[R/dEploidTools.R:1:22:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                     ^
```
[R/dEploidTools.R:1:28:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                           ^
```
[R/dEploidTools.R:2:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L2) *style:* **Variable and function names should be all lowercase.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:2:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L2) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:2:48:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L2) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
                                               ^
```
[R/dEploidTools.R:3:15:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L3) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i+1
              ^
```
[R/dEploidTools.R:3:22:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L3) *style:* **Put spaces around all infix operators.**
```r
        arg_i = arg_i+1
                    ~^~
```
[R/dEploidTools.R:6:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L6) *style:* **Variable and function names should be all lowercase.**
```r
    outPrefix = "dataExplore"
    ^~~~~~~~~
```
[R/dEploidTools.R:6:15:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L6) *style:* **Use <-, not =, for assignment.**
```r
    outPrefix = "dataExplore"
              ^
```
[R/dEploidTools.R:7:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L7) *style:* **Variable and function names should be all lowercase.**
```r
    vcfFileName = ""
    ^~~~~~~~~~~
```
[R/dEploidTools.R:7:17:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L7) *style:* **Use <-, not =, for assignment.**
```r
    vcfFileName = ""
                ^
```
[R/dEploidTools.R:8:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L8) *style:* **Variable and function names should be all lowercase.**
```r
    refFileName = ""
    ^~~~~~~~~~~
```
[R/dEploidTools.R:8:17:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L8) *style:* **Use <-, not =, for assignment.**
```r
    refFileName = ""
                ^
```
[R/dEploidTools.R:9:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L9) *style:* **Variable and function names should be all lowercase.**
```r
    altFileName = ""
    ^~~~~~~~~~~
```
[R/dEploidTools.R:9:17:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L9) *style:* **Use <-, not =, for assignment.**
```r
    altFileName = ""
                ^
```
[R/dEploidTools.R:10:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L10) *style:* **Variable and function names should be all lowercase.**
```r
    plafFileName = ""
    ^~~~~~~~~~~~
```
[R/dEploidTools.R:10:18:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L10) *style:* **Use <-, not =, for assignment.**
```r
    plafFileName = ""
                 ^
```
[R/dEploidTools.R:11:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L11) *style:* **Variable and function names should be all lowercase.**
```r
    excludeFileName = ""
    ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:11:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L11) *style:* **Use <-, not =, for assignment.**
```r
    excludeFileName = ""
                    ^
```
[R/dEploidTools.R:12:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L12) *style:* **Variable and function names should be all lowercase.**
```r
    dEploidPrefix = ""
    ^~~~~~~~~~~~~
```
[R/dEploidTools.R:12:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L12) *style:* **Use <-, not =, for assignment.**
```r
    dEploidPrefix = ""
                  ^
```
[R/dEploidTools.R:13:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L13) *style:* **Variable and function names should be all lowercase.**
```r
    excludeBool = FALSE
    ^~~~~~~~~~~
```
[R/dEploidTools.R:13:17:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L13) *style:* **Use <-, not =, for assignment.**
```r
    excludeBool = FALSE
                ^
```
[R/dEploidTools.R:15:11:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L15) *style:* **Use <-, not =, for assignment.**
```r
    arg_i = 1
          ^
```
[R/dEploidTools.R:16:11:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
          ^
```
[R/dEploidTools.R:16:33:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
                                ^
```
[R/dEploidTools.R:17:14:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L17) *style:* **Use <-, not =, for assignment.**
```r
        argv = args[arg_i]
             ^
```
[R/dEploidTools.R:18:12:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
           ^
```
[R/dEploidTools.R:18:28:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
                           ^
```
[R/dEploidTools.R:19:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L19) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:19:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L19) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:19:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L19) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:19:52:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:20:13:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L20) *style:* **Variable and function names should be all lowercase.**
```r
            vcfFileName = args[arg_i]
            ^~~~~~~~~~~
```
[R/dEploidTools.R:20:25:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L20) *style:* **Use <-, not =, for assignment.**
```r
            vcfFileName = args[arg_i]
                        ^
```
[R/dEploidTools.R:21:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                  ^
```
[R/dEploidTools.R:21:36:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                                   ^
```
[R/dEploidTools.R:22:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L22) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:22:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L22) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:22:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L22) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:22:52:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:23:13:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L23) *style:* **Variable and function names should be all lowercase.**
```r
            plafFileName = args[arg_i]
            ^~~~~~~~~~~~
```
[R/dEploidTools.R:23:26:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L23) *style:* **Use <-, not =, for assignment.**
```r
            plafFileName = args[arg_i]
                         ^
```
[R/dEploidTools.R:24:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                  ^
```
[R/dEploidTools.R:24:35:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                                  ^
```
[R/dEploidTools.R:25:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L25) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:25:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L25) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:25:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L25) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:25:52:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:26:13:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L26) *style:* **Variable and function names should be all lowercase.**
```r
            refFileName = args[arg_i]
            ^~~~~~~~~~~
```
[R/dEploidTools.R:26:25:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L26) *style:* **Use <-, not =, for assignment.**
```r
            refFileName = args[arg_i]
                        ^
```
[R/dEploidTools.R:27:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                  ^
```
[R/dEploidTools.R:27:35:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                                  ^
```
[R/dEploidTools.R:28:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L28) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:28:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L28) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:28:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L28) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:28:52:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L28) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:29:13:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L29) *style:* **Variable and function names should be all lowercase.**
```r
            altFileName = args[arg_i]
            ^~~~~~~~~~~
```
[R/dEploidTools.R:29:25:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L29) *style:* **Use <-, not =, for assignment.**
```r
            altFileName = args[arg_i]
                        ^
```
[R/dEploidTools.R:30:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                  ^
```
[R/dEploidTools.R:30:39:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                                      ^
```
[R/dEploidTools.R:31:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L31) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:31:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L31) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:31:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L31) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:31:52:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L31) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:32:13:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L32) *style:* **Variable and function names should be all lowercase.**
```r
            excludeFileName = args[arg_i]
            ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:32:29:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L32) *style:* **Use <-, not =, for assignment.**
```r
            excludeFileName = args[arg_i]
                            ^
```
[R/dEploidTools.R:33:13:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L33) *style:* **Variable and function names should be all lowercase.**
```r
            excludeBool = TRUE
            ^~~~~~~~~~~
```
[R/dEploidTools.R:33:25:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L33) *style:* **Use <-, not =, for assignment.**
```r
            excludeBool = TRUE
