[.DEploid/utilities/dEploidTools.r:1:22:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                     ^
```
[.DEploid/utilities/dEploidTools.r:1:28:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                           ^
```
[.DEploid/utilities/dEploidTools.r:2:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L2) *style:* **Variable and function names should be all lowercase.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:2:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L2) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:2:48:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L2) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
                                               ^
```
[.DEploid/utilities/dEploidTools.r:3:15:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L3) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i+1
              ^
```
[.DEploid/utilities/dEploidTools.r:3:22:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L3) *style:* **Put spaces around all infix operators.**
```r
        arg_i = arg_i+1
                    ~^~
```
[.DEploid/utilities/dEploidTools.r:6:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L6) *style:* **Variable and function names should be all lowercase.**
```r
    outPrefix = "dataExplore"
    ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:6:15:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L6) *style:* **Use <-, not =, for assignment.**
```r
    outPrefix = "dataExplore"
              ^
```
[.DEploid/utilities/dEploidTools.r:7:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L7) *style:* **Variable and function names should be all lowercase.**
```r
    vcfFileName = ""
    ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:7:17:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L7) *style:* **Use <-, not =, for assignment.**
```r
    vcfFileName = ""
                ^
```
[.DEploid/utilities/dEploidTools.r:8:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L8) *style:* **Variable and function names should be all lowercase.**
```r
    refFileName = ""
    ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:8:17:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L8) *style:* **Use <-, not =, for assignment.**
```r
    refFileName = ""
                ^
```
[.DEploid/utilities/dEploidTools.r:9:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L9) *style:* **Variable and function names should be all lowercase.**
```r
    altFileName = ""
    ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:9:17:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L9) *style:* **Use <-, not =, for assignment.**
```r
    altFileName = ""
                ^
```
[.DEploid/utilities/dEploidTools.r:10:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L10) *style:* **Variable and function names should be all lowercase.**
```r
    plafFileName = ""
    ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:10:18:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L10) *style:* **Use <-, not =, for assignment.**
```r
    plafFileName = ""
                 ^
```
[.DEploid/utilities/dEploidTools.r:11:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L11) *style:* **Variable and function names should be all lowercase.**
```r
    excludeFileName = ""
    ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:11:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L11) *style:* **Use <-, not =, for assignment.**
```r
    excludeFileName = ""
                    ^
```
[.DEploid/utilities/dEploidTools.r:12:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L12) *style:* **Variable and function names should be all lowercase.**
```r
    dEploidPrefix = ""
    ^~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:12:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L12) *style:* **Use <-, not =, for assignment.**
```r
    dEploidPrefix = ""
                  ^
```
[.DEploid/utilities/dEploidTools.r:13:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L13) *style:* **Variable and function names should be all lowercase.**
```r
    excludeBool = FALSE
    ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:13:17:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L13) *style:* **Use <-, not =, for assignment.**
```r
    excludeBool = FALSE
                ^
```
[.DEploid/utilities/dEploidTools.r:15:11:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L15) *style:* **Use <-, not =, for assignment.**
```r
    arg_i = 1
          ^
```
[.DEploid/utilities/dEploidTools.r:16:11:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
          ^
```
[.DEploid/utilities/dEploidTools.r:16:33:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
                                ^
```
[.DEploid/utilities/dEploidTools.r:17:14:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L17) *style:* **Use <-, not =, for assignment.**
```r
        argv = args[arg_i]
             ^
```
[.DEploid/utilities/dEploidTools.r:18:12:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
           ^
```
[.DEploid/utilities/dEploidTools.r:18:28:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
                           ^
```
[.DEploid/utilities/dEploidTools.r:19:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L19) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:19:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L19) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:19:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L19) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:19:52:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:20:13:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L20) *style:* **Variable and function names should be all lowercase.**
```r
            vcfFileName = args[arg_i]
            ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:20:25:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L20) *style:* **Use <-, not =, for assignment.**
```r
            vcfFileName = args[arg_i]
                        ^
```
[.DEploid/utilities/dEploidTools.r:21:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:21:36:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                                   ^
```
[.DEploid/utilities/dEploidTools.r:22:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L22) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:22:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L22) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:22:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L22) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:22:52:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:23:13:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L23) *style:* **Variable and function names should be all lowercase.**
```r
            plafFileName = args[arg_i]
            ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:23:26:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L23) *style:* **Use <-, not =, for assignment.**
```r
            plafFileName = args[arg_i]
                         ^
```
[.DEploid/utilities/dEploidTools.r:24:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:24:35:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                                  ^
```
[.DEploid/utilities/dEploidTools.r:25:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L25) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:25:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L25) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:25:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L25) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:25:52:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:26:13:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L26) *style:* **Variable and function names should be all lowercase.**
```r
            refFileName = args[arg_i]
            ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:26:25:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L26) *style:* **Use <-, not =, for assignment.**
```r
            refFileName = args[arg_i]
                        ^
```
[.DEploid/utilities/dEploidTools.r:27:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:27:35:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                                  ^
```
[.DEploid/utilities/dEploidTools.r:28:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L28) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:28:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L28) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:28:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L28) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:28:52:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L28) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:29:13:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L29) *style:* **Variable and function names should be all lowercase.**
```r
            altFileName = args[arg_i]
            ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:29:25:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L29) *style:* **Use <-, not =, for assignment.**
```r
            altFileName = args[arg_i]
                        ^
```
[.DEploid/utilities/dEploidTools.r:30:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:30:39:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                                      ^
```
[.DEploid/utilities/dEploidTools.r:31:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L31) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:31:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L31) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:31:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L31) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:31:52:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L31) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:32:13:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L32) *style:* **Variable and function names should be all lowercase.**
```r
            excludeFileName = args[arg_i]
            ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:32:29:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L32) *style:* **Use <-, not =, for assignment.**
```r
            excludeFileName = args[arg_i]
                            ^
```
[.DEploid/utilities/dEploidTools.r:33:13:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L33) *style:* **Variable and function names should be all lowercase.**
```r
            excludeBool = TRUE
            ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:33:25:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L33) *style:* **Use <-, not =, for assignment.**
```r
            excludeBool = TRUE
                        ^
```
[.DEploid/utilities/dEploidTools.r:34:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:34:33:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                                ^
```
[.DEploid/utilities/dEploidTools.r:35:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L35) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:35:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L35) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:35:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L35) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:35:52:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:36:13:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L36) *style:* **Variable and function names should be all lowercase.**
