[R/dEploidTools.R:1:22:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L6) *style:* **Use <-, not =, for assignment.**
```r
    outPrefix = "dataExplore"
              ^
```
[R/dEploidTools.R:7:5:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L7) *style:* **Use <-, not =, for assignment.**
```r
    vcfFileName = ""
                ^
```
[R/dEploidTools.R:8:5:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L8) *style:* **Use <-, not =, for assignment.**
```r
    refFileName = ""
                ^
```
[R/dEploidTools.R:9:5:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L9) *style:* **Use <-, not =, for assignment.**
```r
    altFileName = ""
                ^
```
[R/dEploidTools.R:10:5:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L10) *style:* **Use <-, not =, for assignment.**
```r
    plafFileName = ""
                 ^
```
[R/dEploidTools.R:11:5:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L11) *style:* **Use <-, not =, for assignment.**
```r
    excludeFileName = ""
                    ^
```
[R/dEploidTools.R:12:5:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L12) *style:* **Use <-, not =, for assignment.**
```r
    dEploidPrefix = ""
                  ^
```
[R/dEploidTools.R:13:5:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L13) *style:* **Use <-, not =, for assignment.**
```r
    excludeBool = FALSE
                ^
```
[R/dEploidTools.R:15:11:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L33) *style:* **Use <-, not =, for assignment.**
```r
            excludeBool = TRUE
                        ^
```
[R/dEploidTools.R:34:19:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L82) *style:* **Variable and function names should be all lowercase.**
```r
    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~
```
[R/dEploidTools.R:83:17:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:83:17:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L83) *warning:* **no visible global function definition for ‘extractCoverageFromVcf’**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:83:48:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~
```
[R/dEploidTools.R:85:17:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L155) *style:* **Use <-, not =, for assignment.**
```r
    skipNum = 0
            ^
```
[R/dEploidTools.R:156:10:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L205) *style:* **Variable and function names should be all lowercase.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~
```
[R/dEploidTools.R:205:41:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/R/dEploidTools.R#L205) *style:* **Put spaces around all infix operators.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~
```
[R/dEploidTools.R:210:11:](https://github.com/mcveanlab/DEploid-r/blob/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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/01060c85711b19771c1dc160b16ea3530257c392/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)
                                       ~^~
```


Нет, отвратительнейшее форматирование.


It means that if any of the ref updates fails, the whole thing fails. In practice, it means that if master has changed and the push fails, don't delete the PR branch.

Although this situation actually happened to me this morning and GitHub deleted the PR branch anyway 😱


I dont understand this change. Seems backwards.

This RE will match if snapshots should be destroyed for a task.
Say you have one task for "tank" and it is recursive, final RE will be: ^((tank)@|()[@/])
So a snapshot named tank/foo@auto-whatever will not match and will not be destroyed.


Сделай лучше


fast-forwarding riak_ts-develop to borshop-integration-1496-jbg-feature-ts-where-is-null = e5f179e3


sgGiveaway.Copies = int.Parse(price.InnerText.Replace(",", "").Replace(" Copies)", "").Split('(')[1]).Replace(",", "").Replace(" Copies)", "").Split('(')[1]).Replace(",", "").Replace(" Copies)", "").Split('(')[1]).Replace(",", "").Replace(" Copies)", "").Split('(')[1]);


That's a bit dangerous. mkdir could fail and thus, rm all files in current dir.


Очень смешно


No, because they are chained with &&
So should mkdir fail, the remaining is not executed.

At least, thats my understanding of it.

@bigzaymetheceo can confirm


Done


Точка под точкой в правой части выражения и будет ок.


Actually, `bulk_add_subscriptions` and `bulk_remove_subscriptions` do take Iterables; the problem here isn't that.

The issue mypy flagged here is that the `subscribers` variable on line 284 is a different type depending on which code path has been followed, which is confusing and creates risk of future bugs.


That change was unintentional.  I was trying to get recursive tasks first in the list and didn't see the ^.  It should have been backed out.


