[.DEploid/utilities/dEploidTools.r:1:22:](https://github.com/mcveanlab/DEploid-r/blob/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.DEploid/utilities/dEploidTools.r#L82) *style:* **Variable and function names should be all lowercase.**
```r
    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:17:](https://github.com/mcveanlab/DEploid-r/blob/b6968b57db9bc60e7872eea57a63447c449d3e5b/.DEploid/utilities/dEploidTools.r#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:17:](https://github.com/mcveanlab/DEploid-r/blob/b6968b57db9bc60e7872eea57a63447c449d3e5b/.DEploid/utilities/dEploidTools.r#L83) *warning:* **no visible global function definition for ‘extractCoverageFromVcf’**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:48:](https://github.com/mcveanlab/DEploid-r/blob/b6968b57db9bc60e7872eea57a63447c449d3e5b/.DEploid/utilities/dEploidTools.r#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:17:](https://github.com/mcveanlab/DEploid-r/blob/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.DEploid/utilities/dEploidTools.r#L193) *style:* **Variable and function names should be all lowercase.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:193:41:](https://github.com/mcveanlab/DEploid-r/blob/b6968b57db9bc60e7872eea57a63447c449d3e5b/.DEploid/utilities/dEploidTools.r#L193) *style:* **Put spaces around all infix operators.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~
```
[.DEploid/utilities/dEploidTools.r:198:11:](https://github.com/mcveanlab/DEploid-r/blob/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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/b6968b57db9bc60e7872eea57a63447c449d3e5b/.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);
                                                                            ^
```


```js
const { combineReducers, createStore } = require('redux');
```


/cc @taisel Thanks very much for re-licensing GameBoy-Online to permit this.


Thanks for the advice. My own testing shows that the `should_escape` version is slower though 🤔 A more realistic benchmark may say otherwise, but without concrete evidence I'm keeping the code as is.

Good point with the single quotes. I found that removing that line doesn't affect performance in a noticeable way, so I'll probably bundle it with the next batch of breaking changes.


```js
const { Component } = React;


```js
const { connect, Provider } = require('react-redux');
```


Maybe a sign that you need to start splitting the code into multiple files.


@rutgerkok tested and works :)


Sorry, @MrCK1.
But you did get the honor of having the first psxmode issue! ;p


elimine archivo


Another idea that solves the issue in a clean way, is to make a new tiled range class that is specifically tailored for the needs of QC.


I probably knew that somewhere in the back of my mind. At least there's a reference for later


Dude you cannot rename existing textures. This will break WORLDS. Not only will we have missing textures because you decided to rename them to something they aren't called in code. But they will be considered entirely different food by the game, breaking things if they update.


After discussion with mareko, he thinks we should really get gain with csmt, but we really need to have all calls that could be non-blocking to be non-blocking.
For vertex-buffer locks, nooverwrite means we can write the data without waiting the draw calls to be scheduled. As for discard, we just need to reference the vertex buffer resource when scheduling the draw calls. When we do discard, we'd create a new resource, and use that one for later draw calls. For better performance, we can use u_upload_mgr to do sub-allocation with big buffers.


the pipe_context probably needs to be encapsulated into a pipe_context with mutexes for thread safety.


Added comment for while loop purpose.


Wow, thumbs up!


This isn't DiscordVoiceWS :p


Read HANS' source


@raven sorry, that was a mistake, just created a new PR


I tried that code, but there was a problem with the SCL map registers. I see your code fixed it. ONe more thing atmega328p is the same with lilyPad right?


is this line needed? why is it commented out?


You probably don't need this in `deroff.py`; it doesn't import anything but stdlib modules.


I think this has to go before `from deroff import Deroffer`.


use the `currency(at: Int)` function here instead of direct array access `currencies[row]`?


It's true we don't normally run deroff.py directly as part of building and packaging fish but it is setup so that you can run it directly (presumably for testing its behavior).


better to keep all this 💩 outside this layer. it makes the tests super verbose w all the immutable.js boilerplate, plus eventually i want other ppl to be able to easily reuse various parts of the loading/saving infrastructure without needing to learn immutable.js. so, try to keep that stuff in the higher-level app code


When you run a Python script directly, Python doesn't write bytecode (which is why a `create_manpage_completions.pyc` doesn't get written).  Bytecode for a module is written only when a module is imported.