                        ^
```
[R/dEploidTools.R:34:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                  ^
```
[R/dEploidTools.R:34:33:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                                ^
```
[R/dEploidTools.R:35:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L35) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:35:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L35) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:35:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L35) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:35:52:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:36:13:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L36) *style:* **Variable and function names should be all lowercase.**
```r
            outPrefix = args[arg_i]
            ^~~~~~~~~
```
[R/dEploidTools.R:36:23:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L36) *style:* **Use <-, not =, for assignment.**
```r
            outPrefix = args[arg_i]
                      ^
```
[R/dEploidTools.R:37:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                  ^
```
[R/dEploidTools.R:37:40:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                                       ^
```
[R/dEploidTools.R:38:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L38) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:38:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L38) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:38:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L38) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:38:52:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:39:13:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L39) *style:* **Variable and function names should be all lowercase.**
```r
            dEploidPrefix = args[arg_i]
            ^~~~~~~~~~~~~
```
[R/dEploidTools.R:39:27:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L39) *style:* **Use <-, not =, for assignment.**
```r
            dEploidPrefix = args[arg_i]
                          ^
```
[R/dEploidTools.R:44:15:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L44) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i + 1
              ^
```
[R/dEploidTools.R:51:8:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
       ^
```
[R/dEploidTools.R:51:10:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L51) *style:* **Variable and function names should be all lowercase.**
```r
    if ( plafFileName == "" ){
         ^~~~~~~~~~~~
```
[R/dEploidTools.R:51:28:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
                           ^
```
[R/dEploidTools.R:58:12:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
           ^
```
[R/dEploidTools.R:58:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
                  ^
```
[R/dEploidTools.R:58:35:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L58) *style:* **Variable and function names should be all lowercase.**
```r
    return ( list ( vcfFileName = vcfFileName,
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:59:35:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L59) *style:* **Variable and function names should be all lowercase.**
```r
                    refFileName = refFileName,
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:60:35:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L60) *style:* **Variable and function names should be all lowercase.**
```r
                    altFileName = altFileName,
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:61:36:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L61) *style:* **Variable and function names should be all lowercase.**
```r
                    plafFileName = plafFileName,
                                   ^~~~~~~~~~~~
```
[R/dEploidTools.R:62:33:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L62) *style:* **Variable and function names should be all lowercase.**
```r
                    outPrefix = outPrefix,
                                ^~~~~~~~~
```
[R/dEploidTools.R:63:37:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L63) *style:* **Variable and function names should be all lowercase.**
```r
                    dEploidPrefix = dEploidPrefix,
                                    ^~~~~~~~~~~~~
```
[R/dEploidTools.R:64:39:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L64) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeFileName = excludeFileName,
                                      ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:65:35:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L65) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeBool = excludeBool) )
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:65:47:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L65) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    excludeBool = excludeBool) )
                                              ^
```
[R/dEploidTools.R:69:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L69) *style:* **Variable and function names should be all lowercase.**
```r
fun.dEploidPrefix <- function ( prefix ){
^~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:81:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L81) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.coverage <- function ( inputs ){
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:82:17:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L82) *style:* **Variable and function names should be all lowercase.**
```r
    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~
```
[R/dEploidTools.R:83:17:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:83:17:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L83) *warning:* **no visible global function definition for ‘extractCoverageFromVcf’**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:83:48:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~
```
[R/dEploidTools.R:85:17:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:85:17:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L85) *warning:* **no visible global function definition for ‘extractCoverageFromTxt’**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:85:48:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                               ^~~~~~~~~~~
```
[R/dEploidTools.R:85:68:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                                                   ^~~~~~~~~~~
```
[R/dEploidTools.R:109:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:109:38:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~
```
[R/dEploidTools.R:109:51:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:110:9:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L110) *style:* **Use <-, not =, for assignment.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
        ^
```
[R/dEploidTools.R:110:22:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L110) *style:* **Variable and function names should be all lowercase.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[R/dEploidTools.R:111:9:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L111) *style:* **Use <-, not =, for assignment.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
        ^
```
[R/dEploidTools.R:111:22:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L111) *style:* **Variable and function names should be all lowercase.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[R/dEploidTools.R:112:39:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L112) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = ref[,1],
                                      ^
```
[R/dEploidTools.R:113:37:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L113) *style:* **Commas should always have a space after.**
```r
                         POS = ref[,2],
                                    ^
```
[R/dEploidTools.R:114:42:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L114) *style:* **Commas should always have a space after.**
```r
                         refCount = ref[,3],
                                         ^
```
[R/dEploidTools.R:115:42:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L115) *style:* **Commas should always have a space after.**
```r
                         altCount = alt[,3] )
                                         ^
```
[R/dEploidTools.R:120:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L120) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
^~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:120:34:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                 ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:120:51:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:121:10:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L121) *style:* **Variable and function names should be all lowercase.**
```r
    if ( excludeBool ) {
         ^~~~~~~~~~~
```
[R/dEploidTools.R:122:39:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L122) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool,
                                      ^~~~~~~~~~~
```
[R/dEploidTools.R:123:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L123) *style:* **lines should not be more than 80 characters.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:123:51:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L123) *style:* **Variable and function names should be all lowercase.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
                                                  ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:125:39:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L125) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool ))
                                      ^~~~~~~~~~~
```
[R/dEploidTools.R:147:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:147:38:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                     ^~~~~~~
```
[R/dEploidTools.R:147:47:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                              ^~~~~~~~~~~~
```
[R/dEploidTools.R:150:12:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L150) *style:* **Place a space before left parenthesis, except in a function call.**
```r
