[.DEploid/utilities/dEploidTools.r:1:22:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                     ^
```
[.DEploid/utilities/dEploidTools.r:1:28:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                           ^
```
[.DEploid/utilities/dEploidTools.r:2:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L2) *style:* **Variable and function names should be all lowercase.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:2:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L2) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:2:48:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L2) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
                                               ^
```
[.DEploid/utilities/dEploidTools.r:3:15:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L3) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i+1
              ^
```
[.DEploid/utilities/dEploidTools.r:3:22:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L3) *style:* **Put spaces around all infix operators.**
```r
        arg_i = arg_i+1
                    ~^~
```
[.DEploid/utilities/dEploidTools.r:6:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L6) *style:* **Variable and function names should be all lowercase.**
```r
    outPrefix = "dataExplore"
    ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:6:15:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L6) *style:* **Use <-, not =, for assignment.**
```r
    outPrefix = "dataExplore"
              ^
```
[.DEploid/utilities/dEploidTools.r:7:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L7) *style:* **Variable and function names should be all lowercase.**
```r
    vcfFileName = ""
    ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:7:17:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L7) *style:* **Use <-, not =, for assignment.**
```r
    vcfFileName = ""
                ^
```
[.DEploid/utilities/dEploidTools.r:8:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L8) *style:* **Variable and function names should be all lowercase.**
```r
    refFileName = ""
    ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:8:17:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L8) *style:* **Use <-, not =, for assignment.**
```r
    refFileName = ""
                ^
```
[.DEploid/utilities/dEploidTools.r:9:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L9) *style:* **Variable and function names should be all lowercase.**
```r
    altFileName = ""
    ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:9:17:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L9) *style:* **Use <-, not =, for assignment.**
```r
    altFileName = ""
                ^
```
[.DEploid/utilities/dEploidTools.r:10:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L10) *style:* **Variable and function names should be all lowercase.**
```r
    plafFileName = ""
    ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:10:18:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L10) *style:* **Use <-, not =, for assignment.**
```r
    plafFileName = ""
                 ^
```
[.DEploid/utilities/dEploidTools.r:11:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L11) *style:* **Variable and function names should be all lowercase.**
```r
    excludeFileName = ""
    ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:11:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L11) *style:* **Use <-, not =, for assignment.**
```r
    excludeFileName = ""
                    ^
```
[.DEploid/utilities/dEploidTools.r:12:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L12) *style:* **Variable and function names should be all lowercase.**
```r
    dEploidPrefix = ""
    ^~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:12:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L12) *style:* **Use <-, not =, for assignment.**
```r
    dEploidPrefix = ""
                  ^
```
[.DEploid/utilities/dEploidTools.r:13:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L13) *style:* **Variable and function names should be all lowercase.**
```r
    excludeBool = FALSE
    ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:13:17:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L13) *style:* **Use <-, not =, for assignment.**
```r
    excludeBool = FALSE
                ^
```
[.DEploid/utilities/dEploidTools.r:15:11:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L15) *style:* **Use <-, not =, for assignment.**
```r
    arg_i = 1
          ^
```
[.DEploid/utilities/dEploidTools.r:16:11:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
          ^
```
[.DEploid/utilities/dEploidTools.r:16:33:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
                                ^
```
[.DEploid/utilities/dEploidTools.r:17:14:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L17) *style:* **Use <-, not =, for assignment.**
```r
        argv = args[arg_i]
             ^
```
[.DEploid/utilities/dEploidTools.r:18:12:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
           ^
```
[.DEploid/utilities/dEploidTools.r:18:28:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
                           ^
```
[.DEploid/utilities/dEploidTools.r:19:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L19) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:19:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L19) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:19:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L19) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:19:52:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:20:13:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L20) *style:* **Variable and function names should be all lowercase.**
```r
            vcfFileName = args[arg_i]
            ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:20:25:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L20) *style:* **Use <-, not =, for assignment.**
```r
            vcfFileName = args[arg_i]
                        ^
```
[.DEploid/utilities/dEploidTools.r:21:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:21:36:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                                   ^
```
[.DEploid/utilities/dEploidTools.r:22:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L22) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:22:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L22) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:22:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L22) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:22:52:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:23:13:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L23) *style:* **Variable and function names should be all lowercase.**
```r
            plafFileName = args[arg_i]
            ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:23:26:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L23) *style:* **Use <-, not =, for assignment.**
```r
            plafFileName = args[arg_i]
                         ^
```
[.DEploid/utilities/dEploidTools.r:24:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:24:35:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                                  ^
```
[.DEploid/utilities/dEploidTools.r:25:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L25) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:25:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L25) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:25:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L25) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:25:52:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:26:13:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L26) *style:* **Variable and function names should be all lowercase.**
```r
            refFileName = args[arg_i]
            ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:26:25:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L26) *style:* **Use <-, not =, for assignment.**
```r
            refFileName = args[arg_i]
                        ^
```
[.DEploid/utilities/dEploidTools.r:27:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:27:35:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                                  ^
```
[.DEploid/utilities/dEploidTools.r:28:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L28) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:28:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L28) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:28:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L28) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:28:52:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L28) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:29:13:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L29) *style:* **Variable and function names should be all lowercase.**
