will get `unfold` back soon. The new `dunfold` has the prefix `d` because it guarantees the resulting expression is definitionally equal to the original one. The new `dunfold` is based on the equational lemmas produced by the equation compiler. The goal is to get a more sensible result when we unfold something like `list.append`. BTW, I'm not very happy with the name `dunfold`. I'm also using `dsimplify` for the simplifier that guarantees the resulting expression is definitionally equal to the input.

The new `unfold` (working-in-progress) will also apply equational lemmas that do not hold definitionally. This is particularly important for functions defined by well founded recursion where none of the equational lemmas hold definitionally.


yup, nice catch!


Many thanks for this!


Very nice 😉


Tohle je asi teoreticky mozne, ale tak nejak jsem pocital s tim, ze to budou cela cisla. Dava pak smysl i uzivatelum zobrazit informaci, o kolik mesicu se jim predplatne prodlouzi. Nastavil bych to na 0, 1 a 2.


@markasammut release is out now.


"http://yourdomain.com" # the base hostname & protocol for your site


Visual Regression Testing found a difference between new version and the baseline.
Check the diffs [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-pr-check/742/).
Accept the new baseline [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-update-baseline/parambuild?branch=ember).


Can I have markers of two different colors, say few markers of red color and few of green. I am struggling to make it work. Please help.


Don't forget `--fastparser` 😄


you're right


> without actually affecting anything

That's not quite true. If I have another stylesheet which uses `o2-plugin-styles` as a dependency I'd need to change the handle based on `is_rtl()` too, even if the additional stylesheet doesn't require a RTL version.


@joseph-robertson FYI


I think there was a typo here.


// (BOF - EDIT) ZCA Responsive Components for 1.5.5

      $db->Execute("insert into " . TABLE_LAYOUT_BOXES . "
                  (layout_template, layout_box_name, layout_box_status, layout_box_location, layout_box_sort_order, layout_box_sort_order_single, layout_box_status_single, show_box_min_width)
                  values ('" . zen_db_input($template_dir) . "', '" . zen_db_input($file) . "', 0, 0, 0, 0, 0, 0)");

// (EOF - EDIT) ZCA Responsive Components for 1.5.5


No big deal, these things happen. An explicit notice in the assembly of the authorship (commit author or otherwise) would be nice.


https://github.com/zackhsi/dotfiles/commit/a5d1ccc4529f60626d87070b40cfbabcc2492fed :)


Definitely!


maybe it would be better to use /sim/time/delta-sec rather than assuming a fixed frame rate


Nice, would you mind if I cherry pick this one?


Closes issue #25


Awww yeah! :D Looking good!


TBC

                    int32 bonusDamage = m_caster->SpellBaseDamageBonusDone(GetSpellSchoolMask(m_spellInfo))
                        + unitTarget->SpellBaseDamageBonusTaken(GetSpellSchoolMask(m_spellInfo)); // Does Amplify Magic/Dampen Magic influence flametongue? If not, this must be removed.
                    float weaponSpeed = (1.0f / IN_MILLISECONDS) * m_CastItem->GetProto()->Delay;
                    int32 bonusDamage = m_caster->SpellBonusWithCoeffs(m_spellInfo, bonusDamage, 0, 0, SPELL_DIRECT_DAMAGE, false); // apply spell coeff
                    int32 totalDamage = (damage * 0.01 * weaponSpeed) + bonusDamage;

Explanation: BonusDamage contains spell damage from gear. I was wrong above.

wotlk version in a moment.