         if( any( grepl( "gzfile connection", w) ) )
           ^
```
[R/dEploidTools.R:154:9:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L154) *style:* **Use <-, not =, for assignment.**
```r
    gzf = gzfile(vcfFile, open = "rb")
        ^
```
[R/dEploidTools.R:154:18:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L154) *style:* **Variable and function names should be all lowercase.**
```r
    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~
```
[R/dEploidTools.R:154:18:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L154) *warning:* **no visible binding for global variable ‘vcfFile’**
```r
    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~
```
[R/dEploidTools.R:155:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L155) *style:* **Variable and function names should be all lowercase.**
```r
    skipNum = 0
    ^~~~~~~
```
[R/dEploidTools.R:155:13:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L155) *style:* **Use <-, not =, for assignment.**
```r
    skipNum = 0
            ^
```
[R/dEploidTools.R:156:10:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L156) *style:* **Use <-, not =, for assignment.**
```r
    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
         ^
```
[R/dEploidTools.R:156:49:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L156) *style:* **Put spaces around all infix operators.**
```r
    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                               ~^~
```
[R/dEploidTools.R:156:61:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L156) *style:* **Put spaces around all infix operators.**
```r
    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                           ~^~
```
[R/dEploidTools.R:158:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L158) *style:* **Commented code should be removed.**
```r
        if (grepl("##", line )){
                    ^~~~~~~~~~~~
```
[R/dEploidTools.R:159:13:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L159) *style:* **Variable and function names should be all lowercase.**
```r
            skipNum = skipNum+1
            ^~~~~~~
```
[R/dEploidTools.R:159:21:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L159) *style:* **Use <-, not =, for assignment.**
```r
            skipNum = skipNum+1
                    ^
```
[R/dEploidTools.R:159:23:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L159) *style:* **Variable and function names should be all lowercase.**
```r
            skipNum = skipNum+1
                      ^~~~~~~
```
[R/dEploidTools.R:159:30:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L159) *style:* **Put spaces around all infix operators.**
```r
            skipNum = skipNum+1
                            ~^~
```
[R/dEploidTools.R:163:14:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L163) *style:* **Use <-, not =, for assignment.**
```r
        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
             ^
```
[R/dEploidTools.R:163:53:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L163) *style:* **Put spaces around all infix operators.**
```r
        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                   ~^~
```
[R/dEploidTools.R:163:65:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L163) *style:* **Put spaces around all infix operators.**
```r
        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                               ~^~
```
[R/dEploidTools.R:167:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L167) *style:* **lines should not be more than 80 characters.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:167:10:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L167) *style:* **Use <-, not =, for assignment.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
         ^
```
[R/dEploidTools.R:167:31:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L167) *style:* **Variable and function names should be all lowercase.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                              ^~~~~~~
```
[R/dEploidTools.R:167:45:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                           ~^~
```
[R/dEploidTools.R:167:46:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L167) *style:* **Variable and function names should be all lowercase.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                             ^~~~~~~
```
[R/dEploidTools.R:167:61:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                           ~^~
```
[R/dEploidTools.R:167:77:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                           ~^~
```
[R/dEploidTools.R:167:119:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                                ~^~
```
[R/dEploidTools.R:169:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L169) *style:* **Variable and function names should be all lowercase.**
```r
    sampleName = names(vcf)[10]
    ^~~~~~~~~~
```
[R/dEploidTools.R:169:16:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L169) *style:* **Use <-, not =, for assignment.**
```r
    sampleName = names(vcf)[10]
               ^
```
[R/dEploidTools.R:171:9:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L171) *style:* **Use <-, not =, for assignment.**
```r
    tmp = vcf[[sampleName]]
        ^
```
[R/dEploidTools.R:171:16:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L171) *style:* **Variable and function names should be all lowercase.**
```r
    tmp = vcf[[sampleName]]
               ^~~~~~~~~~
```
[R/dEploidTools.R:172:11:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L172) *style:* **Use <-, not =, for assignment.**
```r
    field = strsplit(as.character(tmp),":")
          ^
```
[R/dEploidTools.R:172:40:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L172) *style:* **Commas should always have a space after.**
```r
    field = strsplit(as.character(tmp),":")
                                       ^
```
[R/dEploidTools.R:174:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L174) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/dEploidTools.R:174:15:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L174) *style:* **Use <-, not =, for assignment.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
              ^
```
[R/dEploidTools.R:174:44:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L174) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
                                           ^~~~~~~~~~~~
```
[R/dEploidTools.R:175:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L175) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
    ^~~~~~
```
[R/dEploidTools.R:175:12:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L175) *style:* **Use <-, not =, for assignment.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
           ^
```
[R/dEploidTools.R:175:36:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L175) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                   ^~~~~~~~~
```
[R/dEploidTools.R:175:47:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L175) *style:* **Commas should always have a space after.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                              ^
```
[R/dEploidTools.R:177:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L177) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/dEploidTools.R:177:14:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L177) *style:* **Use <-, not =, for assignment.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
             ^
```
[R/dEploidTools.R:177:41:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L177) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
                                        ^~~~~~
```
[R/dEploidTools.R:178:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L178) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/dEploidTools.R:178:14:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L178) *style:* **Use <-, not =, for assignment.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
             ^
```
[R/dEploidTools.R:178:41:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L178) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
                                        ^~~~~~
```
[R/dEploidTools.R:180:39:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L180) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = vcf[,1],
                                      ^
```
[R/dEploidTools.R:181:37:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L181) *style:* **Commas should always have a space after.**
```r
                         POS = vcf[,2],
                                    ^
```
[R/dEploidTools.R:182:37:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L182) *style:* **Variable and function names should be all lowercase.**
```r
                         refCount = refCount,
                                    ^~~~~~~~
```
[R/dEploidTools.R:183:37:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L183) *style:* **Variable and function names should be all lowercase.**
```r
                         altCount = altCount )
                                    ^~~~~~~~
```
[R/dEploidTools.R:204:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L204) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
^~~~~~~~~~~
```
[R/dEploidTools.R:204:12:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L204) *style:* **Put spaces around all infix operators.**
```r
extractPLAF<- function ( plafName ){
          ~^
```
[R/dEploidTools.R:204:26:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L204) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
                         ^~~~~~~~
```
[R/dEploidTools.R:205:25:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L205) *style:* **Variable and function names should be all lowercase.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~
```
[R/dEploidTools.R:205:41:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L205) *style:* **Put spaces around all infix operators.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~
```
[R/dEploidTools.R:210:11:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
         ~^~~
```
[R/dEploidTools.R:210:19:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                 ~^~