```r
            altFileName = args[arg_i]
            ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:29:25:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L29) *style:* **Use <-, not =, for assignment.**
```r
            altFileName = args[arg_i]
                        ^
```
[.DEploid/utilities/dEploidTools.r:30:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:30:39:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                                      ^
```
[.DEploid/utilities/dEploidTools.r:31:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L31) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:31:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L31) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:31:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L31) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:31:52:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L31) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:32:13:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L32) *style:* **Variable and function names should be all lowercase.**
```r
            excludeFileName = args[arg_i]
            ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:32:29:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L32) *style:* **Use <-, not =, for assignment.**
```r
            excludeFileName = args[arg_i]
                            ^
```
[.DEploid/utilities/dEploidTools.r:33:13:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L33) *style:* **Variable and function names should be all lowercase.**
```r
            excludeBool = TRUE
            ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:33:25:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L33) *style:* **Use <-, not =, for assignment.**
```r
            excludeBool = TRUE
                        ^
```
[.DEploid/utilities/dEploidTools.r:34:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:34:33:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                                ^
```
[.DEploid/utilities/dEploidTools.r:35:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L35) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:35:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L35) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:35:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L35) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:35:52:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:36:13:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L36) *style:* **Variable and function names should be all lowercase.**
```r
            outPrefix = args[arg_i]
            ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:36:23:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L36) *style:* **Use <-, not =, for assignment.**
```r
            outPrefix = args[arg_i]
                      ^
```
[.DEploid/utilities/dEploidTools.r:37:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                  ^
```
[.DEploid/utilities/dEploidTools.r:37:40:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                                       ^
```
[.DEploid/utilities/dEploidTools.r:38:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L38) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[.DEploid/utilities/dEploidTools.r:38:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L38) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:38:21:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L38) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:38:52:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[.DEploid/utilities/dEploidTools.r:39:13:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L39) *style:* **Variable and function names should be all lowercase.**
```r
            dEploidPrefix = args[arg_i]
            ^~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:39:27:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L39) *style:* **Use <-, not =, for assignment.**
```r
            dEploidPrefix = args[arg_i]
                          ^
```
[.DEploid/utilities/dEploidTools.r:44:15:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L44) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i + 1
              ^
```
[.DEploid/utilities/dEploidTools.r:51:8:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
       ^
```
[.DEploid/utilities/dEploidTools.r:51:10:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L51) *style:* **Variable and function names should be all lowercase.**
```r
    if ( plafFileName == "" ){
         ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:51:28:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
                           ^
```
[.DEploid/utilities/dEploidTools.r:58:12:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
           ^
```
[.DEploid/utilities/dEploidTools.r:58:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
                  ^
```
[.DEploid/utilities/dEploidTools.r:58:35:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L58) *style:* **Variable and function names should be all lowercase.**
```r
    return ( list ( vcfFileName = vcfFileName,
                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:59:35:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L59) *style:* **Variable and function names should be all lowercase.**
```r
                    refFileName = refFileName,
                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:60:35:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L60) *style:* **Variable and function names should be all lowercase.**
```r
                    altFileName = altFileName,
                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:61:36:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L61) *style:* **Variable and function names should be all lowercase.**
```r
                    plafFileName = plafFileName,
                                   ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:62:33:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L62) *style:* **Variable and function names should be all lowercase.**
```r
                    outPrefix = outPrefix,
                                ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:63:37:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L63) *style:* **Variable and function names should be all lowercase.**
```r
                    dEploidPrefix = dEploidPrefix,
                                    ^~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:64:39:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L64) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeFileName = excludeFileName,
                                      ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:65:35:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L65) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeBool = excludeBool) )
                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:65:47:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L65) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    excludeBool = excludeBool) )
                                              ^
```
[.DEploid/utilities/dEploidTools.r:69:1:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L69) *style:* **Variable and function names should be all lowercase.**
```r
fun.dEploidPrefix <- function ( prefix ){
^~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:81:1:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L81) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.coverage <- function ( inputs ){
^~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:82:17:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L82) *style:* **Variable and function names should be all lowercase.**
```r