Even if it were imported, a `sys.dont_write_bytecode = True` inside the module couldn't affect whether bytecode was written, because it was already compiled and imported at that point.


Why comment it out? Just delete it. if you ended up needing it you could re-add it or roll back this commit.


It still says 'Runnint'...


hmm, won't this default to just `bash`? I think we want to see if `/usr/local/bin/bash` exists to ensure we're using the latest bash.


Sorry for troubling you. I just found the solution. I changed some unsigned variable from uint32_t to uint16_t. Thank you for your time >.<


Добавить в класс


При появлении новых постов ответы снова появляются вверху.


Note that this release also includes https://github.com/balderdashy/sails/commit/ab9c2c3431a5298e8fd140e5c1e2ed2c7260526c and https://github.com/balderdashy/sails/commit/0057123a0321be6758845abbeb4290bf418ce542  (we left as-is rather than shift the tag and create confusion.)


Thank you very much!


I was trying to get the tests to pass on travis-ci and tried different things. I didn't even think of just checking to see if the path exists to figure out which bash to use.

The other option for this library is to run a pre-install script on travis-ci to install the latest version of bash, then it might be in the `/usr` path. That would probably give better results for travis-ci. I'm not sure the exact commands to run to get that installed through.


quoi que non c'est la cocaténation je dit de la merde ;)


Hm, this looks to me like some incompatibility between gcc-5.3.0 and musl-1.1.15, that is not actually related to elektra? I would need to look into this in more detail to figure out whats really going on though.


Yes, this makes so much sense. Thank you! I implemented this change with the `article_select` function in the latest commit.

Would it make sense to move this method to `app/helpers/article_helpers.rb` like I did with the `article_params` method that require and permit params? I'm just curious because I'm not sure how private controller methods are different than helpers.

Thanks again, Dave!


That is legacy code form the previous development.  I didn't delete anything, I only moved and occasionally repackaged things.


k, no worries. we'll get it figured out - this will be good to know.


Wow, thank you. This is the kind of stuff I get embarrassed about when I read:

> This has been referred to as breaking one of the oldest rules of programming, dating back to the COBOL, FORTRAN and PL/1 manuals of the 1960s

Thanks again!


I think for many of the variables that are initialized that there should be spaces between the variable and equal and equal and the quotes to decrease confusion and increase organization.


made by Priyank Verma and Tejaswi Susarla.


Mmh, any value returned by a `.then` inside will not be used, and any error will already be handled by an inner `.catch`. So, it looks unnecessary.
However, I would rather keep it as it fits the pattern of promises. If, in the future, we reorganise this code, and a value is expected, finding out where a return was missing can waste a lot of time.


Yeah I messed up the repo somehow. It's fixed now.


Our plane is improving little by little, is this working in the system electrical among other things.
@soitanen you know much about this aircraft, it were well if you join their knowledge of this aircraft with us  We know that you want this aircraft 100% real, but failure while you upload an update for month, i.e., better unite as a team and this aircraft could be improved more @it0uchpods, @legoboyvdlp and I, Do a great job, If you are joining can correct any error for he or my Since you have good information about this plane What I want to say with this Is that if we work together This plane will be very well in the future.
Our plane already has very good things New sounds system electrical That soon will be better, New animations for cabin(pedestal, flightdesk and oh panel)  new engines, wings, new fuselaje etc etc.
You can work more in the systems and instruments Or what you want. @soitanen I hope to have its response Thanks You.


The weakes part in Puppy is the package manager, many packages don't work or break puppy, because puppy was not meant to work that way. So definitely this was the best approach.

All this work would more make sense if puppy was built as a traditional distro from scratch creating it's own packages with many volunteers contributing packages, this never happened, and now it's impossible. The way i see puppy is something that boots everywhere, but you have to do the packaging for your own needs. That's why i never use the ppm..

The current code base, however, can be used to restore the Puppy 4 philosophy. Although supporting slackware this way is good nonetheless, it has all the apps puppy develops scripts for, all the other distros have something wrong, basically systemd and debian's mistakes.

This branch will stay, but i think 2 diffrent build systems may coexist if some tweaks are applied maybe...