```
[R/dEploidTools.R:210:23:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                     ~^~
```
[R/dEploidTools.R:210:24:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L210) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                       ^
```
[R/dEploidTools.R:210:26:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                        ~^~
```
[R/dEploidTools.R:210:28:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                          ~^~
```
[R/dEploidTools.R:211:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **lines should not be more than 80 characters.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:211:8:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
      ~^~~
```
[R/dEploidTools.R:211:23:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                     ~^~
```
[R/dEploidTools.R:211:30:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                            ~^~
```
[R/dEploidTools.R:211:43:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                         ~^~
```
[R/dEploidTools.R:211:44:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                           ^
```
[R/dEploidTools.R:211:46:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                            ~^~
```
[R/dEploidTools.R:211:54:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                    ~^~
```
[R/dEploidTools.R:211:59:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                         ~^~
```
[R/dEploidTools.R:211:72:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                      ~^~
```
[R/dEploidTools.R:211:77:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **Commas should always have a space after.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                            ^
```
[R/dEploidTools.R:211:77:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                            ^
```
[R/dEploidTools.R:211:79:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                             ~^~
```
[R/dEploidTools.R:211:87:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                                ~^~
```
[R/dEploidTools.R:212:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L212) *style:* **lines should not be more than 80 characters.**
```r
    #  llk<-lgamma(fac*f.samp+cov.alt)+lgamma(fac*(1-f.samp)+cov.ref)-lgamma(fac*f.samp)-lgamma(fac*(1-f.samp));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:212:8:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L212) *style:* **Commented code should be removed.**
```r
    #  llk<-lgamma(fac*f.samp+cov.alt)+lgamma(fac*(1-f.samp)+cov.ref)-lgamma(fac*f.samp)-lgamma(fac*(1-f.samp));
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:213:25:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L213) *style:* **Put spaces around all infix operators.**
```r
    if (sum(is.nan(llk))>1){
                       ~^~
```
[R/dEploidTools.R:220:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L220) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.dic.by.llk.var <- function ( tmpllk ){
^~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:221:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L221) *style:* **lines should not be more than 80 characters.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:221:23:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L221) *style:* **Put spaces around all infix operators.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
                     ~^~
```
[R/dEploidTools.R:221:40:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L221) *style:* **Put spaces around all infix operators.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
                                      ~^~
```
[R/dEploidTools.R:221:48:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L221) *style:* **Put spaces around all infix operators.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
                                              ~^~
```
[R/dEploidTools.R:225:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L225) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.dic.by.theta <- function ( tmpllk, thetallk ){
^~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:226:5:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L226) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    DIC.WSAF.bar = -2 * sum(thetallk)
    ^~~~~~~~~~~~
```
[R/dEploidTools.R:226:18:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L226) *style:* **Use <-, not =, for assignment.**
```r
    DIC.WSAF.bar = -2 * sum(thetallk)
                 ^
```
[R/dEploidTools.R:227:1:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L227) *style:* **lines should not be more than 80 characters.**
```r
    return (  mean(-2*tmpllk) + (mean(-2*tmpllk) - DIC.WSAF.bar) ) # D_bar + pD, where pD = D_bar - D_theta, and D_bar = mean(D_theta)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:227:22:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L227) *style:* **Put spaces around all infix operators.**
```r
    return (  mean(-2*tmpllk) + (mean(-2*tmpllk) - DIC.WSAF.bar) ) # D_bar + pD, where pD = D_bar - D_theta, and D_bar = mean(D_theta)
                    ~^~
```
[R/dEploidTools.R:227:41:](https://github.com/mcveanlab/DEploid-r/blob/643c66e166bdf6c22ccad748fc3b8c92b72c47ed/R/dEploidTools.R#L227) *style:* **Put spaces around all infix operators.**
```r
    return (  mean(-2*tmpllk) + (mean(-2*tmpllk) - DIC.WSAF.bar) ) # D_bar + pD, where pD = D_bar - D_theta, and D_bar = mean(D_theta)
                                       ~^~
```


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Temporary.


Wow wait a minute...What happened here ..?

Well, I'll tell you. As mentionned in the **ReadMe**, I'm not the guy behind this.
In fact, I was allowed by the original developper himself to create this repo (and I did it).

But he recently asked me to include his former commits to my repo.
After a _few_ rebase attempts, I finally managed to get something decent.
So here we are, this is a breaking point. Before that, all the original commits from the creator; After that, my contributions to the project.

I'm sorry, this is not perfect, I kinda messed up eveything.


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The file's name should be .travis.yml (starting with a dot)


![](https://github.trello.services/images/mini-trello-icon.png) [Bug de la colonne ID vide](https://trello.com/c/hlkt2ppg/65-bug-de-la-colonne-id-vide)


We both discussed this version of pick_best() two days ago. I know, that std::max_element can be used without opening condition, this is replaced by assert in my previous version.


That's the right way to do it! :clap:

Next time maybe make commit heading a bit shorter, so that it has to break with …, but apart of that, nice commit.


Err #111 not #11


This reminds me that we should soon try to deploy this plugin https://github.com/xjamundx/eslint-plugin-promise


This is a giant change for a point release and it broke me, since we were using eslint 2.


Nice catch, I didn't notice that else. Do you think I should replace that with the old ebcdic string or move the e2a up to the if and elif?


Done 👍


\o/


Up to the if and elif i think would be better.
Then the ebcdic2ascii tool can do its job without us having to revert its changes.


Thank you!


I thought that I already published it


it works to show FAIL dockerme branches


I've just amended a new commit to this one because it didn't work. Hope nobody pulled it in before reading this


more like NOT REALLY initial commit ammirite/??//


pourquoi tu as fait la multiplication deux fois ?


Fixed.


На всякий случай сообщу, что эту величину можно изменять в HouseActor_BP в самом Unreal Editor'е. Тогда не надо будет перекомпилировать код для того чтобы настройка применилась.

Вот пример: https://docs.unrealengine.com/latest/INT/Programming/Tutorials/VariablesTimersEvents/2/


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Аналогично, эту переменную можно менять в блюпринте GameMode_BP.


Incomplete version of instructions


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would say also `(affected, recordType)`...


![](https://github.trello.services/images/mini-trello-icon.png) [item -> tj rocky ... ???](https://trello.com/c/CL6rSyVA/64-item-tj-rocky)


Glad it is out of service, sorry for yelling.


I just did within the last 4 minutes.


i think it should be int? id


Вот эту формулу удобно было бы оформить в виде функции
```cpp
float ComputeOrderPriority(float distance, float timeLeft)
```
А затем внутри цикла позвать ее один раз для вычисления `currentPriority` и переиспользовать эту переменную везде. Тогда и кода меньше будет, и менять его надо будет при изменении формулы только в одном месте.


I see your point about being invulnerable inside a ship/tank wreck, so it makes sense to automatically eject them so they are hurt by the explosion. I think they will be hurt inside the wreck by the explosion now too, but I have to test to confirm.

You can blow up a helicopter just by rolling it over at < 5 km/h speed and < 5m altitude. The fact that it blows up in that situation is already unrealistic, but instantly killing the whole crew is even worse. They should survive that and just take damage from the explosion as they do in normal Arma/DayZ. Otherwise every time a group botches a helicopter take off 5m off the ground their entire team is wiped out.

The same goes for low speed plane and heli crashes where players would normally survive with some minor damage. Instantly killing them is a bad idea.


Yeh, a little, but, we can roll back easily enough, and we'll keep node up
to date, we're not technically running a real prod server yet.

On 13 Oct 2016 15:22, "Wilson Page" <notifications@github.com> wrote:

> DRIVE-BY: Risky using latest and not locking to particular version?
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/mozilla-magnet/magnet-metadata-service/commit/48027acb8278c3e5ee78b3267ccde8cdb9ff0169#commitcomment-19412582>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AAzSjjTRPTh7c_Erp9D4CjSuQzvbv5b2ks5qzj6ugaJpZM4KV8su>
> .