Хотя. я подумал, у меня  в предыдущий раз было 8 итераций :(. В общем, не получилось. :(, зато читабельно стало)


Review again @lalchandmali


Ну пиши тут


one of the reason that the version jumped numbers was that most of the action items that were planned to be developed until December was developed and released earlier.

Hope it make sense. :)


Dude, more updates to your repo!


os_2_0_develop (macumber) - x86_64-MacOS-10.10-clang: Build Failed

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Ops, **my fault!!!** The list is protected by a ``synchronized (zks.outstandingChanges) {`` at line 631-634 (few lines above). Excuse me.


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How can i install ruby on ubuntu ? I keep getting erros with dependencies


@leeight Ahh, yes. I left out a few files for which it would required anything more than a simply `eslint --fix`. I think these two files either raised Flow errors or weren't already requiring `React`. Thanks for pointing them out, though!


Задачи оптимизации мы пока не ставили, а вот читабельность для нас сейчас крайне важна. Боюсь, тут она не сильно выше, чем в прошлой версии)


wow, how did you commit from the future?


@jmesa-sistel that seems to be this VSCode related issue instead https://github.com/angular/angular-cli/issues/2453#issuecomment-252833890


`listFilesFunction` isn't being used


What settings were you using to get the above log?  I think it is supposed to work at either location but I'll try the symlink method when I have some time to tinker.


I think it makes more sense to put stuff like this in your global git ignore. Otherwise we'll soon have this file polluted by a ton of files created by/for development tools.

Put this in your `~/.gitconfig`
```
[core]
    excludesfile = ~/.gitignore
```
Now, you can add arbitrary stuff in your `~/.gitignore`.


It's better to use English whenever possible


Okay, sorry. I thought you get notified on every commit in this rep.


[EN message] Small changes, added credentials include, added STA/AP mode switch.


shouldn't this be `empty($cat)`? now this would be always set.


Я поправил в следующем коммите.


I don't think there's any reason to give this function a capitalized name.


[EN message] Changed millis -> micros (silly mistake), some logging amended.


TeamCity Chorus :: chorus-win32-master Continuous [Build 2.6.279.d475f2bf8839ccbb75f187127965b976a88563e9](http://build.palaso.org/viewLog.html?buildId=77927&buildTypeId=bt2) outcome was **SUCCESS**
Summary: Tests passed: 949, ignored: 50 Build time: 00:28:30


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There are two require functions on lines 6 and 8 that should be changed. I will make another pull request to eliminate need for them.


@chengguoqiang @taylorotwell This change broke my tests.

I am POSTing an array of images with field name `files[]`, like `files[$file1, $file2]`. Specifically I am trying to validate that at least one image was POSTed.

These request validation rules worked fine in 5.3.16:

```php
public function rules(): array
{
    return [
        'files' => 'required|array',
        'files.*' => 'file|image',
    ];
}
```

With the changes in this commit, the validation now stops at `files => required`, since the field does not exist anymore. Not sure if this was intended?


Is there a specific reason not to spell it correctly i.e. `IDD_PREFERENCE_HIGHLIGHT_BOX`?


@oliviertassinari Will this be released with v0.16.1?


test


This should be `kz_json:set_value([Node, <<"default_timezone">>]`.

This issue was also present in my version. Noticed just now when testing your update.


This commit appears to have broken my automation configuration entirely. I reverted back to the commit prior to confirm. I'm including the automation yaml documents in **!include_dir_list automation** format. I suspect this has something to do with the problem, thought I have not yet had time to run through additional troubleshooting. All I have been able to confirm at this time is this commit specifically causes a total failure to start of the HaSS service.


Hi @tobibeer so you're saying that you'd like a separate minimum search string length for the title search and the body search? I'm not convinced that it is worth not only the extra implementation complexity but also the complexification of the user interface itself.

> `$:/config/Search/MinLength/plugin-foo/field-bar`

I'm confused by this example. The minlength hack is only really useful in the particular case of a search string, surely?