    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:17:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:17:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L83) *warning:* **no visible global function definition for ‘extractCoverageFromVcf’**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:48:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:17:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:17:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L85) *warning:* **no visible global function definition for ‘extractCoverageFromTxt’**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:48:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                               ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:68:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                                                   ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:109:1:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:109:38:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:109:51:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:110:9:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L110) *style:* **Use <-, not =, for assignment.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
        ^
```
[.DEploid/utilities/dEploidTools.r:110:22:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L110) *style:* **Variable and function names should be all lowercase.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:111:9:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L111) *style:* **Use <-, not =, for assignment.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
        ^
```
[.DEploid/utilities/dEploidTools.r:111:22:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L111) *style:* **Variable and function names should be all lowercase.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:112:39:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L112) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = ref[,1],
                                      ^
```
[.DEploid/utilities/dEploidTools.r:113:37:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L113) *style:* **Commas should always have a space after.**
```r
                         POS = ref[,2],
                                    ^
```
[.DEploid/utilities/dEploidTools.r:114:42:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L114) *style:* **Commas should always have a space after.**
```r
                         refCount = ref[,3],
                                         ^
```
[.DEploid/utilities/dEploidTools.r:115:42:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L115) *style:* **Commas should always have a space after.**
```r
                         altCount = alt[,3] )
                                         ^
```
[.DEploid/utilities/dEploidTools.r:120:1:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L120) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
^~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:120:34:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                 ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:120:51:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                                  ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:121:10:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L121) *style:* **Variable and function names should be all lowercase.**
```r
    if ( excludeBool ) {
         ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:122:39:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L122) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool,
                                      ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:123:1:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L123) *style:* **lines should not be more than 80 characters.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:123:51:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L123) *style:* **Variable and function names should be all lowercase.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
                                                  ^~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:125:39:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L125) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool ))
                                      ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:147:1:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:147:38:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                     ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:147:47:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                              ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:149:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L149) *style:* **Variable and function names should be all lowercase.**
```r
    catCmd = "cat"
    ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:149:12:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L149) *style:* **Use <-, not =, for assignment.**
```r
    catCmd = "cat"
           ^
```
[.DEploid/utilities/dEploidTools.r:150:1:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L150) *style:* **lines should not be more than 80 characters.**
```r
    if ( grepl("gzip", system(paste("file --mime-type", vcfName), T) ) == TRUE ){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:150:57:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L150) *style:* **Variable and function names should be all lowercase.**
```r
    if ( grepl("gzip", system(paste("file --mime-type", vcfName), T) ) == TRUE ){
                                                        ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:151:9:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L151) *style:* **Variable and function names should be all lowercase.**
```r
        catCmd = "zcat <"
        ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:151:16:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L151) *style:* **Use <-, not =, for assignment.**
```r
        catCmd = "zcat <"
               ^
```
[.DEploid/utilities/dEploidTools.r:154:1:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L154) *style:* **lines should not be more than 80 characters.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:154:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L154) *style:* **Variable and function names should be all lowercase.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
    ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:154:13:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L154) *style:* **Use <-, not =, for assignment.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
            ^
```
[.DEploid/utilities/dEploidTools.r:154:39:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L154) *style:* **Variable and function names should be all lowercase.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
                                      ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:154:47:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L154) *style:* **Variable and function names should be all lowercase.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
                                              ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:154:81:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L154) *style:* **Commented code should be removed.**
```r
    skipNum = as.numeric(system(paste(catCmd, vcfName, " | head -5000 | grep \"##\" | wc -l"), T))
                                                                                ^~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:155:1:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L155) *style:* **lines should not be more than 80 characters.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:155:10:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L155) *style:* **Use <-, not =, for assignment.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
         ^
```
[.DEploid/utilities/dEploidTools.r:155:31:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L155) *style:* **Variable and function names should be all lowercase.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                              ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:155:45:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L155) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                           ~^~
```
[.DEploid/utilities/dEploidTools.r:155:46:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L155) *style:* **Variable and function names should be all lowercase.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                             ^~~~~~~
```
[.DEploid/utilities/dEploidTools.r:155:61:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L155) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                           ~^~
```
[.DEploid/utilities/dEploidTools.r:155:77:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L155) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                           ~^~
```
[.DEploid/utilities/dEploidTools.r:155:119:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L155) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                                ~^~