```r
            outPrefix = args[arg_i]
            ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:36:23:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L36) *style:* **Use <-, not =, for assignment.**
```r
            outPrefix = args[arg_i]
                      ^
```
[.DEploid/utilities/dEploidTools.r:37:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:37:40:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                                       ^
```
[.DEploid/utilities/dEploidTools.r:38:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L38) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:38:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L38) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:38:21:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L38) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:38:52:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:39:13:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L39) *style:* **Variable and function names should be all lowercase.**
```r
            dEploidPrefix = args[arg_i]
            ^~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:39:27:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L39) *style:* **Use <-, not =, for assignment.**
```r
            dEploidPrefix = args[arg_i]
                          ^
```
[.DEploid/utilities/dEploidTools.r:44:15:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L44) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i + 1
              ^
```
[.DEploid/utilities/dEploidTools.r:51:8:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
       ^
```
[.DEploid/utilities/dEploidTools.r:51:10:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L51) *style:* **Variable and function names should be all lowercase.**
```r
    if ( plafFileName == "" ){
         ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:51:28:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
                           ^
```
[.DEploid/utilities/dEploidTools.r:58:12:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
           ^
```
[.DEploid/utilities/dEploidTools.r:58:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
                  ^
```
[.DEploid/utilities/dEploidTools.r:58:35:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L58) *style:* **Variable and function names should be all lowercase.**
```r
    return ( list ( vcfFileName = vcfFileName,
                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:59:35:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L59) *style:* **Variable and function names should be all lowercase.**
```r
                    refFileName = refFileName,
                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:60:35:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L60) *style:* **Variable and function names should be all lowercase.**
```r
                    altFileName = altFileName,
                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:61:36:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L61) *style:* **Variable and function names should be all lowercase.**
```r
                    plafFileName = plafFileName,
                                   ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:62:33:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L62) *style:* **Variable and function names should be all lowercase.**
```r
                    outPrefix = outPrefix,
                                ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:63:37:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L63) *style:* **Variable and function names should be all lowercase.**
```r
                    dEploidPrefix = dEploidPrefix,
                                    ^~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:64:39:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L64) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeFileName = excludeFileName,
                                      ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:65:35:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L65) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeBool = excludeBool) )
                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:65:47:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L65) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    excludeBool = excludeBool) )
                                              ^
```
[.DEploid/utilities/dEploidTools.r:69:1:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L69) *style:* **Variable and function names should be all lowercase.**
```r
fun.dEploidPrefix <- function ( prefix ){
^~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:81:1:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L81) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.coverage <- function ( inputs ){
^~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:82:17:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L82) *style:* **Variable and function names should be all lowercase.**
```r
    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:17:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:17:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L83) *warning:* **no visible global function definition for ‘extractCoverageFromVcf’**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:48:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:17:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:17:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L85) *warning:* **no visible global function definition for ‘extractCoverageFromTxt’**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:48:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                               ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:68:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                                                   ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:109:1:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:109:38:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:109:51:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:110:9:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L110) *style:* **Use <-, not =, for assignment.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
        ^
```
[.DEploid/utilities/dEploidTools.r:110:22:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L110) *style:* **Variable and function names should be all lowercase.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:111:9:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L111) *style:* **Use <-, not =, for assignment.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
        ^
```
[.DEploid/utilities/dEploidTools.r:111:22:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L111) *style:* **Variable and function names should be all lowercase.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:112:39:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L112) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = ref[,1],
                                      ^
```
[.DEploid/utilities/dEploidTools.r:113:37:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L113) *style:* **Commas should always have a space after.**
```r
                         POS = ref[,2],
                                    ^
```
[.DEploid/utilities/dEploidTools.r:114:42:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L114) *style:* **Commas should always have a space after.**
```r
                         refCount = ref[,3],
                                         ^
```
[.DEploid/utilities/dEploidTools.r:115:42:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L115) *style:* **Commas should always have a space after.**
```r
                         altCount = alt[,3] )
                                         ^
```
[.DEploid/utilities/dEploidTools.r:120:1:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L120) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
^~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:120:34:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                 ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:120:51:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:121:10:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L121) *style:* **Variable and function names should be all lowercase.**
```r
    if ( excludeBool ) {
         ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:122:39:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L122) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool,
                                      ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:123:1:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L123) *style:* **lines should not be more than 80 characters.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:123:51:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L123) *style:* **Variable and function names should be all lowercase.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
                                                  ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:125:39:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L125) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool ))
                                      ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:147:1:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:147:38:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                     ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:147:47:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                              ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:149:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L149) *style:* **Variable and function names should be all lowercase.**
```r
    catCmd = "cat"
    ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:149:12:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L149) *style:* **Use <-, not =, for assignment.**
```r
    catCmd = "cat"
           ^
```
[.DEploid/utilities/dEploidTools.r:150:1:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L150) *style:* **lines should not be more than 80 characters.**
```r
    if ( grepl("gzip", system(paste("file --mime-type", vcfName), T) ) == TRUE ){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:150:57:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L150) *style:* **Variable and function names should be all lowercase.**
```r
    if ( grepl("gzip", system(paste("file --mime-type", vcfName), T) ) == TRUE ){
                                                        ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:151:9:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L151) *style:* **Variable and function names should be all lowercase.**
```r
        catCmd = "zcat <"
        ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:151:16:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L151) *style:* **Use <-, not =, for assignment.**
```r
        catCmd = "zcat <"
               ^
```
[.DEploid/utilities/dEploidTools.r:154:1:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L154) *style:* **lines should not be more than 80 characters.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:154:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L154) *style:* **Variable and function names should be all lowercase.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
    ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:154:13:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L154) *style:* **Use <-, not =, for assignment.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
            ^
```
[.DEploid/utilities/dEploidTools.r:154:39:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L154) *style:* **Variable and function names should be all lowercase.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
                                      ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:154:47:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L154) *style:* **Variable and function names should be all lowercase.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
                                              ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:154:81:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L154) *style:* **Commented code should be removed.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
                                                                                ^~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:155:1:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L155) *style:* **lines should not be more than 80 characters.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:155:10:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L155) *style:* **Use <-, not =, for assignment.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
         ^
```
[.DEploid/utilities/dEploidTools.r:155:31:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L155) *style:* **Variable and function names should be all lowercase.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                              ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:155:45:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L155) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                           ~^~
```
[.DEploid/utilities/dEploidTools.r:155:46:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L155) *style:* **Variable and function names should be all lowercase.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                             ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:155:61:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L155) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                           ~^~
```
[.DEploid/utilities/dEploidTools.r:155:77:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L155) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                           ~^~
```
[.DEploid/utilities/dEploidTools.r:155:119:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L155) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                                ~^~
```
[.DEploid/utilities/dEploidTools.r:157:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L157) *style:* **Variable and function names should be all lowercase.**
```r
    sampleName = names(vcf)[10]
    ^~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:157:16:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L157) *style:* **Use <-, not =, for assignment.**
```r
    sampleName = names(vcf)[10]
               ^
```
[.DEploid/utilities/dEploidTools.r:159:9:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L159) *style:* **Use <-, not =, for assignment.**
```r
    tmp = vcf[[sampleName]]
        ^
```
[.DEploid/utilities/dEploidTools.r:159:16:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L159) *style:* **Variable and function names should be all lowercase.**
```r
    tmp = vcf[[sampleName]]
               ^~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:160:11:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L160) *style:* **Use <-, not =, for assignment.**
```r
    field = strsplit(as.character(tmp),":")
          ^
```
[.DEploid/utilities/dEploidTools.r:160:40:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L160) *style:* **Commas should always have a space after.**
```r
    field = strsplit(as.character(tmp),":")
                                       ^
```
[.DEploid/utilities/dEploidTools.r:162:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L162) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:162:15:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L162) *style:* **Use <-, not =, for assignment.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
              ^
```
[.DEploid/utilities/dEploidTools.r:162:44:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L162) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
                                           ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:163:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L163) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
    ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:163:12:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L163) *style:* **Use <-, not =, for assignment.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
           ^
```
[.DEploid/utilities/dEploidTools.r:163:36:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L163) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                   ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:163:47:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L163) *style:* **Commas should always have a space after.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                              ^
```
[.DEploid/utilities/dEploidTools.r:165:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L165) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:165:14:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L165) *style:* **Use <-, not =, for assignment.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
             ^
```
[.DEploid/utilities/dEploidTools.r:165:41:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L165) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
                                        ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:166:5:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L166) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:166:14:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L166) *style:* **Use <-, not =, for assignment.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
             ^
```
[.DEploid/utilities/dEploidTools.r:166:41:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L166) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
                                        ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:168:39:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L168) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = vcf[,1],
                                      ^
```
[.DEploid/utilities/dEploidTools.r:169:37:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L169) *style:* **Commas should always have a space after.**
```r
                         POS = vcf[,2],
                                    ^
```
[.DEploid/utilities/dEploidTools.r:170:37:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L170) *style:* **Variable and function names should be all lowercase.**
```r
                         refCount = refCount,
                                    ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:171:37:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L171) *style:* **Variable and function names should be all lowercase.**
```r
                         altCount = altCount )
                                    ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:192:1:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L192) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:192:12:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L192) *style:* **Put spaces around all infix operators.**
```r
extractPLAF<- function ( plafName ){
          ~^
```
[.DEploid/utilities/dEploidTools.r:192:26:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L192) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
                         ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:193:25:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L193) *style:* **Variable and function names should be all lowercase.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:193:41:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L193) *style:* **Put spaces around all infix operators.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~
```
[.DEploid/utilities/dEploidTools.r:198:11:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
         ~^~~
```
[.DEploid/utilities/dEploidTools.r:198:19:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                 ~^~
```
[.DEploid/utilities/dEploidTools.r:198:23:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                     ~^~
```
[.DEploid/utilities/dEploidTools.r:198:24:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L198) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                       ^
```
[.DEploid/utilities/dEploidTools.r:198:26:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                        ~^~
```
[.DEploid/utilities/dEploidTools.r:198:28:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                          ~^~
```
[.DEploid/utilities/dEploidTools.r:199:1:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L199) *style:* **lines should not be more than 80 characters.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:199:8:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
      ~^~~
```
[.DEploid/utilities/dEploidTools.r:199:23:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                     ~^~
```
[.DEploid/utilities/dEploidTools.r:199:30:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                            ~^~
```
[.DEploid/utilities/dEploidTools.r:199:43:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                         ~^~
```
[.DEploid/utilities/dEploidTools.r:199:44:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L199) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                           ^
```
[.DEploid/utilities/dEploidTools.r:199:46:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                            ~^~
```
[.DEploid/utilities/dEploidTools.r:199:54:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                    ~^~
```
[.DEploid/utilities/dEploidTools.r:199:59:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                         ~^~
```
[.DEploid/utilities/dEploidTools.r:199:72:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                      ~^~
```
[.DEploid/utilities/dEploidTools.r:199:77:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L199) *style:* **Commas should always have a space after.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                            ^
```
[.DEploid/utilities/dEploidTools.r:199:77:](https://github.com/mcveanlab/DEploid-r/blob/9a9bb7379fa30e7bfcede6168df970b9e57dc953/.DEploid/utilities/dEploidTools.r#L199) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                            ^
```


die Aufgabe4 ist noch nicht fertig, habe gerade angefangen


@roalcantara I dunno... LGTM 👍


vps? also i can get you a vm on my server for hosting servers


HUMM... I guess the could include another option since the dynamic_form is required. `include_blank: false`


Agreed - see line 34


ls -al ~/.ssh


Why did you reorder the back-ends? They made sense and were consistent with everything else that way :v


You could also use nounces or sha256 hashes to allow the inline JS.