Possible to make this a PR back to https://github.com/paulosuzart/sdkman ?  The parametrized URL for wget is great, and also I'd recommend setting the default $sdkman_url to "https://get.sdkman.io" .


sortedBy() and indexOf() create unnecessary complexity. You can find the operator with the lowest precedence using a single linear scan with index.


hmmm Let me try to regenerate and get back to you.


Remove this


Not sure about the `.assignNoPrototype()` here. You'll lose the prototype for all children of the polyadic expression; don't think this is a good idea.


Final Commit


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background_Color change to backgroundColor


A switch on `operatorType` would be more efficient and error-proof than a string switch.


@Hexik, good luck :+1:


I would add a test to ensure that we don't lose comments in the middle of a polyadic expression.


- Statistics such as the number of installs
  - 43 installs lost -- from packagist.org/packages/u01jmg3/ics-parser -- by swapping back


Got it, I'm working on the drag-drop.
Thank you!

On Fri, Oct 14, 2016 at 11:30 AM, caok2709 <notifications@github.com> wrote:

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amazing !


Thanks all for the clarifications.

On Wed, Oct 12, 2016 at 5:21 AM, Titus von der Malsburg <
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Also, changed win conditions to those asked for by project guidelines. You now win by uncovering all empty cells without touching a bomb.


I think this will produce incorrect results if the left element in a binary expression is a complex expression like `a * b`. In this case parentheses would be required for correct conversion, and you don't add them.


TestPlan our task


`!x.any` is better written as `x.none`


sorry for the slow response, I just got a chance to look at your notebook. You are right about calling quadphase twice the way you have it now. why not just replace the lens_phasor term with your aberration?
Maybe it would help if you can explain a little more what you think your class is going to do differently?


Hello, you must update flash template to version 11.2.202.637


Could you please point me to the part of the guideline which says that jira reference should be removed from license file changes? Sorry I couldn't find it.

On the other hand I guess since rewriting would already affect another commit (couldn't catch this mistake early) we have to live with it.


This issue has several duplicates; it's worth looking at the duplicates and including the examples from them as test cases.


Error when no params is present (which happens whenever someone resets or first goes to admin/orders)
![image](https://cloud.githubusercontent.com/assets/7496190/19395621/5d17b86a-91f3-11e6-88ba-91e85e3c685a.png)

Also even when params are present, search_form_for still doesn't repopulate form fields by reading from params:
https://github.com/mancrates/titan/pull/155#issuecomment-253091236

I started an /mancrates branch to try to fix it:
https://github.com/mancrates/ransack
....but I wasn't having luck getting my local to actually the patched gem, and my local is broken because of Sierra OS so I can't nuke my gemsets. I'm putting a ticket in the backlog and I'm not going to include patching ransack on this PR.


The control knobs are unfortunately not perfect. However, they can be double-clicked on to bring up a dialog which allows for keyboard input. For the first integration, I would recommend using an integer knob (should be fine to only allow multiples of a single USD/EUR/whatever) and simply set the upper bound to Integer.MAX_VALUE (which should also be enough).


Маленькое приложение - html хватает, учитывая, что тут одна страница.


You even added a new symbol! That's great! +1


@obaid I added `hasAttachments` function to check attachments is empty or not.
In [7964d54](https://github.com/CasperLaiTW/laravel-fb-messenger/blob/7964d54546b5ab6ebf379705ed9f47fc352c6033/src/Messages/ReceiveMessage.php#L68), attachments is mixed(array or bool).


Yeah, it would be great to do it this week-end.


memory wise it is best to define the variables in the first part of a for loop


You'll see in a later commit that I've gone with the roots going down analogy now...


test file: http://pasteall.org/blend/index.php?id=43954


Nice one love the save code 👍


yes for easy use with json api in lua scripts

I have tried to do it with lua and json.lua but I don't know why, it's hanging
`-- get group/scene idx
function groupIdx(device)
	local getallgroups = assert(io.popen(curl..'"'..domoticzURL..'/json.htm?type=scenes"'))
	local readallgroups = getallgroups:read('*all')
	getallgroups:close()
	alldecoded = json:decode(readallgroups)
	allgroups = alldecoded.result
	for n, group in pairs(allgroups) do
		if (group.Name == device) then
			return group.idx
		end
	end
end