```
[.DEploid/utilities/dEploidTools.r:157:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L157) *style:* **Variable and function names should be all lowercase.**
```r
    sampleName = names(vcf)[10]
    ^~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:157:16:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L157) *style:* **Use <-, not =, for assignment.**
```r
    sampleName = names(vcf)[10]
               ^
```
[.DEploid/utilities/dEploidTools.r:159:9:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L159) *style:* **Use <-, not =, for assignment.**
```r
    tmp = vcf[[sampleName]]
        ^
```
[.DEploid/utilities/dEploidTools.r:159:16:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L159) *style:* **Variable and function names should be all lowercase.**
```r
    tmp = vcf[[sampleName]]
               ^~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:160:11:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L160) *style:* **Use <-, not =, for assignment.**
```r
    field = strsplit(as.character(tmp),":")
          ^
```
[.DEploid/utilities/dEploidTools.r:160:40:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L160) *style:* **Commas should always have a space after.**
```r
    field = strsplit(as.character(tmp),":")
                                       ^
```
[.DEploid/utilities/dEploidTools.r:162:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L162) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:162:15:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L162) *style:* **Use <-, not =, for assignment.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
              ^
```
[.DEploid/utilities/dEploidTools.r:162:44:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L162) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
                                           ^~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:163:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L163) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
    ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:163:12:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L163) *style:* **Use <-, not =, for assignment.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
           ^
```
[.DEploid/utilities/dEploidTools.r:163:36:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L163) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                   ^~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:163:47:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L163) *style:* **Commas should always have a space after.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                              ^
```
[.DEploid/utilities/dEploidTools.r:165:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L165) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:165:14:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L165) *style:* **Use <-, not =, for assignment.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
             ^
```
[.DEploid/utilities/dEploidTools.r:165:41:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L165) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
                                        ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:166:5:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L166) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:166:14:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L166) *style:* **Use <-, not =, for assignment.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
             ^
```
[.DEploid/utilities/dEploidTools.r:166:41:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L166) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
                                        ^~~~~~
```
[.DEploid/utilities/dEploidTools.r:168:39:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L168) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = vcf[,1],
                                      ^
```
[.DEploid/utilities/dEploidTools.r:169:37:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L169) *style:* **Commas should always have a space after.**
```r
                         POS = vcf[,2],
                                    ^
```
[.DEploid/utilities/dEploidTools.r:170:37:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L170) *style:* **Variable and function names should be all lowercase.**
```r
                         refCount = refCount,
                                    ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:171:37:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L171) *style:* **Variable and function names should be all lowercase.**
```r
                         altCount = altCount )
                                    ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:192:1:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L192) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:192:12:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L192) *style:* **Put spaces around all infix operators.**
```r
extractPLAF<- function ( plafName ){
          ~^
```
[.DEploid/utilities/dEploidTools.r:192:26:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L192) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
                         ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:193:25:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L193) *style:* **Variable and function names should be all lowercase.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:193:41:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L193) *style:* **Put spaces around all infix operators.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~
```
[.DEploid/utilities/dEploidTools.r:198:11:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
         ~^~~
```
[.DEploid/utilities/dEploidTools.r:198:19:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                 ~^~
```
[.DEploid/utilities/dEploidTools.r:198:23:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                     ~^~
```
[.DEploid/utilities/dEploidTools.r:198:24:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L198) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                       ^
```
[.DEploid/utilities/dEploidTools.r:198:26:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                        ~^~
```
[.DEploid/utilities/dEploidTools.r:198:28:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L198) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                          ~^~
```
[.DEploid/utilities/dEploidTools.r:199:1:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L199) *style:* **lines should not be more than 80 characters.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:199:8:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
      ~^~~
```
[.DEploid/utilities/dEploidTools.r:199:23:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                     ~^~
```
[.DEploid/utilities/dEploidTools.r:199:30:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                            ~^~
```
[.DEploid/utilities/dEploidTools.r:199:43:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                         ~^~
```
[.DEploid/utilities/dEploidTools.r:199:44:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L199) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                           ^
```
[.DEploid/utilities/dEploidTools.r:199:46:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                            ~^~
```
[.DEploid/utilities/dEploidTools.r:199:54:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                    ~^~
```
[.DEploid/utilities/dEploidTools.r:199:59:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                         ~^~
```
[.DEploid/utilities/dEploidTools.r:199:72:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L199) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                      ~^~
```
[.DEploid/utilities/dEploidTools.r:199:77:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L199) *style:* **Commas should always have a space after.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                            ^
```
[.DEploid/utilities/dEploidTools.r:199:77:](https://github.com/mcveanlab/DEploid-r/blob/ca3767ad5f056a24fd82861ff92f3a71909ef0d7/.DEploid/utilities/dEploidTools.r#L199) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                            ^
```


oh weird, wasn't working for me originally, didnt even see that call in the * catch all. Perhaps I had a copy of a blank page in memcached


That is not possible.