![dont work](https://cloud.githubusercontent.com/assets/6472084/19224368/e2af6d70-8e5a-11e6-9238-c86aef25b0ca.png)

The new code is crashing.


Awesome :)


Does this work with other characters besides UTF-8?


btw, to clarify about the path. Bash 4.3 is needed for some of the tests (only because I'm doing a real-time comparison of actual bash results versus results from this module), so neither of our approaches is really going to be sufficient.

I'm not sure what travis is capable of. Can we have travis install homebrew then do `brew install bash`? If so that's the way to go. We would need to use the path still as well (`/usr/local/bin/bash`)


I wonder that why it's not merged yet into the main project!

thanks for your great job.


In this case I think it makes sense. Other contracts that do not deal with Ether could instead `throw`. In Solidity 0.4 the fallback function throws by default anyway.


Small but mesurable progress against Sungorus 1.4:
```
demolito vs sungorus_1.4: 2263 - 6512 - 1225  [0.288] 10000
ELO difference: -157.62 +/- 6.93
```
Same testing conditions as before (without timemargin which isn't necessary anymore):
```
./cutechess-cli \
  -each proto=uci tc=8+0.08 option.Hash=8 \
  -openings file='./book5.epd' format=epd -repeat \
  -engine cmd=$1 name=$1 \
  -engine cmd=$2 name=$2 \
  -pgnout $3 \
  -concurrency 7 -rounds 10000 -ratinginterval 25 -recover \
  -draw movenumber=40 movecount=8 score=20 \
  -resign movecount=3 score=900
```


Главное сам на этом твоем коммите так прокололся...


One of the tickets that could be closed via this commit is #5920.


This is a meta test plz ignore this too


BTW meta


@LarryEitel Hi, hope you are doing well.

I was trying to test the multiple site feature that you added, but couldn't get it to work, could you please help me write a documentation for it:

Note: I'm using the term app1 instead of site_a.

## Running Multiple Laravel Apps with single LaraDock:

1. create the following folder structure:

```
- projects
   - laradock
   - app1
   - app2
```
2. open `docker-compose.yml` file and mount all your apps:

    volumes_source:
        image: tianon/true
        volumes:
            - ./app1/:/var/www/app1
            - ./app1/:/var/www/app2

3. open the `nginx/sites/` folder and create your apps nginx config files:

`nginx/sites/app1.conf` and `nginx/sites/app2.conf`, here's an example of what should your `app1.conf` container (do the same for `app2.conf`..):

```
server {

    listen 80;
    listen [::]:80;

    server_name app1;
    root /var/www/app1/public;
    index index.php index.html index.htm;

    location /app1 {
         try_files $uri $uri/ /index.php$is_args$args;
    }

    location ~ \.php$ {
        try_files $uri /index.php =404;
        fastcgi_pass php-upstream;
        fastcgi_index index.php;
        fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
        include fastcgi_params;
    }

    location ~ /\.ht {
        deny all;
    }
}
```

Note: I added `location /app1 {` it was `location / {` in your PR.

4. go to `http://127.0.0.1/app1/` and voila :D

I am getting **404 Not Found** here! can you tell me what I'm missing?

Thanks.


Ok, we'll port this stuff when the time is right..


development only.


bad iso date


I'm Rick Harrison, and this is my pawn shop. I work here with my old man and my son, Big Hoss. Everything in here has a story and a price. One thing I've learned after 21 years - you never know what is gonna come through that door.


"http://www.freedesktop.org/standards/PolicyKit/1/policyconfig.dtd"

This URL is broken for me or does it not matter?


@BoatsAreRockable Can you believe this has been here since 2015 and we've not noticed it?


This constant can be removed. I can't find out where it is called.


```ruby
  def current_user
      @current_user ||= User.find_by(id: current_user_id)
  end
```


Just `params`  is ok.


Wow that was fast! Thanks!


vol.php est bug(offset 0 ) on peut peut peut être cacher ça ?


I should be remained, The information is too much as for the default 404 error of grape.


NB I've created a `3-stable` branch off this commit, since it's assumedly where we want to start 4.*. There's also a `4-stable` branch that tracks master currently.


thank you! now corrected


## Things need to be done:

* grape 的日志格式完善。
* 报错返回的 json，是不是用 error 报一层就可以了，而不是一个数组。虽然 jsonapi 的规范要求使用error 数组，但是觉得必要性不大。
* test.