-- switch On a group or scene
function groupOn(device)
	local idx = groupIdx(device)
	os.execute(curl..'"'..domoticzURL..'/json.htm?type=command&param=switchscene&idx='..idx..'&switchcmd=On" &')
end

-- switch Off a group
function groupOff(device)
	local idx = groupIdx(device)
	os.execute(curl..'"'..domoticzURL..'/json.htm?type=command&param=switchscene&idx='..idx..'&switchcmd=Off" &')
end
`
then I could use in lua script groupOn('myGroup') instead of commandArray['Group:myGroup']
the goal of this is reduce delay in action
that's perfect working for switchs with otherdevices_idx

sorry for my english again, I hope you understand me better now


@ObaniGemini Go for it :smile:


Instead of exposing the raw bucket during initialization, I would prefer an extensible options object that is passed into the open function.


any workaround you can think of? can we just skip it altogether? or create a new id_rsa key instead of using the one you have added below?


Single variable name.


variable names


unnecessary parentheses


ok, this is good sample


Using `0` as `root` user, this will always work and it will **always** be root anyway.


"""Oh"""


wow did i just commit the .exe


needs to cut these lines


> how to add style


## good ##


WARNING: This commit was written as part of a conversation and just with illustrating purposes. It isn't stable and raised a few problems with the managed entities, as duplicating them when disabling and enabling CiviRules multiple times. It shouldn't be sent as pull request or used in production.


# Add


Where is this variable `grade` coming from?


If you're going to go through all the trouble of providing your own message for a ValueError, make it descriptive of the actual process. Here you're trying to remove a teacher. The message should be something along the lines of "The teacher you are trying to remove does not exist at the given grade level"


s/add/adds


Thanks Ben for the update. I really appreciate the work you are doing. I don't mean to press, but do you have any sense for timeline? This week? This month?


You could modify that `before_install` line to say:

```
test -z "$DEPLOY_DOCS" || openssl aes-256-cbc -K $encrypted_6460fd32304f_key -iv $encrypted_6460fd32304f_iv
```

This way -- it will only attempt to run that code IF we are going to deploy docs (which should never happen on a fork branch anyhow). I think that's the best solution =D


* 36 行改为“生成起步包”比较好，和下文呼应
* 40 行开头改为“打开”或者“启动”比较合理吧？起步编辑器感觉不是很符合逻辑
* 89-90 行的代码应该是首字母大写比较合理，现在最新版的 Atom 的命令都长这个样子（打开看看就清楚了），这篇教程是作者去年写的了
* 204 行“软件包可以用时加载”好像有点语病啊。而且作者前面假设了读者都会一点前端的（教程须知），这里用“懒加载”才是比较恰当的
* 378 行愿意指的时 `return {}` 这条语句无法实现，而不是返回文本无法实现，但我在这里貌似用“返回体”也很难看懂
* 711 行貌似我们通常不会说“分叉”吧，开发者惯例都是直接“fork”

还有就是，这篇选题有很多细节的样式和原文是不一样，我后来参照了原文重新改了一遍样式的，不知道应该用哪个样式好。

@wxy


The


Shutdown hooks and unterminated daemon threads result in a classloader leak when redeploying web applications.


s/only/following/
s/tracked are/are tracked/


s/code/code,/


TODO: Add command to show how to run the tests!


YAY! Documentation! 📝 🎊


Can you describe your experiments with Begin/endScene ?


UPDATE spell_affect SET SpellFamilyMask=0x0000000000200000 WHERE effectId = 1 AND entry=16266;


also twice under `test/` https://github.com/JuliaLang/Iterators.jl/search?utf8=%E2%9C%93&q=compat


@themsaid A slight variation of the `testMultipleFileUploads` test above could probably test this:

```php
public function testValidationFailsWhenRequiredFilesAreMissing()
{
    $trans = $this->getIlluminateArrayTranslator();
    $v = new Validator(
        $trans,
        ['files' => []],
        [
            'files' => 'required|array', // should fail here
            'files.*' => 'file' // should be ignored
        ]
    );
    $this->assertFalse($v->passes());
}
```

From the `testMultipleFileUploads` method in the commit above: I doubt the required rule has any effect here, other than checking for empty values:

```php
$v = new Validator($trans, ['file' => [$file, $file2]], ['file.*' => 'Required|mimes:xls']);
```


this chunk and others in this file belong to the previous commit, instead of the documentation commit.