>


Все-таки **retrieve** это грамматически правильный вариант ;)


Ok, you're the one to maintain this code


Этот индекс можно было с легкостью запомнить в предыдущем цикле (который ищет заказ с максимальным `priority`) и избавиться от еще одного прохода.


There is probably way better way to do what I was trying to do here, but had no idea what :)
But it's working :+1:


I've quickly tested receivings with my latest change, looks ok here.


Once you use the unsigned version, the error message does not match anymore:
"Expected positive argument" : stroul will always return a positive argument.
Also, the tests "tmp < 0" will always be true.

Instead, we should use the signed int.._t type for tmp.


Yes I have created an algorithm for irregular section channel I'm my [https://github.com/alexiusacademia/ChannelFlowLib](url). Kindly check it out. I have included a sample usage at the bottom of the file irrig_channel.py


"listed below" is necessary for emphasis.
Also, as the page linking behavior works today, if I click the link, the page doesn't advance to that section to display it at the top of the page. I only see that the link is working if I right-click the link and open it in a new tab, in which case the new page does open with the destination section displayed at the top.


HTML test runners tests pass.


I fixed the rest of rendering bugs and merged it.


je me suis trompé :3


firt mod


Наоборот: `t.string :name`.


I'd probably `show_help=False` since this doesn't do anything and is deprecated (?)


The `UnaryFunctions` should probably be passed by reference so that they can potentially be updated. I had compilation errors while trying to do this though.


@rsanchez-wsu Good commit :D


did you mean to commit this file (probably not) -- should this have gone through a PR ?


@mjksmith


misspelled header incorrectly


Здесь, очевидно, должно быть `railway_stations_routes`.


Good commit message. It offers a brief but comprehensive summary of the changes made, and the methods that were added. I've been making some effort myself to document student-written methods on the wiki.


Please adopt the indentations used in each file, this means use 4 spaces and not tabs for this file.


Изглежда сте готови :D


i get this randomly while breaking blocks on dedicated then it just stops ticking

java.util.ConcurrentModificationException
        at java.util.ArrayList$Itr.checkForComodification(ArrayList.java:901)
        at java.util.ArrayList$Itr.next(ArrayList.java:851)
        at net.codepixl.GLCraft.world.entity.EntityManager.update(EntityManager.java:164)
        at net.codepixl.GLCraft.world.WorldManager.update(WorldManager.java:232)
        at net.codepixl.GLCraft.world.CentralManager.update(CentralManager.java:643)
        at net.codepixl.GLCraft.GLCraft.update(GLCraft.java:377)
        at net.codepixl.GLCraft.GLCraft.commonInitializer(GLCraft.java:239)
        at net.codepixl.GLCraft.GLCraft.<init>(GLCraft.java:121)
        at net.codepixl.GLCraft.GLCraft.main(GLCraft.java:406)

Exception: java.awt.HeadlessException thrown from the UncaughtExceptionHandler in thread "main"


This causes an erroneous log message in dev mode:
    ERROR play - Restart: Need to restart Play because <path>\application.conf has been changed

because when detectChange() is first executed the value of long configLastModified has not been properly initialized yet.  It's value is 0.  So the ConfigurationChangeWatcherPlugin will think a change has occurred to the application.conf when it it fact has not occurred.   The value of configLastModified only gets initialized later when onConfigurationRead() is called.


yes dooo itttt


NO IT WASN'T, IT WASN'T EVEN COMMITTED ON A BRANCH AAAAAAAAAAA


STAGE3 uptime was 27h


While I agree doing a 'compressed' state change list to send to the other thread would be superior solution and lower overhead, I think it should be already good with the current way where you send a list of calls.

How do you explain we don't get gains when game is having ideal lock usage (at beginning of frame) ?


Здесь смысл в том что билет принадлежит именно к станции начальной и конечной, не к маршруту.


This commit provided functionality that will be important to the overall program as it progresses. Without this it would not be possible for two clients to connect at once.


Nicely done! Though it looks like HUDK4050 is causing your person-person graph to be a bit skewed. If you remove HUDK4050 you may see a more interesting structure.


Great Description!!

From,
Team 4


Source map tests pass. Publishing.


Here is a snippet from my log file showing the order in which these methods were called:

17:51:19,355  INFO play:308 - detectChange()
java.lang.Throwable
	at play.ConfigurationChangeWatcherPlugin.detectChange(ConfigurationChangeWatcherPlugin.java:24)
	at play.plugins.PluginCollection.detectChange(PluginCollection.java:598)
	at play.Play.detectChanges(Play.java:641)
	at play.Invoker$Invocation.init(Invoker.java:199)
	at play.server.PlayHandler$NettyInvocation.init(PlayHandler.java:264)
	at play.Invoker$Invocation.run(Invoker.java:285)

17:51:19,474  INFO play:308 - onConfigurationRead()
java.lang.Throwable
	at play.ConfigurationChangeWatcherPlugin.onConfigurationRead(ConfigurationChangeWatcherPlugin.java:14)
	at play.plugins.PluginCollection.onConfigurationRead(PluginCollection.java:610)
	at play.Play.readConfiguration(Play.java:356)
	at play.Play.start(Play.java:489)
	at play.Play.detectChanges(Play.java:659)
	at play.Invoker$Invocation.init(Invoker.java:199)
	at play.server.PlayHandler$NettyInvocation.init(PlayHandler.java:264)
	at play.Invoker$Invocation.run(Invoker.java:285)
	at play.server.PlayHandler$NettyInvocation.run(PlayHandler.java:303)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)


Including the issue that was fixed is an excellent precedent to set. It helps keep work easily to reference. Including the method names in the commit is a nice touch. It will provide an at a glance line of development evolution.


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"the above stated" is there for emphasis.
The statement "This ability to use REST API..." can be misleading, if the customer skims and only reads the highlighted yellow note on the page.
IMO this feature, as it debuts, has "gotchas" here and there, and some customers are likely to run into these inconsistencies. This is a good opportunity and a necessity for the docs is to put enough emphasis where customers can possibly run into problems.


Calling wrong method?
```java
public boolean post(Event event, boolean allowClientThread) { }
public boolean post(Event event, boolean allowClientThread, boolean fireModEvents) { }
```


This commit was very descriptive and its title is very clear with what it accomplished.