Okay accepted


The zero values statement has been removed before your comments started, so I am not sure what you still believe needs to be changed. It currently reads:

Validation results may include, as a value of the property sh:value, a specific node that has caused the result.


Thank you, for considering my request.

On 10/8/16, Peter Schrott <notifications@github.com> wrote:
> Hi, I can try to find it.
> But I am in holiday. If I don't get back to you in 3 weeks, buzz me.
>
> Peter
>
> On Wed, Oct 5, 2016, 2:35 PM asdspal <notifications@github.com> wrote:
>
>> Do you still have this dataset with you? Unfortunately, Kaggle has
>> removed
>> it from their website.
>>
>> —
>> You are receiving this because you authored the thread.
>> Reply to this email directly, view it on GitHub
>> <https://github.com/peedeeX21/axa-driver-telematics/commit/5baeb8383a874d19f193300ff40ae3d82d5b667d#commitcomment-19307978>,
>> or mute the thread
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--
Thanks & regards
Ashwini kumar pal
09919169021


Probably should make jackson-module-jsonSchema and json-schema-validator `<optional>true</optional>`, so they are not pulled down by default.

I'm thinking that If users want schema support, they should add those dependencies to their own pom.


It this an accidental leftover from debugging?


Maybe consider creating a new `getFieldSchema()` method that by default returns `new StringSchema()`.  Then some subclasses would just need to override `getFieldSchema()` if they wanted to not use StringSchema


FYI, this inspired me for [a similar branch on my fork](https://github.com/jgonggrijp/pip-review/commit/a08ee67c7e5c670267f90f7b992ede2107a9cde8), which is now incorporated in [version 0.5](https://pypi.python.org/pypi/pip-review/0.5) of the standalone pip-review. Thank you for setting me on the right track.


Hi quasar1 firstly your contribution has been very helpful in allowing me to set up my boxeebox, I was not sure if there was anything useful left in the hardware that was worth keeping it for... great effort!
I have a question: is there any further updates to this software planned? I applied this laterst release however Kodi is not updating to the latest version (Jarvis 16.1) and I am not sure how to do this through the Kodi interface. A message comes up in Kodi saying that there is a newer version available, perhaps you know a way to update also from the interface?


It is, good catch!


fixed.


Hmm.  This doesn't seem like a good candidate for a StaticSchemaProvider, since the fields within the object are all dynamic.


Same comment as above.  This doesn't seem like a good candidate for a StaticSchemaProvider, since the fields within the object are all dynamic.


No, this is a unit test. It is meant to be included in the repository.


Seems like this should implement `StaticSchemaProvider` directly, since it's not taking advantage of anything provided by `AbstractSchemaAwareFieldJsonProvider`


Looks to me like this is pure green (0,0,255,0) in original POI files.


This should be a String (lowercase too). See [Firebase's documentation](https://firebase.google.com/docs/cloud-messaging/http-server-ref#downstream).


@ROCKNROLLKID, Yes, I also tested it with ASCII (normal) characters

On Sun, Oct 9, 2016 at 5:01 PM, Alex <notifications@github.com> wrote:

> Does this work with other characters besides UTF-8?
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/az0/bleachbit/commit/b30558e63d3aca9184c6f71fea252866517fd1e9#commitcomment-19355518>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AA4_MCw9FN-d1E8O7jeE5xJeqA0_EqhUks5qyXJCgaJpZM4KSJCB>
> .
>


Потому что куда его там засовывать? В logging.info? Только при -v будет видно, также это не warning и не error, а видно должно быть при запуске с любыми параметрами.


As is, there is no benefit for this class to extend `AbstractSchemaAwareFieldJsonProvider`, since it is overriding addToSchema.

However, this is a case where it would be useful to have `getFieldSchema()` method defined in `AbstractSchemaAwareFieldJsonProvider`, so this class could just override it.

Same comment goes for any other classes that extend `AbstractSchemaAwareFieldJsonProvider` but also override `addToSchema` just to change the field schema type


hi ，i don't known how to use the example munin.go ，and the function，can you explain？thank you


I don't think `"strictNullChecks": true` is a good way to solve this problem, because in principle this (or any) library can be consumed by non-typescript code. You'd still need to check for the nulls as File can be created supplied outside of ts.