I haven't experimented with it. Just wondered about msdn. Looks like no draw calls are possible after endscene, allowing some optimizations.


@kolovsky setup your GIT properly ;)


Awesome! 👍


double empty line


@tnabtaf We can remove this workaround style and just use regular styling and h1.  I had autotoc ignoring h1s already -- it only selects for h2, h3, h4 per https://github.com/dannon/galaxy-site/blob/master/build.coffee#L49.


r+


#1 Added label


@evilaliv3 You took out the display of the file errors. Come on!!


The answers to the following questions `are` either missing or invalid.


I've seen an nvidia dev presentation saying that some games do not respect it (some do not even call beginScene and endScene at all).
In theory you are not allowed to do some operations like StretchRect inside beginScene and endScene


saw approval from jedmccaleb
at https://github.com/vogel/stellar-core/commit/c9a19c00361d7372e9fdead7af1bb1055ea11e83


merging vogel/stellar-core/fix-delete-non-existing-offer = c9a19c00 into auto


vogel/stellar-core/fix-delete-non-existing-offer = c9a19c00 merged ok, testing candidate = 8ee9ba8f


Couldn't you do:
```python
for teacher in list_teachers:
    dict_grade_teacher[teacher.grade_level].append(teacher)
```


@jatows  или в левое меню, или на странице как раньше. + Открепляемая шапка в планах чтоб показывалась при  скролле вверх.


@tkelman now removed from runtests.

Perf is a legacy performance benchmark suite and is not run as part of tests. I'll be completely replacing it for 1.0 but I didn't want to delete it until that happened.


`s/* / */`


The list of students would never be `None`. An empty list is a falsey value, as is `None`, but neither of them are actually equal to False or each other.


So, generate Markdown H1's instead of <div class="title">?  I can do that easily.


-
user research
-
 3 research method

-
 Online survey

-


Don't you have a function for calculating GPAs?


Well... we are planning to integrate dzVents with Domotics and then you get all this for free.

/me looks at Giz....


:+1: :+1: :+1: :+1: :+1:

I've been waiting for this. Rebuild a cache into a second database, then atomically swap it into production. Love it.


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`self.students` will never be `None`


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Comment added from mobile application


I think we should build it into the metadata, and display it on the page via the template.  How about that?


Relevant code snipet
https://github.com/CyanogenMod/android_hardware_qcom_keymaster/blob/cm-13.0/keymaster_qcom.cpp

    ALOGD("keymaster app got loaded at attempt number %d", attempt_num);
    ret = (*km_handle->QSEECom_start_app)((struct QSEECom_handle **)&km_handle->qseecom,
                        "/vendor/firmware/keymaster", "keymaster", KM_SB_LENGTH);
    if(ret)
        ret = (*km_handle->QSEECom_start_app)((struct QSEECom_handle **)&km_handle->qseecom,
                        "/firmware/image", "keymaste", KM_SB_LENGTH);
    if (ret) {
        ALOGE("Loading keymaster app failed");
        free(km_handle);
        return -1;
    }

My reading of this would be that either location, with the correct naming scheme should work.