![wp_000115](https://cloud.githubusercontent.com/assets/5588621/19325005/7a6d6764-90c4-11e6-9205-f4fcbd911be7.jpg)
Antichi sentieri per le campagne della Sardegna.


Si ça ne peut pas marcher avec la valeur par défaut, il faut ajouter dans ce cas un truc dans le code du genre :

```js
if (!status) status = 200;
```

sinon, ça change le fonctionnement du programme et ça peut être embêtant.


норм


Setting the `required` value enables browser-based validation which forces the user to pick an option.


This just turns auto-suspend back on, going by what happened in @josephoaks' windows essentials class. I will file a ticket for this.


This message gets shown when the user selects something wrong.


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

![Build Badge](http://img.shields.io/badge/build%20status-failing-red.svg) ![Test Badge](http://img.shields.io/badge/tests%20passed-NA-red.svg)


I imagine this is going to cause it to just request it twice.


We set up a new `ReactiveVar` for this template containing the error message, and a helper for the template to access it.


If the answer is wrong, we set the error message, which then shows up automatically.


![wp_000111](https://cloud.githubusercontent.com/assets/5588621/19325085/d8ddf566-90c4-11e6-94af-3b4d6a03c3ed.jpg)
Falco pellegrino cacciatore di Sardegna.....


@alicexigao: I set up the quiz to respond with an error message when answered incorrectly. Let me know if you have any questions.


That 10% needs some proof :) You might be right on the bonustaken but this isnt really @Phatcat fault since he only tried to refactor, not change logic.


It's these 4 lines causing the process hang. I'll keep looking into it later https://github.com/UniversalMediaServer/UniversalMediaServer/commit/98b2e8a1fcce4caf071200a4b1bd6b27cbd50bb2#diff-67a73f91e7ae978447b6dc02fe38997dR374


TeamCity SayMore :: SayMore pull requests [Build *.*.1.1133ccd214622210a125ed533d787be9e0a63221](http://build.palaso.org/viewLog.html?buildId=77756&buildTypeId=SayMore_SayMorePullRequests) outcome was **UNKNOWN**
Summary: Canceled Build time: 00:00:13


:trollface:


Attention, this part has changed. The return value of getBarcode callback now is an object instead of barcode number.
The return value now is:
address:{
  "addressBarcode" : "024782135864",
   addressComponents: {
    "primary_number": "86",
      "street_name": "Frontage",
      "street_suffix": "Rd",
      "city_name": "Belmont",
      "state_abbreviation": "MA",
      "zipcode": "02478",
      "plus4_code": "2135",
      "delivery_point": "86",
      "delivery_point_check_digit": "4"
  }
}
addressComponents includes valid address components


![](https://github.trello.services/images/mini-trello-icon.png) [(3) Create Plunkr template [5]](https://trello.com/c/YwlholHt/28-3-create-plunkr-template-5)


```
function doPhysicalWeaponskill(attacker, target, wsID, tp, primary, action, taChar, params)
     if (params == nil) then
        print("Phys wsID: "..wsID.." has nil params.")
    end
    local criticalHit = false;
    local bonusTP = 0;
    if (params.bonusTP ~= nil) then
        bonusTP = params.bonusTP;
    else
        print("Phys wsID: "..wsID.." has nil params.bonusTP")
    end
```
Did same thing in all 3 weaponskill functions in the global. And here's the resulting prints:
```
12/Oct] [15:46:02][LUA Script] Phys wsID: 144 has nil params.bonusTP
12/Oct] [15:46:06][LUA Script] Phys wsID: 23 has nil params.bonusTP
12/Oct] [15:46:37][LUA Script] Mag wsID: 19 has nil params.bonusTP
12/Oct] [15:46:44][LUA Script] Phys wsID: 16 has nil params.bonusTP
12/Oct] [15:46:50][LUA Script] Phys wsID: 31 has nil params.bonusTP
12/Oct] [15:47:03][LUA Script] Phys wsID: 31 has nil params.bonusTP
12/Oct] [15:47:23][LUA Script] Phys wsID: 23 has nil params.bonusTP
```
Params is not nil. only the element was nil. Or both would have printed.