What is this?


If the getters/setters don't do any transformation we might as well make those members public.


Thank you so much!


Eu sei que deveria fazer isso, o próprio Android recomenda, e não é a toa. Eu vou fazer isso no meu próximo commit. Valeu pela dica <3


Should move this to CompositeJsonFormatter so it can be exposed in both the CompositeJsonEncoder and CompositeJsonLayout


Should this be `vibrate` or `sound`?


Should allow the IOException to propagate out of this method.


@sfarmer15 so your using this variable `r` here without declaring it in any scope, which eslint will highlight now. What happens when you do this is called "leaking globals"—a variable gets created in the global scope, which right now doesn't cause any problem, but you're probably expecting this variable `r` and its current value to only exist in the current scope, but it will leak into other scopes and possibly overwrite values in other places down the line when you don't expect it.


Oops, those should be tabs. fixing now.


declear -> declare :)


Is this already implemented? Because the viewer count bug is still present


>  But you did get the honor of having the first psxmode issue! ;p

If you don't count https://github.com/PCSX2/pcsx2/issues/1608
:p


Including the cmd to print the kernel name would be useful


Only optional?  Seems like that reduces the usefulness of this feature.  Wouldn't it make sense to support required properties?


@sfarmer15 you'll notice in your console right now that clicking outside the canvas still creates circles in irrelevant positions relative to whatever element you clicked on. Remember, `document` isn't the only element you can attach events to—you also have a reference to your canvas element in `c` already


gyro check the slacko beta thread. billtoo reports that puppy doesn't find the sfs files when there is strange usb device plugged... SSD, sound card, that's what he says.

the id string was used to identify the boot partition -vmlinuz- and puppy just searched all over the place, i guess that's why it could handle any possible error, then a logic would set the pmedia maybe? haven't looked closely at the old init.

i have a new probedisk script for the initrd, just in case. to be used once so it can be part of the debug log. it can also return the pmedia value for a device argument... something like, i think this is the boot partition.. give me something for pmedia..

so maybe, if the boot media is a cd or unknown or empty, should puppy  in every partition  even in subdirs if psubdir was not specified? then when if it finds the puppy sfs, in case pmedia was not specified.. set an appropriate pmedia. this way it's unlikely to fail again.

let's say the more info you give to puppy, the less searching it will do. it can be a rogue machine or boot directly following params, i guess that can be regression or something?

so what do you think?


I'm leaning towards no getters/setters as well. I'll leave the implementation as is until the other modules come together, and see if there is any good reason to keep the getters/setters.


Added several parameters to the GUI to play with this. I set the defaults to as close as I could get in the time I had to an original POI .png file. I created a new "drawGlyphText"  method that is basically a copy of your drawBlurredText, that needs to be refactored at some point (I tried to use optional params to drawBlurredText, but I could get that to work yet). Added ability to change transparency level for the glyph mask and added a "colorPicker" method to be able to call colorDialogs from the GUI to be able to adjust the colors more easily......Will push tonight.


我们发现你的应用程序的一个或多个错误，当回顾在iPhone运行iOS 10.0.2 Wi-Fi连接到IPv6网络。
具体来说，你的应用程序显示了一个错误信息登录和浏览时，我们无法访问您的应用程序的功能。
我们已经附上截图（S）为您的参考。
接下来的步骤
请运行您的应用程序在设备同时连接到IPv6网络（所有的应用程序必须支持IPv6）识别问题（S），然后修改并重新提交你的应用程序的审查。
如果我们误解了您的应用程序的预期行为，请回复此消息在分辨率中心提供这些功能是如何工作的信息。
对于新的应用程序，从一个设备卸载你的应用程序的所有以前的版本，然后安装并按照步骤来重现这个问题（S）。


Yeah, I'm slowly revising the code and experiment files. Only the GMM one is done so far, but the LDS one is almost done (in the reviving-lds-dots branch). If you go back to earlier commits of the code you can see the original files. I recommend waiting for the more polished versions though, which I intend to have done by the time we present the paper at NIPS.

Let me know if there's a particular experiment you wanted to look at and I can probably point you to the best git commit.