You could get unique grades by using a `set`


Сегодня будет фикс


With kernel 4.8 I had to resort to this "activate-governors" script to force-load the governors at boot time.Otherwise only one governor would show in the cpufreq applet:

```
#!/bin/sh
# -*- mode: shell-script; indent-tabs-mode: nil; sh-basic-offset: 4; -*-
# ex: ts=8 sw=4 sts=4 et filetype=sh

modprobe cpufreq_ondemand
modprobe cpufreq_conservative
modprobe cpufreq_userspace
modprobe cpufreq_powersave
#echo userspace > /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor
echo ondemand > /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor

exit 0
```
I've got it installed in /usr/bin along with a systemd unit to fire it up.

```
[Unit]
Description=startup routine for linux 4.7 and later governors

[Service]
ExecStart=/usr/bin/activate-governors
```

The governors would usually load if Ubuntu's indicator-cpufreq was started, and could then be used from mate's cpufreq applet but were not loaded at boot. This was the clue telling me to write the script.
It works in all of my AMD machines plus an Intel Atom netbook but I suspect this is the old governors still being available rather than the new ones. I don't know a whole lot about the kernel CPU governors though


What's so embarrassing about this code? Looks fine to me...


ah you just do that here.


Justo metí yo eso en la pull 😋  jajajajaj. Arreglé otras cosas lo miras porfa 😉


Tin liên quan


Но ведь время существования этой копии очень невелико (т.к. маленькая область видимости - тело функции). По крайней мере такое поведение помню по C#. Или в C++ она висит в памяти до завершения программы?


Couple things. Again, you have a function for calculating GPAs already. Second, you could just build up a dictionary of lists of grades, then apply your `calc_avg_gpa` function to every list in that dict. A lot simpler than passing around values here.


Sounds good, thanks for the feedback!


I wouldn't blame `pyserial` too fast. What I believe is happening is that `write()` returns immediately because there are enough byte available in the transmit buffer of the serial driver (i.e. in the computer) to allow for another `write()` call to happen right away.

We have two options:

1. wait for the worst case
2. have the mote send an ACK

Obviously, option 2 is the right one, but option 1 is faster to implement. In any case, we will have to implement option 2, but you might implement option 1 as a temporary work-around while creating a separate issue to implement option 2.


@dpgeorge : FYI


Right now the code generates both a title: element in the YAML and a div title in the page.  It would be easy to suppress the div title entirely.

(But, right now, the code also puts Markdown in the YAML title element, so that still needs fixing.)


If you're just returning the `results` dict no matter what, what's the point of your `if self.teachers != None:` block?


Или вы имеете ввиду процессорные затраты на её создание (используется инструкция копирования)? Так ведь они ничтожны. А читаемость, на мой взгляд, несколько лучше.


Awesome @JimWatV1


I'll drop the generation of the title text in the page text.


So not actually merged?


@udeved: this commit broke **mt-0.13.x**. I've restored the old **manjaro-efi-shell** now. People still use the old branch. Also there is no conflict with **manjaro-efi-utils** at all.


Hello,
I follow your coding but unable to fetch loan.csv file. Would you please help me in this matter?


```
rails new myAPIName --api -d postgresql
rails g scaffold modelName attributeName:dataType
```
then add seed data


I don't know what that means, but this was reverted because it spams endless presence notifications to anyone on a "federated" channel.


I like that you pulled out the lambda function here. Nice job!


An empty directory is better than no directory.


(so, more concretely, something like this should replace it: https://github.com/dannon/galaxy-site/commit/2893948a11d553751402d6734245c69dcbc7b987)


I'm not really sure how I managed to make a branch, commit to both it and the master, and then commit them both. Just ignore this whole mess. Its not worth the work to get rid of.


Allow for cross origin resource sharing. Add the rack cors gem. Bundle install. Copy and paste the code into application.rb. Should have included methods for update and delete from the start but ended up doing that in a later commit when I realized I missed that.


Wait, you're not talking about editing the conversion again, right?  We can't touch that again.


My guess is that your Neovim is outdated. The change that `haslocaldir()` takes 2 arguments was made 5 months ago, which is very long in Neovim time. ;-)

If if you don't use master, upgrading Neovim to its latest release 0.1.5 will make this work.


Хм, даже не подумал об использовании std::multimap (слышал только о std::unordered_map вариации std::map). Кажется, я вас понял. Код чуть позже обновлю.
Под циклом сортировки вы имели в виду последний цикл? Просто там сортировки как таковой не происходит, только поиск максимального значения.