Looks like same thing as https://github.com/TeoTwawki/darkstar/commit/4e9b4722aa16291b2b82a7fbaaab29b33fddc86a#diff-c21711a7901ec1db18ca1dfca46f8216L13 to me


Is this a cron job? It doesn't appear to be hooked up via crontab. The file also isn't chmod'ed to be executable. It also goes against directory convention by having the `rb` extension.


It is not meant to be the most secure thing ever. Plus people are confused because the password changed. We just need to keep not alpha testers out.


Fais attention à tes noms, plus bas dans ton code ta fonction s’appelle `createAbuse` et ici `createAbuseReport`. Il faut que ce soit le même partout. (Après, mon avis personnel serait de la nommer `reportAbuse`, ce qui est encore plus trivial comme nom.)


If you have a minute, could you benchmark both the  [mastert](https://github.com/Stebalien/horrorshow-rs/tree/0e87b1a74c3b067c33e3550b15a962faf912a673) and [revert-opt](https://github.com/Stebalien/horrorshow-rs/tree/a5ae8cfc1edd1e002b32e9d05861428a0798f273) horrorshow branches (I'm applying the same optimization)?


Hello,
 First of all its great work now i am able to understand torch framework and benchmark till some extend.
 Im trying to see the difference between running on gpu and cpu.
 I built the torch and my desktop spec are intel i7 with Pascal Titan-X.
 I was able to run on GPU but as far as running on CPU when i issue the command
 python run_cnn_benchmarks.py --gpus -1 --models Torch_Ref/distro/cnn_bench/cnn-benchmarks/models/alexnet/alexnet.t7 --batch_sizes 1 --use_cudnn 1

Im getting following error "
 re/lua/5.2/torch/File.lua:343: unknown Torch class "

May i missing something here while running on CPU only.


Si ton schéma s’appelle `abuseReportedSchema`, il est judicieux d’appeler le modèle `AbuseReported` tout court pour éviter les confusions. (Mon avis personnel serait de parler d’`AbuseReport` et non d’`AbuseReported`, ce qui est plus correct en terme de langue, mais ça ne change rien au fonctionnement du programme, c’est juste plus compréhensible.)


Has this not made it to the master branch yet? I can't see to see it in my npm install huboth-aws --save on a fresh hubot?


Pour que le `abuse.save()` fonctionne après, il manque encore deux champs obligatoires à renseigner :

* le contenu abusif qu’on rapporte ;
* le type de contenu dont il s’agit.


TeamCity SayMore :: SayMore pull requests [Build *.*.2.3dad968f316c1cc48da6edaa7f721fa7acc1d74f](http://build.palaso.org/viewLog.html?buildId=77757&buildTypeId=SayMore_SayMorePullRequests) outcome was **FAILURE**
Summary: Compilation error: src\SayMore\SayMore.csproj (new); compilation error: src\SayMoreTests\SayMoreTests.csproj (new) Build time: 00:01:15


Je pense (à voir), que le req.body est vide, tu peux donc initialiser abuse comme suit :

```js
var abuse = new AbuseReported();
```


No I don't think its merged but the PR is there


Please switch this to be a single line per export like so:

```erlang
-export([
    maybe_start_profiler/1,
    maybe_start_profiler/2,
    maybe_terminate_profiler/1,
    maybe_terminate_profiler/2
]).
```

This accomplishes two things: 1) it keeps the line under the maximum 80 character line length, and 2) it makes future additions to this module cleaner in that each additional export will show up as a dedicated line item in the git diff, making it much clearer what has been changed.


Will add it to my .gitignore


Can we add two new rules? These are basic, yet powerful suggestions.
```
        // Having comments and todo's should warn as these are unfinished thoughts.
        "no-warning-comments":[
      		1,
      		{ "terms": ["todo", "fixme"],
      		"location": "anywhere" }
    		],
    		// Debuggers should never leave local enviornments!
    		"no-debugger": [
      		2
    		]
```


yeah, I only really user Remove, Move, SudoWrite


This is a great starting point


LOL, I just saw this commit as I was preparing to clone, checkout and submit a pull request for this exact problem.

(I had just fixed it locally and was preparing to submit a patch...)

Thank you and have a nice day!

Nick


Unicode与音标对照表


I think you ment for this to be i < arrsze. If I enter an array size of n, your loop will run for n+1 times and throw an error


when indexing an array, remember arrays start counting from 0 so you always want to be one less than the array. i.e. not i<=j but i<j.