This seems like a very helpful commit. All of these elements are useful and give a good basic start to our DTD. Might be helpful to add a little more to the description but it is fairly straightforward after reading the code. It is also helpful that you fixed the issue as well with the commit. As Roberto said, nice work with this.


Calling wrong method?


I'll leave that up to @kaisen


It is a nice start for the GUI Interface

From,
Team 4


This is a large amount amount of commented out code to commit.  It can become unclear what the code is doing.


too long of a variable name try to shorten


Comments aren't consistently placed. Great job on commenting on what everything is, making it easily followable.


Проверь как работает эта ассоциация.


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I had to do this so the numbers wouldn't confuse the rest of the program. (when confused ```:)```= 😔 and various other confusing and seemingly random things.


This commit is very descriptive, has plenty of comments for clarity, and is very clearly titled.


Let's keep this "API" singular. In general, let's not split hairs on this. If we need to emphasize the plurality, we can clarify with "API sets".


Well documented, also cites the related issues that it closes/works on.


Very well polished code.  Sock vs. socket variable names are a little close.  Also leaves room for improvements.


No description on this commit. Reading title without looking into the code doesn't really tell others what exactly has been committed here.


No description on this commit. Doesn't reference issue.


Hello


we still have unresolved issue if system username will be longer then 14 chars. Where will be no place for  db username. Any ideas?


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@alexey-sidnev  Task about number sequence.


that seems to have been the problem...works now for me.


@Hexik, so why don't you use it as in your previous version?


so you want us to make a new package with these 3 classes in it?


@iwilsonq   did you mean to write `48rem`?


I did change this, but I am willing to change it back.


WOOOOO @enormandin


@swayand
That parent_logical_file_name logical file name is not working for you does not mean that it is not need for a correct DBS3 publication. You are currently breaking parentage information in DBS and should you probably think of fixing your parentage problem in another way.

Cheers.
Manuel


I changed the name of this out of preference. It seemed to fit better.


oh I didn't mean it that way, I was talking in general that sources should be mendtioned in future commits regarding game mechanics/scalings. I know that you didnt change any scaling here so it is not needed here.

As for the internal discussed sources it doesn't make much sense to not include them in the future commits since the sourcecode is already open source. Having a policy to enforce sources would generally lead to a higher quality codebase, with commits beeing easier to check and less prone to introducing errors.


![](https://github.trello.services/images/mini-trello-icon.png) [Gestión de Usuarios](https://trello.com/c/QJfkLbrL/8-gestion-de-usuarios)


![](https://github.trello.services/images/mini-trello-icon.png) [Gestión entrenadores](https://trello.com/c/UZNgyttq/9-gestion-entrenadores)


I want to join this project. Chuck-


This line doesn't seem to work.


@skurudo suggested we can cut username, like a cPanel does... but... it will be large modification of source code because we must also change a functions that check owner permissions (to avoid mixing with other users that has username that begin with the same letters)


Sweet!


next time, tell me you stole it directly from Prism kay?
really not a good idea to steal shit from other people


I agree with Brand. If you list the variables to the Java documentation, you may be able to remove some of the comments. I do like the amount of documentation, but if you consolidate it, it may help the code. In addition to moving the variables to Javadocs, you can probably combine some comments for the process into groups of steps.

Writing the comments as the steps occur helps to an extent, but if you put the majority of the documentation in a doc and reference the doc, it can help to do more with less.


It would be better if you broke up the title and the description. Instead it got word wrapped awkwardly.  Perhaps the title could be "fixed an issue with the filecommand method" and the rest could be the description.


I feel that this commit message was too brief. Why was the push made, for instance? Taking at least a couple sentences to explain the logic behind your changes would be beneficial to everyone involved in this project.


It might be more descriptive to explain your reason why you removed it in the commit message.


Curiosity: why is this needed and does it actually belong in the client instead of the brokerage?

We may want to save this thread for the dispose method as well.


What data base are you using ? MongoDB?


Why was DTD moved to the com package? What kind of effect will moving it there have? Also, offer some examples of HOW you expanded on the DOS and POSIX file attributes.


What exactly is the change here? A method and a function is the same thing.


Marco reject it, so I am testing something more readable, actual test result is along my expectation, something above 1 elo
I plan next test with better version which has higher speedup potential


I think having a description or body for this commit would help understanding a lot.


The title is self-explanatory, however I would like to see a brief explanation of what changes are being merged. This would make it easier for other teams to quickly understand what is being merged.


many of these variable names are quite descriptive although some of the variables may need some help such as instead of a two letter variable name try being more descriptive on those variable names. I also like how the beginning brackets are put on the same line as the method to avoid getting some errors. Also remember to use the rules for declaring variables so it will not confuse anybody. Also, the formatting is really great.


Good commit. However, there is no description. But overall good.


"The yarn.lock file lists every dependency and the exact version of that installed dependency ... When yarn installs from a yarn.lock file, it installs the exact same code, everywhere."

Everyone gets the same version of dependencies.


Doesn't say it fixes or references this issue.


I should mention that i am really new to github...
Sorry...
Error message:
error: pathspec 'ustream-websocket' did not match any file(s) known to git.


LGTM


Broke commit.


I'll remove it, don't worry 😄


@cooladam201212 you'll have to use a different dircolors (`$LS_COLORS`) color scheme I bet. For example here's a [solarized color scheme](https://github.com/seebi/dircolors-solarized) for ls.


this is a kick ass method - very cool.

Where did you get the header spec from? I'm assuming wac2wav source code? can you link to it?


TaskCluster: https://tools.taskcluster.net/task-graph-inspector/#MSJb6Gz4QEKoL9fo3939lg/


The first try


I think this should have been 0.9.0. Too late?


OK, you've gotta switch to the ustream-websocket branch.
Try
```
git checkout -b ustream-websocket origin/ustream-websocket
```


looks good :) one thing I'm not sure about is: Are castcustomspell spell's still subject to applying total percentage damage modifiers? like http://wowwiki.wikia.com/wiki/Elemental_Weapons?oldid=1354476 which increase the total flametongue dmg.
If not it could be sth that needs to be done manually here too


общие рекомендации:
- разнести js в js файлы, css в css, html оставить в html файлах
- убрать onxxx хендлеры. юзать addEventListener()
- сделать из этого кода модуль (читай тут: http://largescalejs.ru/module-pattern/)
- хранить внутри модуля\компонента ссылку на главный контейнер (сейчас это форма) и относительно него осуществлять поиск.