All clear, thank you very much @jermolene


wotlk

                    int32 bonusDamage = m_caster->SpellBaseDamageBonusDone(GetSpellSchoolMask(m_spellInfo))
                        + unitTarget->SpellBaseDamageBonusTaken(GetSpellSchoolMask(m_spellInfo)); // Does Amplify Magic/Dampen Magic influence flametongue? If not, this must be removed.
                    float weaponSpeed = (1.0f / IN_MILLISECONDS) * m_CastItem->GetProto()->Delay;
                    int32 bonusDamage = m_caster->SpellBonusWithCoeffs(m_spellInfo, bonusDamage, 0, 0, SPELL_DIRECT_DAMAGE, false); // apply spell coeff
                    int32 totalDamage = ((damage + bonusDamage) * 0.01 * weaponSpeed);


Missing `,` here


TBC SQL needed

INSERT INTO spell_bonus_data VALUES('8026', '0.1', '0', '0', '0', 'Shaman - Flametongue Weapon Proc Rank 1');

DELETE FROM spell_chain WHERE first_spell=8026;
INSERT INTO spell_chain VALUES
(8026, 0, 8026, 1, 0),
(8028, 8026, 8026, 2, 0),
(8029, 8028, 8026, 3, 0),
(10445, 8029, 8026, 4, 0),
(16343, 10445, 8026, 5, 0),
(16344, 16343, 8026, 6, 0),
(25488, 16344, 8026, 7, 0);


Should we use a $global-inuit-breakpoint-separator, to use in every partials that needs it, following the decision on issue #166?


Should be just: `taskcluster/(exchanges|queues)/${newNamespace.namespace}/.*` (extra spaces and plus signs now that you use back ticks).


the sumatrapdf head honchos are sadomachists - they have to be - they compile with /w4 (!).  that means any warning is treated as error.  so the other change you have to do if you want it to pass muster is to qualify your 0.4 as float with 0.4f.

Other than that, if the font changes aren't necessary to what you want to implement, you are better off removing them to increase your chances. of the commit going through  I was reading a comment recently from Kovid Goyal (calibre guy) that once you start maintaining a big project like his, you suddenly become extremely conservative and reticent to changes.  It sounds very true to me.

The other factor is having to deal with a userbase that is ready to pick a fight over the stupidest things ... like the highlight color for example.  [There was so much drama over that yellow!](highlight|selection color site:forums.fofou.org)  it was too bright, then too brown, then the border was wrong, etc.  I would have told everyone in the forum to fuck off and hardcoded it to cyan or something equally ugly if it had been me.


WOTLK SQL needed

INSERT INTO spell_bonus_data VALUES('8026', '3.85', '0', '0', '0', 'Shaman - Flametongue Weapon Proc Rank 1');

DELETE FROM spell_chain WHERE first_spell=8026;
INSERT INTO spell_chain VALUES
(8026, 0, 8026, 1, 0),
(8028, 8026, 8026, 2, 0),
(8029, 8028, 8026, 3, 0),
(10445, 8029, 8026, 4, 0),
(16343, 10445, 8026, 5, 0),
(16344, 16343, 8026, 6, 0),
(25488, 16344, 8026, 7, 0),
(58786, 25488, 8026, 8, 0),
(58787, 58786, 8026, 9, 0),
(58788, 58787, 8026, 10, 0);


upnew


@monsta
Can you please bump version in NEWS too for further packages?   :)
Otherwise distcheck fails when creating the tarball for testing changes.


I dont know if i understood correctly, please check


What was the point of this change? I reverted this and I no longer get the null error I was able to reproduce.


Bah, fuck, I forgot to stage that before I amended to add that :<


Question: Do we care to support all possible usecases? For example, there methods can also accept an object (e.g. `{[token: Ng1Token]: IProvider}`). Should `ngUpgrade` be able to handle? I guess not, right?


Yeeesss


Added prop - float. Allows buttons to float left towards the label or right towards end of container.


kljklj


this block missing test coverage


Visual Regression Testing found a difference between new version and the baseline.
Check the diffs [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-pr-check/743/).
Accept the new baseline [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-update-baseline/parambuild?branch=ember).


Why did you remove the function here? Breakpoints are no longer filtered.


How are we testing the ng2 testability?


Cursos? Pra que commitar manterCurso.jsp ? Esse foi o exemplo do Marco de como fazer as telas, e elas foram feitas, essa pagina deve ser apagada @fdotf97pb


It gave weird issues. I thought it only read in the stack regions anyway...