See https://csp-evaluator.withgoogle.com/ and https://csp.withgoogle.com/docs/index.html.


A condition always has a fixed size fingerprint: 256 bits, at this time.


Woops, must have been rustfmt?


Yeah the v3 is available for preorder at Robotshop


`http://www.hackreactor/.com`
This is probably a typo


@rajeshdalsaniya was unable to do more that this today. Documentation file is [here](https://github.com/askmike/gekko/blob/stable/docs/trading_bot/talib_indicators.md).


Hey Marie @mhilpl ,

When you are adding supporting materials for an HTML/JADE file, can you please add it to public/[images/stylesheets/javascript] directory. This will keep views directory consistent.

Regards,
Jayant Arora


My workaround when experiencing this issue, rather than deleting this div, was to assign it an id that I then suppressed display of in my CSS.


Słabo poprawiłem ten ostatni błąd. Muszę go przemyśleć.


I wonder why this did not have:
isset($config['system']['use_mfs_tmpvar'])
in the conditional.
Was there an issue that dhcp6leases is not restored on reboot on a full install with use_mfs_tmpvar?
It just looked a bit surprising that this code was only done for nanobsd.


right?


250 in stock here at SparkFun: https://www.sparkfun.com/products/14032


Let's leave the app bundle in, but make the js file blank.


Thanks! I think this non-inline approach is fine, though.


Do you also need to add com.sun.jersey.jersey-test-framework to the group? To support http://search.maven.org/#artifactdetails%7Ccom.sun.jersey.jersey-test-framework%7Cjersey-test-framework-core%7C1.19.2%7Cjar


I see.

I've been quite concerned about the `include_blank: false` option, tho.

Lemme explain it:

By not using this option, the user is required to choose (actively) the dynamic_form. Whereas by using such an option, the user will be able to create a new task without selecting a dynamic_form. And that's why I didn't let this option.

Could this be a problem?

What do you reckon?


This line is redundant and should be removed, given the check below. No?


Rustfmt doesn't format TOML :v
It is,


#1 completed


@CarlosFer27  @DulceVallejo
Ya esta nuestra primer clase

Saludos :+1:


Sure do, will release a patch version.


Revised this thing for Diane


Thanks for accepting me.
Hello my name is miss jennifer i got your E-mail through github please there is something very important i would like to tell you.
(Nezjennifer@outlook.com)


Done, thaanks =)


ahhahah eu refiz a estrutura de botões, para centraliza-los, ai copiei o CANCEL, do SAVE, ai nem percebi que ficou com este parametro a mais


Nah it's good I'm using digitalocean, it's cheap and reliable

On Wed, Oct 12, 2016 at 5:16 PM, Spike11302000 <notifications@github.com>
wrote:

> vps? also i can get you a vm on my server for hosting servers
>
> —
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> Reply to this email directly, view it on GitHub
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TaskCluster: https://tools.taskcluster.net/task-graph-inspector/#Xd5aWZhqR5yYby6r-ayWxQ/


Start


is obsolete in current pear version:

        if (!$addr) {
            return $this->raiseError('$addr cannot be empty');
        } else if (strspn($addr, ':.0123456789') == strlen($addr)) {
            $this->addr = strpos($addr, ':') !== false ? '['.$addr.']' : $addr;
        } else {
            $this->addr = $addr;
        }


If `filter_expression` is `None` (and it will be `None` the first time one of these `if` statements runs), we will get an `AttributeError`. `__iand__(..)` is not defined for `None`. See [here](https://docs.python.org/2/reference/datamodel.html) for more on Python operator overloading.


I Really wana know the code from the fake lostcore... I want to fix it. xD


I've adopted this changed. :+1:


Already fixed. :+1:


Great, this fixes issue https://github.com/ClearControl/DockFX/issues/6


related #136


Adopted :+1:


ok


This is missing an #include "win32/time.h" for the Windows side of things, as we have our own implementation in win32/time.c


Just the skeleton of the website including an awesome logo.


Yes, thanks!


Thanks for accepting me.
Hello my name is miss julite i got your E-mail through github please there is something very important i would like to tell you.
(julitebemba@outlook.com)


@metion


mate one of them says "speedk"


Shouldn't it be 'DELETE FROM tweets WHERE.....'


If you're doing just upstream updates, feel free to push them directly to master.


dont use foo


If I may ask, what is this about? I don't think I have ever intentionally left an unused `var _;` lying around.

And if there is a case where this make sense, is it really common enough to deserve to live here?


That's an interesting question.  I'm trying to come up with a case where that isn't true.  I know it's true for a tree, but not necessarily a graph.


can you provide a code sample?


So, I tried to see how topological sort works, and I have no idea what it's doing.  Is there a description anywhere?


Nice job adding this in and using the `action (mut propertyName)` construct.