To be clear, these experiment files were the ones we used to generate the figures in the paper, but they don't work anymore because I improved some parts of the code and the experiments need to be updated accordingly. The newer code makes the experiments a lot cleaner.


По-идее, stackTopOffset - это смещение внутри самого стека, которое хранится в переменной, смещение которой мы здесь должны задать. Предлагаю, чтобы не было путаницы, различать Address - абсолютное смещение относительно начала RAM и Offset - относительное смещение, например относительно заголовка стека или, другой пример, относительноего верхнего кадра. Address-переменные являются настоящими переменными C#. Offset-переменные применяются в двух случаях: как C#-переменные,  в которых храняться смещения динамических переменных для методов и в качестве вспомогательных переменных самой программы, которые хранятся в памяти-массиве.  являются вспомогательными переменными самой программы и хранятся в массиве-памяти.

По таким правилам, получается, что varAddress - это смещение статической переменной var, её значение можно получить как RAM[varAddress], а m1VarOffset - это относительное смещение динамической переменной m1Var (кстати, думаю, лучше будет для динамических переменных использовать в качестве префикса название метода, при вызове которого они создаются), а значение этой переменной можно получить, как RAM[stackTopAddress + m1VarOffset].

ushort stackTopOffsetAddress = ... ; // Адрес переменной, в которой мы храним смещение верхушки стека. Из этой переменной состоит заголовок стека. В команде InitStack этот адрес передаётся процессору

// Эти вычисления производятся уже внутри процессора при выполнении команд
ushort stackHeaderSize = 1; // Размер переменной (заголовка стека), в которой мы храним смещение верхушки стека
ushort stackBeginAddress = stackTopOffsetAddress + stackHeaderSize;
ushort stackTopOffset = RAM[stackTopOffsetAddress];
ushort stackTopAddress = stackBeginAddress + stackTopOffset;


I've never had a look at this branch before. But i think this build system has to be adapted to the current tree, or at least be safe in one of the maintained branches even if it's not used anymore. Maybe in a new dir: woof-next or something

I guess this was meant to be something like debiandog?? Well it looks quite interesting.

I see ./build.sh ./builders and the rest is the same i guess... so should i push those files to rationalise or am i missing something?


I suggest you review how the data is treated when using panda.

That seems to be the biggest challenge with this program.


You can enter the submodule folder and run 'git fetch' to fetch new commits.  But normally you don't need to do that.  To fix your local depot. the best way is:
1 'git reset --hard HEAD'  // this command would reset your working folder and remove all you changes,
2 'git submodule sync --recursive'
3 'git submodule update --init --recursive' // the above two command would reset submodule.
4 'git pull'  // pull new commits from github
Then, if the submodule changed in Github depot. your could see modified status in your local working folder if you run 'git status'.
Then you have to run step#2 and #3 again to update your working folder.

IMPORTANT!  Please don't use "git commit -am "xxxx"" to commit you changes.  You'd better split it into:
'git add xxxx' and 'git commit -m' to manually add your changes.  Then if you don't need to modified submodules, never 'git add submodule/path'.  And if you see submodules show changed status run upper Step#2 and #3 to update them.


wat


C


testing.


当时抽出来只是为了结构更清晰，formatPostParam只在这一个函数中使用，这样看来是不是画蛇添足了？


> ..will Nicola eine Methode zu entwickeln ,...
(btw, Nicola and Nikola were mixed in a text I recently translated, and I'd decided to stick with Nikolas)
may go like: **will Nikolas eine Methode entwickeln, die Worte in Gedichten sucht.**


first submission


确实有点难理解了，不把这个函数里的逻辑封装在一个函数里， 应该会更好吧


I prefer (\n) directly after "Newline-Character"
....**in dem Zeilen durch den "Newline-Character" (\n) getrennt werden.**


"Ya fue mejor pusheo todo de frente"


Correct


这个怎么简单呢？ 求指点，需要筛选出 name为"couponRadio" 且被选中的checkbox; 只想到这种方法还有使用循环的方法


嗯对


There's tons of work hat has to be done before this branch can be merged :(


用户自己选择 不使用优惠劵


Немного перестаралась) Я не говорил, что смещения переменных нужно тоже в явном виде использовать (задавать - да, а вот использовать лучше через переменные, не зря же мы их создаём?)