Bah, I've looked at the log.Logger docs a bunch of times and never noticed Output, nice find.


I think we want format/values as parameters here, so that we're not taking the cost of building the string at log levels that don't log.


@Hexik, Marco didn't explain properly why he rejected. I think it's not very respectful from him. But if it passes Fishtest, I think he will accept.


Sorry I just saw your comment here. I will be following this closely. Also,
i can also revert my change last night which violates this.

Navi

On Tue, Oct 11, 2016 at 2:49 PM, Randy Westlund <notifications@github.com>
wrote:

> You really need to separate your commits. This combines at least three
> different kinds of changes:
>
>    - content additions
>    - section reordering
>    - whitespace changes (indenting)
>
> These should all be in separate commits. Most importantly, separate the
> commits that have no effect on the rendered document (such as line wrapping
> or indentation) and mark them as such. When everything is lumped together
> like this it makes it really difficult for me to help.
>
> I had to re-edit every line you touched (#40
> <https://github.com/vanallen/writeup/pull/40>) because I couldn't tell
> where the content changes were. Your commit message didn't even say
> anything about what you were changing!
>
> Keep your commits small and specific.
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/vanallen/writeup/commit/72fe869245fa9e2721a4f0d4dad0a004bd070224#commitcomment-19385413>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AChRzJFSmBBvgkrJOZYwUuqeahaNrB_Mks5qzAR7gaJpZM4KUIwu>
> .
>


все функции сейчас живут в windows - то есть, они глобальны. это не очень гуд. лучше использовать неймспейсы для этого. я буду объяснять это на уроках. сейчас можно сделать так:
```javascript
var HW = {};
HW.addItem = function () {}
HW.delItem = function () {}
```


Make sense, will update.


I somehow missed it in the docs but saw it capitalized in the code.


The new login Modal was added in this commit


будет лучше, если поиск будет не глобальный, а относительно рутовой ноды (сейчас это форма).


![](https://github.trello.services/images/mini-trello-icon.png) [Butoane](https://trello.com/c/p56UnK8q/8-butoane)


умные мира сего рекомендуют не использовать таблицы в верстке. дивы - лучше и будет работать быстрее.


onclick() - это плохо. юзай addEventListener()


He may think the speed benefit is too small. But if we show it's higher, he will probably accept the patch. Moreover, look at the implementation of the insertion_sort function above. It uses a similar style.


@afk11 its a untested concept WIP ,  but probably yeah `mod(n)`


it would be good to clarify what `le16` means - as near as I can figure - from context - it is a 16-bit little endian number... but the docs do not seem to agree http://ruby-doc.org/core-2.3.0/String.html#method-i-unpack


Published.


```ruby
class ArticlesController < ApplicationController
  def index
    @articles = Article.all
  end
end
```

```slim
12 - @articles.each do |article|
13    = article.title
```

trace
```ruby
undefined method `each' for false:FalseClass
```
```
/gems/mongoid-fc71fb5451c6/lib/mongoid/contextual/mongo.rb:123:in `each'
/gems/mongoid-fc71fb5451c6/lib/mongoid/contextual.rb:20:in `each'
app/views/articles/index.slim:12:in `_app_views_articles_index_slim__1313783805182157651_70172427483080'
```


I was not able to spin up a vagrant environment for running the tests on this, but I did try using this new version on my project, and it ran with no trouble and made the deprecation messages go away. I believe those methods were [deprecated](http://rspec.info/documentation/3.4/rspec-expectations/RSpec/Matchers/DSL/Macros/Deprecated.html#failure_message_for_should-instance_method) in rspec-expectations 3.4.


This Commit needs to be made the Main branch


лучше отталкиваться от кликнутого элемента. его можно получить через `event.target`


![](https://github.trello.services/images/mini-trello-icon.png) [Remove old tileset options and add Mapbox satellite tiles](https://trello.com/c/rGOSmk9M/148-remove-old-tileset-options-and-add-mapbox-satellite-tiles)


$http.get('/users')
.then


![](https://github.trello.services/images/mini-trello-icon.png) [HomePage - BG la video-uri sa fie mai dark](https://trello.com/c/jJtdK5pq/11-homepage-bg-la-video-uri-sa-fie-mai-dark)


rundundant


same


Avoid using <br> in html. Use div / css rules for such cases


d


add aliases for controllers like:
controllerAs: 'userListCtrl'


![](https://github.trello.services/images/mini-trello-icon.png) [Hi](https://trello.com/c/WVuSCxNJ/1-hi)


Updated in 16ffd13. If you're a fan, I think you can fast-forward https://github.com/superfell/raft/tree/logging_itf to 16ffd13 to update hashicorp/raft#180


This fix works perfectly on my big set of non-ascii files.


Don't do things like this in JSON. Comments and future Additions belong as Issues in the main repository, not in the file itself. What will happen is the auto-parser will attempt to load this tag like it is one of the measurements and will fail because the data does not match the schema (same fields with the same datatypes in them).


thanks.
I havent had much time to look into the sql.js stuff yet but hopefully within the next couple weeks. I dont think websql support is being dropped for a while so we have some time.


their?


`list` is the name of the Python built-in list. You should never use this as a variable name.


this line raises an `AttributeError: can't set attribute` error


They are, BUT since wotlk DBC shows that dummy should take care of applyspellmod, we will need to add that too.

                    if (Player* playerCaster = dynamic_cast<Player*>(m_caster))
                        playerCaster->ApplySpellMod(m_spellInfo->Id, SPELLMOD_DAMAGE, totalDamage);

will do the trick.


This whole function could've just been a one-liner.
```python
avg_gpa = sum(list) / len(list)
```


This line is unnecessary.


jodaor


This function has nothing to do with students, new or otherwise. It also needs documentation.


git checkout -b ustream-websocket origin/ustream-websocket
fatal: Cannot update paths and switch to branch 'ustream-websocket' at the same time.
Did you intend to checkout 'origin/ustream-websocket' which can not be resolved as commit?

I have no idea why that happened..
Running this also did not work.

`git checkout -b origin/ustream-websocket
Switched to a new branch 'origin/ustream-websocket'
snipe:streamlink sneakysniper$ git checkout ustream-websocket
error: pathspec 'ustream-websocket' did not match any file(s) known to git.`


What's the point of this function if it doesn't return anything?


Use parentheses for all your `print` statements.


Worked with @csan21


This doc string line is entirely too long.