Also, you don't need j here


solution week 2-find_company
email=raw_input("enter your email:")
a=email.find('@')
b=email.find('.')
c=email[a+1]
for i in range(a+2,b):
    c=c+email[i]
print c


solution week 2 -leap year
year=int(raw_input('What year:'))
if year%400==0:
    print year,'is a leap year'
elif year%4==0 and year%100!=0 :
    print year,'is a leap year'
else:
    print year,'is not a leap year'


Mixed tabs and spaces.


Yes it should be fine, I did it manually and innosetup compiles the archive just fine.


This function calculates the range correctly, but not the average. An array of [0, 2, 4 ,8] should return an average of 7


solution week 2- convert
temp=float(raw_input('Enter a temperature'))
convert=raw_input('Convert to (F)ahrenheit or (C)elsius? ')
if convert=='F' or convert=='f':
    tempf = (9.0 / 5) * temp + 32
    print temp,' C = ',tempf,' F'
elif convert=='C' or convert=='c':
    tempc = (5.0/9)*(temp-32)
    print temp,' F = ',tempc,' C'
else:
    print 'you type wrong, please type again'


solution week 2-fibonacci
def print_fib(n):
    a, b = 0, 1
    if n == 0:
        print a
    elif n == 1:
        print a, b
    else:
        print 0, 1,
        for i in range(2, n):
            c = a + b
            a, b = b, c
            print c,
n=int(raw_input('Enter n'))
print 'the Fibonacci Sequence is:'
print_fib(n)


Patched in @9bb2390d181c59d73851310ef58383444dbf5cd9


Should they considered equal if both `NULL`? It's not really clear from the problem description.


Patched in @4efc4c7631f36dc7cc8eb98910c7ee2106c5e834


That's a brilliant idea!


| [eradestiramayani](https://eradestiramayani.github.io/) | ![eradestiramayani](https://projecteuler.net/profile/eradestiramayani.png) | 1, 2, 3, 4, 7, 9, 58 | [Era Desti Ramayani](https://id.wikipedia.org/wiki/Pengguna:Era_Desti_Ramayani) | ![Era Desti Ramayani](http://stackoverflow.com/users/flair/7001715.png) | [unila/unila.github.io](https://github.com/unila/unila.github.io)


Does a `@base_url` module attribute make sense as well in this case?


coursera single page web development using angular js, johns hopkins


Avoid using the ambiguous `it is`. Not clear if the second sentence is explaining __why__ `r` does not have to be an integer, or, perhaps orthogonally, what `r` "represents".


> Which tools besides Node itself lookup .json?

Browserify at least, but all of them should. If it works in Node.js it should work with the packer. Otherwise the tool is fragmenting the community and annoys maintainers by users opening issues about it not working with their tool. You have no idea how many dumb webpack issues I've gotten on my repos because webpack v1 wasn't fully compatible with the Node.js resolution algorithm. IMHO, but rollup should bundle the `rollup-plugin-json` by default. Users shouldn't have to know or care that a module in their dependency tree is using `require('./package')` pointing at a JSON file. Hope you'll open an issue on Rollup about this, and thanks for bringing it up :)


Patched in @9bb2390d181c59d73851310ef58383444dbf5cd9#diff-fbb5bc11492fbd314735f1cef1cf1ba7R1157


TeamCity Xbim :: Xbim Exchange :: XbimExchange [Build 192](http://xbimbuilds.cloudapp.net/viewLog.html?buildId=1293&buildTypeId=Xbim_XbimExchange_XbimExchange) is now running


A message containing letters from A-Z is being encoded to numbers using the following mapping:

'A' -> 1
'B' -> 2
...
'Z' -> 26
Given an encoded message containing digits, determine the total number of ways to decode it.

For example,
Given encoded message "12", it could be decoded as "AB" (1 2) or "L" (12).

The number of ways decoding "12" is 2.


Not sure if this change is whats doing it but looks like other items that have stats attached act a little funky when they roll exceptional or legendary http://puu.sh/rFZ46/4bbdf90d58.jpg


Mixed tabs and spaces.


TeamCity Xbim :: Xbim Exchange :: XbimExchange [Build 192](http://xbimbuilds.cloudapp.net/viewLog.html?buildId=1293&buildTypeId=Xbim_XbimExchange_XbimExchange) outcome was **SUCCESS**
Summary: Running Build time: 00:00:49


Mustafa. What if the array had a new element added to it:

"E"

How should your code change so it won't break?


I would consider making the struct values only what's different about the urls (file name in path) and create a function that transforms them along with `@base_url` into what you require for the comprehension.