Should include update and delete from the start so you don't need to figure out your error later.


Huh I thought I tested that, sorry. So the state of talk presence is still
"anyone who joins stays joined forever", yes?

On Friday, 14 October 2016, Raymond Pasco <notifications@github.com> wrote:

> I don't know what that means, but this was reverted because it spams
> endless presence notifications to anyone on a "federated" channel.
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/urbit/arvo/commit/5e3b34de7672c5a4c1a6faad56c4b00403c460fd#commitcomment-19432040>,
> or mute the thread
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Nice @pratibhamansinghka  - I just came back from travel and was about to start on this, and you have done it. Please get the PR done quickly as well.


please consider this message is not suitable since the file is already created, this commit is made for basic configuration changes, you can see it by comparing files


Script sql3


I'd say that under ["omit needless words"](https://swift.org/documentation/api-design-guidelines/#omit-needless-words) we can get rid of the `request:` label:

```swift
APIClient().perform(signInRequest)
```


@tbodt, i'll take that as a compliment. But it's missing any form of documentation. I've updated the article with a better example, regardless. Check now and be horrified 😄


I believe so.


Bekomme:

Notice: Use of undefined constant __DIR - assumed '__DIR' in /volume1/web/game/opensoccer/einstellungen.php on line 6 Warning: require_once(__DIR/controller/teamController.php): failed to open stream: No such file or directory in /volume1/web/game/opensoccer/einstellungen.php on line 6 Fatal error: require_once(): Failed opening required '__DIR/controller/teamController.php' (include_path='.') in /volume1/web/game/opensoccer/einstellungen.php on line 6


What's the reason for changing the import from the global identifier to a local identifier?
Just looking at [Hugo](https://github.com/spf13/hugo/blob/master/commands/hugo.go) I think you are supposed to use the global identifier.


Fehler in Zeile 6

muss heißen: `require_once(__DIR__.'/controller/teamController.php');`


Test failed.
Output:
```
Welcome to OpenCV 3.1.0
java.io.IOException: Unable to invoke main method
        at org.kneelawk.helloopencv.CPControl3.launch(CPControl3.java:139)
        at org.kneelawk.helloopencv.HelloOpenCVLaunch.main(HelloOpenCVLaunch.java:34)
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.kneelawk.helloopencv.CPControl3.launch(CPControl3.java:125)
        ... 1 more
Caused by: java.lang.UnsatisfiedLinkError: org.opencv.core.Mat.n_Mat(IIIDDDD)J
        at org.opencv.core.Mat.n_Mat(Native Method)
        at org.opencv.core.Mat.<init>(Mat.java:63)
        at org.kneelawk.helloopencv.HelloOpenCV.main(HelloOpenCV.java:11)
        ... 6 more
```


@Salaboy do we need this?


adding info


Got it, so I should use pagetitle instead of title.

And yes, I an talking about editing the conversion scripts.  What I won't do is a wholesale copy of pages.  It just strikes me that for many pages it will be easier (and less error-prone) to copy a bug-free version instead of manual edits.

I'll submit a PR with a few updated pages today to give you an idea of what that will look like.  I've been finding lots of bugs in my generated code.


NB: was $(bindir)


> I'm not convinced that it is worth not only the extra implementation complexity but also the complexification of the user interface itself.

Especially for title prefixes it is **crucial** (for me) to be able to search by one character. However, I do not want this to force me to enable full text search for a single character.

>> $:/config/Search/MinLength/plugin-foo/field-bar

> I'm confused by this example. The minlength hack is only really useful in the particular case of a search string, surely?

The example related to a plugin availing a custom search tab where appropriate, e.g. in the sidebar or in advanced search.


@psiroky can you give me what exactly version of shrinkwrap? and.. what would be the possibility to have ip-bom updated to swarm version of shrinkwrap?


Notice how the previous .kinvey file had combined the metadata from the BL CLI and DLC-CLI. This will work and let you deploy legacy BL side by side with KMR


all tests pass:
success: https://travis-ci.org/stellar/stellar-core/builds/167709199


Actually, ideally we just use title, which is already used elsewhere -- I just picked pagetitle because I saw it already applied to pages in question.