I executed this script and encountered few syntax errors. Will update that give a pull request.


TaskCluster: https://tools.taskcluster.net/task-graph-inspector/#RBOzCYTHTaKLWIm2z2vwGQ/


missiong javadocs?


Modified comment


mountain dew


LGTM


@bersace There's a typo here: `treu`


Why the `outer` and `middle` divs?  They don't seem to have any styling or functionality attached.

(They also triggered my "must indent every nested div" instinct, although occasionally a team will be okay with having wrapper stuff like this be cause for indentation)


This was the trick @garethrees https://github.com/openaustralia/righttoknow/commit/3c85154f23eaa08d1a6775a52ee88aa9d4603884

I could add that to the docs, or write something to include any .js put into /assets/javascripts . That would make the current docs correct and probably be easier for people. You still need to link to these files in your app, so we wouldn't be automatically serving stuff to users, which was a concern for me.


This should be the final version. Hooray!


Recommend using `JUnitMockeryRule` instead and remove `@After` method.


Was this console.log intended?


why did you change the signature of the Main from accepting  (string[] args) ?


Looks very nice now. :) Could you push a little further in the direction you have gone with `inAlphabeticalOrder` and have a single function that includes the comparison conditions for both the score and the name? Ideally we would like just a single if line in the body of the for loop.


Можно классы какие-нить детектить. Она там дохрена созадет всего.
А про кнопки че-то не понял. Если она включена, то и кнопки будут, Или ты о чем?


> классы

стили в смысле


Toggle is not implemented yet, but will essentially be to turn off an already playing audio clip. I still need to play around with it and see what happens. Also AudioSource is public so that the user can drag in a custom Audio SOurce if theud like, otherwise it will make one for them


By convention, I want semicolons on all labels (I'll get around to it)
because per the standard, you can only label statements.  So it's
irritating when the thing after is a declaration to have to put a dummy one
in, and then someone without warnings turned up gets suspicious and deletes
it.  If *all* labels have it, it calls attention to the rule.

I just haven't propagated the rule everywhere yet!

On Oct 11, 2016 8:46 PM, "Shixin Zeng" <notifications@github.com> wrote:

> Is this semicolon intentional? It looks dubious
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
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>


>Или ты о чем?

Когда без куклы то построить кнопки как у куклы, если включена то не строить.


Agree this should be NaN


Так если она выключена, она и кнопки не создает


I mainly did it for creating additional training data. The next thing I have been thinking about adding with this is automatic truth labeling for datasets which have annotations. So it would sort the crops into class folders based on those annotations.


変更済みとのことでしたｗ


18行目のCSSファイル、マウスオン時の＋マック表示用です。削除してもいい気がします。
その他は削除しても画面の表示に影響がなさそうで、削除しました。


У них там какие-то инлайн-картинки вроде


Correction: The bullet point in the commit `Use box images in the base-files folder, rather than make another copy. Also add new images to this folder.` was not added in this commit. It requires changes to the box-translation and box-rotation interactives (see issue #393).


Там картинки закодированы в base64


Your version is definitely a better way to do that.

I have a bad memory so the various string formatting codes and things never stick. As a consequence I don't use them and often forget to even check if they give an easier way of doing things.


А вообще не советую этим заморачиваться. Помимо тредов тут еще много где посты отображаются (в админке, в tudo, в жалобах)


Подобные вещи надо стилями делать, а не переводом )


そこはあまり自信ないです。今更IE8使う人いますかね。。。


`getRealmName()` => `getRealmNames()`


good job, he working


Lets keep `<realm-name>` bounded at `1` and add a new element for `<realm>` that is `unbounded`, then merge them together with `<realm-name>` value before `realm` values in the resolver.


Но детект нужен по любому. Коррекцию времени надо отключать, плюс апи ее заюзать для новых постов.


@syzygy1 I still didn't look at this in a deep way, I will give this topic
a detailed look later this week (when I have time and fresh mind).

On Tue, Oct 11, 2016 at 11:45 PM, syzygy1 <notifications@github.com> wrote:

> The STC test for the revert passed more quickly than I had feared.
>
> @mcostalba <https://github.com/mcostalba>
> Would you like me to schedule an LTC test?
> (I have some hesitation to spend considerable resources on an attempt to
> revert a patch that does not seem to harm Elo-wise, even though I do think
> that the patch is problematic. So if you prefer to keep the patch and save
> the resources, then I won't argue against that. But if you say schedule,
> then I'll schedule ;))
>
> —
> You are receiving this because you were mentioned.
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Fix early access feature description for multiple realms.


いや、どこか使ってるかもです。タイトルのフォントは変わりました。
調整します。


you don't use num anywhere in your function


why are you limiting this to 5 ?


What happens after a server restart? Will the client send requests using the wrong version?


Shouldn't be removed.


Regarding your customGroup#.sqf scripts, the randomSoldierLoadout is in the incorrect position. See -> http://pastebin.com/uub56has for the correct way (the code [_unit] call randomSoldierLoadOut; must be within the for "_i" loop, and the redundant code can be removed). I hope that helps. -soul.


I've created a hotfix that's already in master. Should be fine.


@xfra35

Without looking at the framework internals, `$f3->set('LANGUAGE','en',3600);` would convey the following meaning: cache the language setting for an hour. This does not make sense for a mutilingual site.

A TTL for `FALLBACK` would be more appropriate - but this variable (along with `LANGUAGE`) should ideally be defined before the `LOCALES`.

The intent of this commit is to allow a TTL setting in config primarily for the purpose of caching the dictionary files. I think we can just mention the repercussions of misusing the TTL  in variables like LANGUAGE and FALLBACK as caveats in the documentation.