Good shot, congrats!


Don't like the repetition of "Verschlüsselung". What you think of linking _Buch- oder auch Ottendorf-Verschlüsselung_ together to wiki, or dropping the trivia Ottendorf?


Mr-huangzhen commit first time;


xxxxxxxx


Ещё, думаю, помогла бы такая штука, как выравнивание в памяти. Это когда адреса идут не максимально плотно, а кратно некоему минимальному размеру. Так как размер команды у нас тут выбран в 8 байт, то давай и размещать все команды на адресах, кратных 8. То есть, если у нас получилось всего переменных на 10 байт, то давай зарезервируем за ними область в 16 байт, с 8 по 23. Чтобы первая команда после них шла с адреса 24. То что там какое-то количество байт окажется ничем не занятых - не страшно, зато нам это даст более читабельные адреса (просто делим в уме на 8 и сразу понимаем порядковый номер команды) и к тому же это соотносится с тем, что в реальных процессорах память тоже выравнимается согласно разрядности (32 и 64 бита, соответствеено 4 и 8 байт), так как процессор и вся его переферия в принципе не может работать с объёмами данных, меньше 4 или 8 байт.


note: don't clone players


咔 这么快  我还想pull request一发哈哈


哈哈哈哈哈


didn't notice, jazakAllah khairan!


sssssssss


> @harshavardhana hi, is this available in pip? I saw documentation wasn't updated.

It is not available pip right now @muminoff - Will be publishing a new version today.


Shouldn't overwrite the player town cap based on the full claim cap. Should probably make an eventual maximum. That way people don't end up getting a hundred players and getting ludicrously many claims; a hard cap is still fair enough


굳굳


allocating a buffer for curve25519 secret key, but the size of ed25519 secret key!


"1,321 additions, 1,302 deletions"
how did that happen exactly


Scriptname: `spell_hun_lock_and_load_dummy` spell (Id: 56342) is ranked spell. Perhaps not all ranks are assigned to this script.


Please report the build error on issues. This code shall be built successfully.


Дублирование строчки 32


dsadsadsa


oh i was merging e.t.'s pull here https://github.com/po-devs/po-server-goodies/pull/1510

it was mostly just shifting commands around/tidying stuff up


Concerned by the empty string in `addItemToUser(email, '', pending)`

Intentional?


Дублирование строчки 104. Зачем?


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

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


## Description
DOL 框架描述(随着实验进行迭代添加、修改)
![image](https://cloud.githubusercontent.com/assets/22589015/19217664/45194f82-8e13-11e6-8c76-be07557b449b.png)
## How to install
 DOL 安装笔记

1. [下载文件](http://jingyan.baidu.com/article/c33e3f48a5c153ea15cbb5b2.html)(使用Vmware虚拟机，也可以从主机拷贝到虚拟机中)：
sudo wget http://www.accellera.org/images/downloads/standards/systemc/systemc-2.3.1.tgz
sudo wget http://www.tik.ee.ethz.ch/~shapes/downloads/dol_ethz.zip1

2. 解压文件
新建dol的文件夹
$	mkdir dol
将dolethz.zip解压到 dol文件夹中
$	unzip dol_ethz.zip -d dol
解压systemc
$	tar -zxvf systemc-2.3.1.tgz

3. 编译systemc
解压后进入systemc-2.3.1的目录下
$	cd systemc-2.3.1
新建一个临时文件夹objdir
$	mkdir objdir
进入该文件夹objdir
$	cd objdir
运行configure(能根据系统的环境设置一下参数，用于编译)
$	../configure CXX=g++ --disable-async-updates
运行完之后如下图
![image](https://cloud.githubusercontent.com/assets/22589015/19217770/f6237cd8-8e15-11e6-957f-60b47f8f65cf.png)
$	sudo make install
编译完后文件目录如下($ cd ..        $ ls)，能看到include, lib-linux64(对于32位系统，这里是lib-linux)
![image](https://cloud.githubusercontent.com/assets/22589015/19217778/2a0d6824-8e16-11e6-8107-8a3fd2b16856.png)
记录当前的工作路径(会输出当前所在路径，记下来，待会有用)
$	pwd
![image](https://cloud.githubusercontent.com/assets/22589015/19217781/495dfe28-8e16-11e6-90d3-44e57a069cbe.png)
这里表示我当前的工作路径为 /home/wang/systemc-2.3.1