I'm skeptical wrt; rerunning and copying in changed pages, but approach it however you want :)  I did not have luck with that, it was far easier for me to write extra code to iterate over the existing corpus.


![](https://github.trello.services/images/mini-trello-icon.png) [Content-ul e prea wide](https://trello.com/c/xIqGpoFm/10-content-ul-e-prea-wide)


This thing is amazing.


Thank you @nmccready 😄


TaskCluster: @escapewindow does not have permission to trigger tasks.


OK, I'll stick with title.


fast-forwarding next-db-and-proto to auto = 8ee9ba8f


Did you connect to MySQL directly. I'd recommend doing this to ensure you know what you're connecting to. Additionally this is important for your ability to troubleshoot when on site with the team you're training.


Remove all but one of these. You can keep one to explain the idea and why we do this, otherwise the SDK will do this for you.


Cool.  I went ahead and swapped pagetitle->title for existing files (which should merge cleanly with any other changes you make).


Query the actual database and return. Also support:
- onGetById
- onGetCount
- onInsert
Bonus points for
- onUpdate
- onDeleteById


It would be cool to have this commit included in a new 3.1.6 release and NuGet package.


Thanks!


Hello, I just cloned gpac and tried to compile mp4box and it failed. It looks like there is a problem with the ifndef GPAC_DISABLE_3D (when not defined) block removing the declaration of nb_views,nb_layers and nb_frames. They are used directly below  outside of the ifdef block.  (in lines 1030 - 1044). Just thought thought that I should mention this since you just changed the file right before I cloned it!.
thanks


Looks like you need a backslashed quote between the /bin/www and the final quote on line 9.


Great I will do it - thanks for the help! :)


OMG the documentation!


OMG YOU'RE AWESOME VARUN!!!


@nairdo Did this get into the hotfix migration (v6.1) also?


@wesleycoder , você tem alguma sugestão de como posso abstrair isso? A lógica que foi aplicada foi:

- Model: carrega as informações base (atributos e alguns métodos específicos)
- Controller: carrega os elementos e as ações mais generalizadas
- View: render do HTML

Em outra lógica, como ficaria?


Ich wollte auch gerade eine PR erstellen. :-)


@cclaessens Tuning the DDC frequency will now return the actual center of the 100MHz wide digital channel as discussed.


Да, что то я тут пропустил это отсечение значения после запятой. Ну тогда вот
`(int)double.Parse(param, CultureInfo.InvariantCulture)`
Просто поясню, Replace - это из разряда регулярных выражений, которые не очень хорошо использовать.


Meant to write something but I pressed enter and it just sent ^^.
I will try to push myself into doing this more in the future.Right now I just wanted to commit a fix I have done three times over now due to my new notebook screwing up and me loosing the files.At least it's finally safe now :P.There's also some jumping attack work which I started last week but hit a wall with, which is part of the reason I didn't commit anything in such a long time.


![](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)


Whats happening so far: We're importing angular, ui router, and angular resource. We aren't using the latter yet. The body tag's attribute is our entry point to our app: it points to our tunr module which is defined in script.js. That module is injected with ui router which is configured with stateprovider. state providers callback function defines a state called artistIndex which uses a template found in js/artists/index.html whenever we go to (localhost8080)/#/artists. The ui-view directive in index.html shows where the template should go.


Почему "не очень хорошо использовать"?


@Jermolene, most importantly, I think it needs to be implemented in:

$:/core/ui/DefaultSearchResultList

...and I would actually split it the results in three lists:

# title matches
# text matches
# tag matches

whereas I would not constrain both title or tag matches by default, but only text matches.


I don't think we can actually just swap these. What happens when we try to compose the composite with another composite?


For store inbox or depot inbox?


> Back to fist grade then :D :-P
*first :laughing:


`block in <main>': undefined method `first' for nil:NilClass (NoMethodError)


В чем проблема баллонов?