@giansique
On my 3+Silver, i can choose ISO only from 70 to 1300.
The second two values you shall use "5" that it's equivalent to 7.7sec (see sheet: http://chernowii.com/gopro-longexp)

Also, for the code to work on my 3+SILVER i had to change "still_exp" to "exp".
So the code I use is:
**t app appmode photo
sleep 1
t ia2 -ae exp P X Y
sleep 1
t app button shutter PR
sleep A
d:\autoexec.ash
REBOOT ye**

Where P must be between 70 and 1300, X and Y must be the same number, between 2 and 1000 and A is the number of seconds between the photos.

I also had success with this other code for single stills:
**sleep 2
t app appmode photo
sleep 1
t ia2 -ae exp P X
sleep 1
t app button shutter PR
sleep A
poweroff yes
reboot yes**


Look, fair enough. The only real reason it surprised me was was that it made reference to "ball" so I felt it didn't belong in this section. That being said, is there any difference between this and what's output by the `naive_harris_function`?


Cool. Thanks.


Ahh, ok. I actually have a branch that's got an annotation method in it.

Maybe take a look around [https://github.com/SamCB/VisionTest/tree/newAnnotationProgram](https://github.com/SamCB/VisionTest/tree/newAnnotationProgram). Of special interest, `annotator.py` that can just be run with `python annotator.py <args go here try -h for details>`.


Removed. (use Recommend\.travis.yml)


天哪我竟然没发现v2有这个bug


I was on this website pretty much every day in my first year of learning python: https://pyformat.info/

Still go there if there's some weird edge case I need.


Got it, Thank you!


$daysToDeleteMessasges misspelled.


Hi, i have a doubt in function Server::_session_logged, line 389. Is there any possible that line 387 has been executed, but line 389 have been not, in this moment, client send an CEPH_SESSION_REQUEST_OPEN(due to some reason, client doesn't know about the preexisting session which has not been closed successfully), mds begin to process this request, in MDS::ms_verify_authorizer(), it find there is a session in mds->sessionmap, so it bind the current connection  with this session whose state is CLOSED waiting to be removed from mds->sessionmap. Every thing seems be ok, until function Server::handle_client_session(), this function will add a session to mds->sessionmap, which will lead to an ASSERT failure since we have had a session related to this client in mds->seesionmap.

Since Server::_session_logged is executed in a separated thread different with mds, so the situation described above should has a possibility. And indeed i have encounter a assert failure in Server::handle_client_session() due to adding a session to sessionmap,  when handle CEPH_SESSION_REQUEST_OPEN . Although restart mds worked and problem no more occurred, i still don't know why.


Yes, yes you do!


Suggest removing `REALM_AUTHENTICATION_...` resource options from `HttpResourceAddress` and replace with an `REALM_AUTHENTICATION_TOKEN_EXTRACTOR` of type `AuthenticationTokenExtractor` which behaves much like `DefaultAuthenticationTokenExtractor` but internally knows which `headers`, `parameters` and `cookies` to extract.


完成了基本折线图、柱状图、饼图的绘制。支持双y轴、柱状折线图、组合柱状图，新增加了鼠标移进移出的交互事件。


PHPcs: code style for method name should not be prefixed with an underscore to indicate visibility.


Ah, yeah the Keras imports should be commented out. Then line 64 should read "    return ROIFindColour". That should let you all use my ROI finder. Sorry I messed up so much in this. I thought I was paying attention to what I was doing, but apparently not.


Is `HttpResourceAddress.REALM_AUTHORIZATION_MODE` still used anywhere? If not, we should remove it too.


Why gopher like abbreviation?


Right back at you!


PHPCS: missing blank line before return statement.


## **William Law**

**_Student_**
## High School of Telecommunication Arts and Technology

## [williaml1886@hstat.org](https://sites.google.com/a/hstat.org/williaml1886sep11/)

William Law was raised and grew up in Brooklyn, New York. He went to P.S. 503 elementary school and I.S. 259 middle school, but currently attends High School of Telecommunications. He also serves as a bowling team player in High School of Telecommunications for 3 years now.

Schedule:

1. Software Engineering

2. English 5

3. Physical Education

4. Advanced Algebra and Trig

5. Spanish 5

6. Physics

7. U.S. History

8. Lunch


`**``William Law**`

_**Student**_

**High School of Telecommunication Arts and Technology**

[williaml1886@hstat.org](https://sites.google.com/a/hstat.org/williaml1886sep11/)

William Law was raised and grew up in Brooklyn, New York. He went to P.S. 503 elementary school and I.S. 259 middle school, but currently attends High School of Telecommunications. He also serves as a bowling team player in High School of Telecommunications for 3 years now.

Schedule:

Software Engineering

English 5

Physical Education

Advanced Algebra and Trig

Spanish 5

Physics

U.S. History

Lunch


Interesting that HXCPP_GC_DEBUG_LEVEL  still fails - rules out some thread
stuff.
If you get a crash in the marking, with HXCPP_GC_DEBUG_LEVEL, then the
native call-stack can provide more information about exactly which object
is actually dodgy.  I will see if I can dig up a complex project that fails.

On Wed, Oct 12, 2016 at 9:54 AM, Luke <notifications@github.com> wrote:

> HXCPP_GC_DEBUG_LEVEL doesn't seem to catch anything further for me; Same
> kind of failings it seems. I'm not able to provide a test case
> unfortunately (my project is a compiler :S), although I did try putting one
> together. It seems simple allocation loops aren't enough to trigger it.
> Something to do with more complex memory layouts.