Marco explain it, as you wrote, I have prepared bad arguments about performance. Basic hardcoded benchmark is only for rough estimation, if you need better result, it is important to use much bigger set of FENs.
Next time I will be prepared better ;-)


Bad variable names. What are you passing in as `d`? What are you populating this dictionary with?


In this case, we are ignoring utsakta not because it is long, but because it is simply an exemplar  (in form of ppp) of the prefixed verb ud + saYj.  This is a case where, as @drdhaval2785 suggested elsewhere, it would be better to have the digitization to be
```
-<P>- {#ud#}, {#utsakta#}
rather than
-<P>- {#ud, utsakta#}
```
As it is, we are excluding things after a comma.  The only cases we've examined thus far indicate this is a 'safe' exclusion, in that we are not losing any prefixes.

There is in fact a list of all such adjustments (286 of them) embedded in [preverb1_log.txt](https://github.com/sanskrit-lexicon/alternateheadwords/blob/master/data/PWGpreverb/preverb1_log.txt).

@gasyoun  You could examine this list to see if there are any exclusions that are unwarranted.


https://github.com/BlocklandGlass/BlocklandGlass/tree/development

probably should've told you first, sorry.


![](https://github.trello.services/images/mini-trello-icon.png) [Favicon + Titles (am sa ti-l dau eu)](https://trello.com/c/ELqgPpxy/19-favicon-titles-am-sa-ti-l-dau-eu)


Lmao here we go again A kang panda production


this would be gr8 to auto build our commits


this nice111!!!!


@kito-cheng done


This doesn't appear to be working 😕


I think it is gonna work! I have compared everything to https://travis-ci.org/ImagicalCorp/ImagicalMine and the logs are almost exactly the same! It should definitely work!


fun times with computers


Yup, direct from the source code


diff --git a/custom/mupen64plus-core/api/config.c b/custom/mupen64plus-core/api/config.c
index 596ab79..7382688 100644
--- a/custom/mupen64plus-core/api/config.c
+++ b/custom/mupen64plus-core/api/config.c
@@ -31,7 +31,8 @@

 #define M64P_CORE_PROTOTYPES 1
 #include "callbacks.h"
-#include "config.h"
+
+#include "../../../mupen64plus-core/src/api/config.h"
 #include "m64p_config.h"
 #include "m64p_types.h"
 #include "main/util.h"

that's all that's missing, it's building and working fine with the change


I noticed there wasn't an update last week. Are you dropping support for this? If so, I would be willing to take over if you can give me a short HOW-TO. It doesn't look at that difficult and I have a strong programming/technical background.


No, the changes to FW are not strictly required by SGW. When SGW depends on something new in FW then I'll update its include statement.


This is the first C# class I have written, so I am sure there are a couple mistakes in regards to proper protocols in naming conventions or setting and getting values. Any input and comments are appreciated.


Yay!


Probably not out of the box, but shouldn't be hard to make it work.


Do you want a link in the code, or in the comments here? https://github.com/QutBioacoustics/wac2wavcmd/blob/master/wac2wavcmd.c


Although, if I remember correctly, it took at least an hour for Travis-CI to upload the build to gh-pages, so its gonna be a while until we know if it worked or not. And, if it doesnt work, I will only be able to fix it tomorrow after i do my hw... But it will definitely be done by Tomorrow at this time!


how do I add this to my heroku app?


#1 完成


I was surprised as well, sadly that code is not in the API library but was in the IB sample app.
It is required, otherwise no events will be fired.
Internally the library pushes received messages into a queue, this thread does the dequeuing.


That's definitely a link to grunt, not gulp


@Otann I don't like the resulting syntax here (with true meaning false), but I decided to stick with it for now as the semantics of LOCKED_IN_CLAIMED_CHUNKS=true (and not the opposite) was more intuitive for me.

Please feel free to refactor this snippet and/or rename the constant.


This should still be deleted.


Did you intend to do if(is_exact) ?

Without really understanding the code, logically I can deduce, at least for the Holo blend case, that cur_k is not initialized unless is_exact is true. so I'm not sure how this can be correct.


I'll add more to this sometime on the weekend if I can.


The switch to px-functions-design 0.3.3 appears to introduce a SASS import loop, as px-functions-design now (starting from 0.3.0?) [imports px-defaults-design](https://github.com/PredixDev/px-functions-design/commit/cc6f8656958b9cf4ac372646f99a8b4d2f65ee17) ... Or am I missing something?


You misspelled "canola"!


Done in https://github.com/QutBioacoustics/baw-audio-tools/commit/2e3551fb30a4e455f04d9dfa7cef241adc6ebba6#diff-943dd8a6728774c4f056227a89fa7713


please wrap this in a `if __name__ == "__main__"`


2.1.1 and 1.8.1 are out. 2.1.0 and 1.8.0 are unpublished. Sorry for the drama.


Move this method to the EventSimulator class. This should be done when the program was initialized.


Hmm this is hardcoded.


You need to check if the table is already created or not.


Parentheses


@Deav10: I already made the classes and the package, as you can see above :) But of course, you guys should populate them. We're still trying to figure out who's doing what :P


TeamCity Xbim :: Xbim Geometry :: XbimGeometry [Build 295](http://xbimbuilds.cloudapp.net/viewLog.html?buildId=1301&buildTypeId=Xbim_XbimGeometry_XbimGeometry) is now running


A better name for the `max` attribute is `at_capacity`


@jlblancoc  Did you mean else on line 611?


Could it be uploaded to the releases or could the raw phar data be uploaded to another branch?


Right.  Doing.


We're really in synch :-)

Look at this commit, almost exactly for the exact instant you were typing this:
https://github.com/MRPT/mrpt/commit/25d50c05a40e2a4a15a2e040d7e04f835408bb03

You're right, this was not correct. This being used for logging purposes only, I didn't pay the required attention and...
Well, at least it's now fixed, hopefully. As usual, thanks for being watchful.
Cheers,


CurrentTick not CurrentTicks


fdfsdf


**zczxc czcz__**


`c zxczx sacasc`


I think the cleanest way to do the csmt thing is to have some MACROS for where we need to sync (which would check first if csmt is enable, and then if the flush/whatever is needed).
Then the required device9 functions would be wrapped by a version that would record the state changes instead (all the functions that set/read something in nine_state structure). We should try to have all the other functions as is, modulo a few MACROS to introduce the syncs.