On Thu, 13 Oct 2016 at 20:14 Nukem <notifications@github.com> wrote:

> Why did you remove the function here? Breakpoints are no longer filtered.
>
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Trying to lead this to success! :)


Alyssa Sanchez


No, we closed this PR, this fix wasn't sufficient. This implementation only adds the first part of what I call the "indirection sandwich", which is the `Node` wrapper. I never found a good way to determine, at run-time, what the inner fragment should be, e.g. `... on Feedback` or `... on Story`, in this example. You can see https://github.com/facebook/relay/pull/1000 for a short discussion on this


o Fernando commitou esse manter curso tbm.. pra que? nós não salvamos curso, isso foi u exemplo q o marco antonio deu, essa pagina deve ser apagada


you can add it. just pass some invalid hex.  the error check above can be hit by passing an incomplete hash.


I say, you should also include the full line I ended up using:
`install_github('RGLab/ncdfFlow', ref='trunk', args='--configure-args="--with-hdf5=<path-to-hdf>"')`


I do not understand who did make a decision regarding such migration.
It is a direct push without review by @reviewbybees , @jenkinsci/code-reviewers and no threads in the mailing lists. What is the reason?


the commit that makes the fix is 02594aff943242ce6016021cb58c801a1d5b5cf7 .
But in doing that I noticed this issue, `order_by` is not in-place, so I have to assign the result back to `self._results`.


Asi máš pravdu. Ještě mě napadá, že by bylo fajn uživatelovi zobrazit, nějaký přehled svých referrovaných. Ukládáme to? Jinak si někého měsíce navíc ani nemusí všimnout.


@alexey-sidnev, доделанная задача с последней пары про последовательность.


Name: Alyssa Sanchez


@Xylemon: I created a PR to fix that segfault. In case it doesn't get merged soon, you can check out my fork at [jgriebler/dunst](https://github.com/jgriebler/dunst).


1.) on kezan- sniffs i have seen some area-trigger that use phaseGroup on same way as phaseIds..
you can only trigger this area by sending a phaseGroup id.. ( on same way as done with phaseId)..
2.) take allways a phaseGroup and use its phaseIds in SetVisible: give no possible visual results in Kezan..

so i think: the way some devs thinking: how phasing is working: Is definitely wrong..

kezan was the only reason, i changed from phaseMask to phaseId..
devs can only know about phasing: if there  **creating the complete zone of kezan.**

the way i have done it now, make it possible to create all quest in kezan..
for mostly other zones, i think, old phaseMask, was able to handle them all..

a note:
so maybe: best way is to do both.. is a way in the middle..
a phaseId is allways only a phaseId
a phaseGroup can be both..
it can be used as a phaseid.. (insertes in column phaseid) (this is the state of now, for arkania)
but it can be used as phasegroup to, and means then: a group of phases ( and insertes in column phaseGroup) and should uses: **only to reduce place in phaseIds..**

on the moment it is not neccessary to do so..
inside the core, its expanding the group to id's.. so the core has same work to do..


The Dream Home suggestion system, developed in CLIPS suggests the best house suitable for you based on your choices


That makes sense. I'll switch them to the same handle then. Thanks for
elaborating on that.

On Oct 13, 2016 11:02 AM, "Dominik Schilling" <notifications@github.com>
wrote:

> without actually affecting anything
>
> That's not quite true. If I have another stylesheet which uses
> o2-plugin-styles as a dependency I'd need to change the handle based on
> is_rtl() too, even if the additional stylesheet doesn't require a RTL
> version.
>
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> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
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http://i.imgur.com/OlEnech.png

this time cant even click morgrim console after morogrim killed


klm;


![](https://github.trello.services/images/mini-trello-icon.png) [Make introduction summary](https://trello.com/c/e1kNMODI/9-make-introduction-summary)


tks for the answer, I'll avoid union and interface until Relay 2