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/HaxeFoundation/hxcpp/commit/628c9f23544c1608e8ffa5851881ecc2cec958e7#commitcomment-19387676>,
> or mute the thread
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> .
>


PHPCS: Public method must be set before the Protected method, final is the Private method.


Then change `HttpResourceAddress.REALM_NAME` to `HttpResourceAddress.REALMS`, where each realm is of type `HttpRealm` which has a `name`, `description`, `challenge scheme`, `tokenExtractor` (of type `AuthenticationTokenExtractor`) and `LoginContextFactory`.


Innecesario solicitar el objeto a transformar cuando el mismo es el objeto


的


objc_setAssociatedObject 的时候用的是 OBJC_ASSOCIATION_ASSIGN，是非持有的，对象可能会被释放。如果对象被释放了，那么 objc_getAssociatedObject 拿出来的时候会默认给对象发 retain 消息（ARC），导致 crash


No problem. Teamwork over git always starts out rough, I think we're starting to get it figured out though.

Though what would actually be great is if we could get this file working the way it works for you, that would be fantastic, otherwise, this looks like it's just another way to use `example_implementations/naive_harris_function.py`. There won't be any problems with others not having keras installed because the test function doesn't even know about this unless you reference it in the command line. As long as they don't expect to use it, it should work fine.

If you've got time to get keras running here, I can try installing it tonight.


調整しました。ご確認をよろしくお願いいたします。


Hello jijie


I convinced myself of the correctness of this code by mentally rewriting it to
```
.where("? <= end_date", self.start_date)
```

In order for there to be overlap of two ranges 1 and 2, start1 <= end2 AND start2 <= end1 which I proved to myself by holding up my pinky and thumb on each hand and moving them back and forth and staring at them like a neanderthal for five minutes.


I would say that SCSS should not take `css` as input, because it should be taking in `scss` instead. CSS and SCSS are not the same format because SCSS has variables, mixins and such.

I don't see why a css minifier shouldn't take in css. If a user doesn't want their css minified, why would they include a css minifier?


基本的に設定ファイルを略さないでください。
スコープが5行くらいのローカル変数まではかろうじて許すでござる


spicy


nit, might want to prefix the title of the commit message with "rocksdb: "


其实还有一个类似的bug，马超铁骑公孙瓒后公孙瓒无法触发义从配音……这种类型的bug可能还有一些，不太想挨个找了


PHPCS: Expected 1 newline at end of file.


makeCacheMatrix <- function(x = matrix()) {
        ## @x: a square invertible matrix
        ## return: a list containing functions to
        ##              1. set the matrix
        ##              2. get the matrix
        ##              3. set the inverse
        ##              4. get the inverse
        ##         this list is used as the input to cacheSolve()

        inv = NULL
        set = function(y) {
                # use `<<-` to assign a value to an object in an environment
                # different from the current environment.
                x <<- y
                inv <<- NULL
        }
        get = function() x
        setinv = function(inverse) inv <<- inverse
        getinv = function() inv
        list(set=set, get=get, setinv=setinv, getinv=getinv)
}

cacheSolve <- function(x, ...) {
        ## @x: output of makeCacheMatrix()
        ## return: inverse of the original matrix input to makeCacheMatrix()

        inv = x$getinv()

        # if the inverse has already been calculated
        if (!is.null(inv)){
                # get it from the cache and skips the computation.
                message("getting cached data")
                return(inv)
        }

        # otherwise, calculates the inverse
        mat.data = x$get()
        inv = solve(mat.data, ...)

        # sets the value of the inverse in the cache via the setinv function.
        x$setinv(inv)

        return(inv)
}


Missing document of class


impressive


eeeee


PHPCS: code style for method name should not be prefixed with an underscore to indicate visibility.


- [ ] 1.


Des fichiers sont rajoutés à la solution, mais non pas été commit.


afasdfasfdasdf


aadfs asfd


this is a comment through the browser in github


PHPCS: Add a coma after each item in a multi-line array.


@elieserdejesus, dê um pull e um checkout na branch "usando-javac" dos 3 projetos: Portugol-Nucleo, Portugol-Studio e Portugol-Studio-Recursos.

Eu implementei toda a parte de compilação do Java e execução dos programas compilados no Portugol Studio. Ou seja, agora o Studio já está executando os programas compilados quando tu aperta no botão "Play" da IDE. As duas coisas que ainda precisa resolver são: passagem por referência e habilitar novamente o passo a passo e pontos de parada do programa. Este último vou tentar resolver em breve.

Só um detalhe, eu fui fazer um rebase nestes branches, e deu tudo certo no Nucleo e Nos Exemplos, mas no Studio, de uma LEVE CAGADINHA, conforme pode ser visto na imagem a seguir. Tens como dar um help?

![cagadinha](https://cloud.githubusercontent.com/assets/709553/19296858/c49c7ec4-9015-11e6-996d-43809188c458.png)


I'm not clear on whats going on here.  It seems that without this the app exits abruptly when the last window is closed.  Does it only terminate on osx? And how does this prevent it from closing, it seems that the logic here will terminate on other platforms.


I think FlipCard may eventually need a mouseListener attached to the first layer of the JLayeredPane (jl1) so that we can tell when to show the equation written on jl2 below. See [this page](https://docs.oracle.com/javase/tutorial/uiswing/components/layeredpane.html) for how to use a JLayeredPane.


@forno
訂正しました.
読みやすさとかどうでしょうか : )


Generally, `hoge >= 1011005` was often used.


Obscure names => Maybe use "testRecommendCreateRender".


The content of the page doesn't look right with the margin:40px in there.
Take a look at the the home pages dashboard table.

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Should use faker.