4. 编译dol
进入刚刚dol的文件夹
$	cd ../dol
修改build_zip.xml文件
找到下面这段话，就是说上面编译的systemc位置在哪里，
<property name="systemc.inc" value="YYY/include"/>
<property name="systemc.lib" value="YYY/lib-linux/libsystemc.a"/>
把YYY改成上页pwd的结果（注意，对于  64位 系统的机器，lib-linux要改成lib-linux64）
然后是编译
$	ant -f build_zip.xml all
若成功会显示build successful
接着可以试试运行第一个例子
进入build/bin/mian路径下
$	cd build/bin/main
然后运行第一个例子
$	sudo ant -f runexample.xml -Dnumber=1
成功结果如图
![image](https://cloud.githubusercontent.com/assets/22589015/19217793/9fade87e-8e16-11e6-8d48-79b3eb18fb92.png)

## Experimental experience
在这次实验中，不但学会了怎样安装DOL，还学会了使用git、markdown，感觉自己的能力和逼格都得到了提升


Congrats!


he want to try best things to do


Mersi de observație @gcbirzan . O să schimb parola chiar acum și o să găsim altă cale să adăugăm parola în fișierul ăsta.

PS: Nu sunt necesare insultele ;)


A+ :D


I feel like this might have a respective bug for sharding if a player was on the same server in a sharding environment and summoned a player and returned them.  Will have to wait ande see :P


It works!! Thats awesome, thanks so much! <3


Yeah, for sure there are some hidden gotchas throughout. Such is development!


Oops, that was a placeholder. It's supposed to be whatever is in the still.


Probably it was fixed with https://github.com/multitheftauto/mtasa-blue/commit/e24b61c81d552d5be6737c2eeed2eca974c96e2a


And slight speedup, maybe


Well, let's say it's an act of preservation... the rk32789 is somewhat modern, so it's worth having something that can be used as a starting point to provide a puppy for this model.

I think i can port some changes to the rationalise branch, then you might want to step in and finish it. as you're the one with the hardware and packages.. Basically most of the commits deal with the config file i guess?? Have to take a closer a look.

UHmm i see there's a special kernel build environment for rk3288, i think these bits can be integrated in the standard script as extras or something..


Hey @basarat ,

Does ts-loader need something like this?  I haven't actually tried to use @types within a project yet and so have no idea.  If I try is it likely to fail because it has to be catered for directly as you have here?

John


Above code gives exception on processing 3.2.1 in my case.
If you could provide processing sketch for Processing 3.2.1/processing 3.1.2/processing 2.2.1
any of the above version, That will be very helpful


This closes #10 issue.


So in my case the file name should be 0001-BFQ-v8r3-v4.8-rt1.patch? Because it fails immediately if I just use this one, but I don't think the patch name matter, it also fails with the bfq version v7. I'm stuck. :(


Mi primer **Merge**. Espero que me haya salido bien.

No sé por qué aparece en este _merge commit_ el archivo `ModelNode.java` con todos los cambios que hizo Andrés marcados como si los hubiese hecho yo. Aparte es raro porque el archivo que Eclipse me marcaba que tenía conflictos ni siquiera era ese; era `Controller.java`.


Markov System patches only output MIDI. Use them to trigger MIDI messages to your D.A.W. Edit your sound configuration and set up a universal MIDI bus, (IAC driver for mac, I'm not sure what its called for windows) then set this as the MIDI I/O's on Pure Data and your D.A.W then you can use the Pure Data patches to trigger any VST/AU you want.


LGTM.  The actual location of the wwivd.service file might change depending on distro, but I don't think we have to sweat that right now.


Не вижу никакой пользы от этих переменных. А если и прописывать динамические переменные (их относительные смещения), то не здесь, а непосредственно перед командами метода


Я понял, что всё-таки нам не хватает команды AssignUInt8ConstStack, которая будет принимать не абсолютный адрес(10), а смещение относительно текущей вершины стека (в данном случае 0, так как предыдущая команда уже подняла верхушку стека). Потому что не можем мы знать абсолютное смещение для динамических переменных (таких, как адрес возврата) во время компиляции.