Executing the daily benchmark build, I will reply here when finished:

@nanosoldier `runbenchmarks(ALL, isdaily = true)`


传 store 是做什么用的？


❤ ❤ ❤   this thumbnail is excellent. @ngokevin MagicaVoxel?


我准备的样式体系里有 autoprefixer，不用写 vendor prefix，会有自动处理。


Check the list of the recommend or the message on the layout.


lol I need a vacation. Thanks for the help.

https://github.com/Fractured-Gaming-Official/Frac_v1.3.Stratis/commit/bbb8adfd2fef193c8ca24e72abd98141b9460473


btw, blake is working on the rate page ... there may be errors as its a
work in progress.

On Tue, Oct 11, 2016 at 8:53 PM, Wayde Gilliam <wgilliam@ohmeow.com> wrote:

> The content of the page doesn't look right with the margin:40px in there.
> Take a look at the the home pages dashboard table.
>
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Yup, just something I quickly whipped together. I might add little blue blocks sticking out of the shopping bag.

May or may not have been based off of my [old work project's logo](http://www.mozillaphilippines.org/slides/firefox-os-app-days/kevin/img/firefox-marketplace_logo-only_RGB.png)


なんだかプログラム側が冗長な気もしますね。
numberの存在意味を感じないので、nameで仮想配列を作ってその下に情報をつけるのが良いのではないでしょうか？


PHPCS: code style for method name should not be prefixed with an underscore to indicate visibility.


Right, I'll take a look at that at some point.


PHPCS: Expected 1 newline at end of file.


いやむしろなぜトップにひとつだけの仮想配列 "waypoint"があるのか謎ですね。


Missing document of class


The naming is a bit misleading. Can you revise the two functions containing "merge"?


To test it for log.
However issue #2 is next.


Did you want to add a Deprecation notice here as well?
As it does seem like getCMSFields is trying to get phased out by this as well.


The frequent invocation of `list_new` causes performance penalty. You can avoid it by introducing [Lazy allocation](https://pdos.csail.mit.edu/6.828/2016/homework/xv6-zero-fill.html) technique.


PHPCS: Public method must be set before the Protected method, final is the Private method.


PHPCS: missing blank line before return statement.


no i just changed the attachment files did not touch any other items if it was related it would have been named "Poison Resistance" not blank and there would be no exceptional at the end


目前没用到`store`，可能后面的开发会用到`store`，所以就传过来了。


ádasd


Already install all necessary packages during make bootstrap. Do not need it here.


Me and @cstill both agreed that it looked far better like that. Up to you though.


Don't do that in `master` branch.


Fix the conflict !


You shall only check in the necessary and dependent files in GIT repository.


Missing page_no param on the document.


How come this is missing `getForm`? (to an extent, `getFormFields` and `getFormActions` as well)


PHPCS: Variable is not in valid camel caps format


So, apparently this was caused by capturing the shared_ptr by reference in the lambda.


辛苦了，这次发布的和2月15发布的相比没什么大改动吧？


no, its up to you guys ... if y'all want to keep the header like that then
the HTML on the matches and home page just needs to be fixed.  Right now
the tables there extend the entire width of the browser and it looks kinda
funny when the header doesn't as well.  I just changed to even to a
previous one so you guys can see.

-wg

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Should remove this.


なるほど、その型の配列を作る時に困るわけですね。
適切な名前に変えておきます。


Should use relative path.
 $Recommend = new RecommendProduct();


Wrong condition in : if (strlen($existProductId > 0)) {


Add a new line for end file


Add new line for end file


add new line for end file


lstm-parser forks stopped working due to this change...


Add license


Using : "if (!$Products)" instead.


Yeah this is README.md material unless you have any objections 😄


where is version 3.0.8 and pgsql?


add new line


PHPCS: Concat operator must not be surrounded by spaces.


Oh, this wasn't specifically for physics. I just used it as a placeholder image if you didn't put an image in your README. I can create a MagicaVoxel for your physics :)


This was responsible for a crasher in my code. I bet this is the reason why this brach is broken


Name 'eccube.admin.order.product.search' ???


Oops! I see now haha. And that makes much more sense. :)


Why is the README.md just a tutorial on forking and pull requests?


I'll recycle something like https://cloud.githubusercontent.com/assets/674727/19173367/d6590832-8bdb-11e6-9336-658b00bc0460.png


d


Cause Auhbro ;)


**Code Quality - Nitpick**
Are you also concerned that a user should own a document and not the role alone.  It will be expensive querying for the document owned by a user if the relationship is not explicitly defined in the model.


Actually, you can just take that and drop it in your README ^


It's down a few lines. :)

The interface doesn't need to promise to return the fields, only the form; This is the promise between this class and the outside world.


We probably can't deprecate it if we don't remove it from the code; Unless we are replacing it across the whole forms api it probably isn't ready to be deprecated (just yet).


Add new line for end file


Use:
if (!$request->isXmlHttpRequest()) {
            return null;
}
to reduce complexity.


no es tan importante diferenciar el #create del #update por ahora. en el caso del proveedor es distinto porque al momento de crear, se genera una aplicación que luego debe ser aprobada/rechazada (y debe emitir notificaciones, etc). Pero en este caso no pasa nada si no existe un `customer_profile`; sólo se lo crea.

en resumen: mejor tener sólo endpoint para `#update` y copias lo que yo tengo en el controlador del carrito: https://github.com/noggalito/porttare-backend/pull/43/files#diff-9775691c4fc08ca2be4437dd86cdbf49R130


💯  thanks!