heh. I had a gut feeling this might be necessary but was unsure since I'm really unfamiliar with the use cases of this gem.


Patched in @25bfb094b5408fee131d27c75b617c66b25d6375


Cheater!! But good job finding these methods for yourself.


what is the `metadata` value?


weight? I dont think thats right, probably meant width? and set it to auto


Patched at @9bb2390d181c59d73851310ef58383444dbf5cd9#diff-fbb5bc11492fbd314735f1cef1cf1ba7R1393


update peserta-universitas.md


Patched in @9bb2390d181c59d73851310ef58383444dbf5cd9#diff-fbb5bc11492fbd314735f1cef1cf1ba7R5718


Thanks! This is far from finished (eventually I want to try a `GenStage` implementation, though not sure how much benefit it'll bring), so I definitely want to circle back and refactor this.


![](https://github.trello.services/images/mini-trello-icon.png) [asdfr](https://trello.com/c/HlDjXW0w/19-asdfr)


Good job getting this to work with numbers. What happens if I enter a letter?


Patched in @9bb2390d181c59d73851310ef58383444dbf5cd9#diff-fbb5bc11492fbd314735f1cef1cf1ba7R5730


Patched here @9bb2390d181c59d73851310ef58383444dbf5cd9#diff-fbb5bc11492fbd314735f1cef1cf1ba7R5781


@ccrisan, I also replied here https://github.com/ccrisan/motioneyeos/issues/554.  Am also seeing ssh problem.  Seems to come and go if I changes the services settings.  Either some writes don't stick or service conflicts.  It's a bit weird, I can get ssh to work everyone in a while if I start enabling/disabling services (SMB/FTP).  Of course I leave SSH enabled.  Not sure what is going on. I am using v919

Let me know if you need me to do any more experiments on my system.  Now it's in a state where I can actually ssh in.  However turning off SSH and reenabling it might not work.


Yes I KNOW. 👻

But how do we choose? We want emoji and international support. We just don't want that insane stuff that can leave its letterbox and haunt the rest of the page. OR DON'T WE? 😆

Maybe `overflow: hidden` on user input areas is good enough to stop the crazies.


Patch at @9bb2390d181c59d73851310ef58383444dbf5cd9#diff-fbb5bc11492fbd314735f1cef1cf1ba7R6180


is there a need for the pull request still? since this commit is going directly to master anyway


you might want to try changing the image size itself if this isn't working


But yes, a `@base_url` and then I guess `@urls` can just use that and concatenate what is different.


s/TiDB/tikv driver/


Patched in @147d3627f5ce2fc17f311df7c09bac48d254a8f3#diff-fbb5bc11492fbd314735f1cef1cf1ba7R4961


@Ryota2017 コミットメッセージは、何の作業をしたのかわかるようにしてください。日本語でも構いません。


@Ryota2017 コミットメッセージは、何の作業をしたのかわかるようにしてください。日本語でもOKです。


test


@Ryota2017 コミットメッセージは、何の作業をしたのか、わかるようにしてください。


this won't match. if you want to catch multiple cases, it needs to be:
```javascript
case 'canplay':
case 'canplaythrough':
...
```


Hello World


@Astilious This no longer works for people who use opencv version 2.4 which only returns 2 elements.

Could you possibly fix this so it checks for tuple length so it'll work for all of us.


Yup, already saw it, makes total sense


Generally, I think it would have been better not to try to reuse this for processing data not provided by the user.

However, this is a great place for a default argument.  It would have spared you changing all the callers that want `silent == false`.


Why not just set `tracker_port` to 0 and let the OS pick a port?


@spboyer  I ported your changes over. I did a copy/paste, I can't see any difference here. No more changes in this repo.


This does not need to be brace-initialized since the one element is immediately assigned a value.


Lord Sri Hari at Tirpupati.


Keep default


Not a big deal, but easier to update if the base url changes. Also improves readability I would think.

:+1: so far


`snprintf` returns the number of characters printed.  There is no need to use `strlen` to recompute it.  If you want to use `strlen`, you should use `pBuf.data()` to get the address of the data.


This brace-initialization looks unnecessary.


This is insufficient capacity for IPv6.


要删除，泄露信息


泄露了信息


This will crash if the input data does not contain `a=`.


Still need to figure out tsconfig.json outDir so that the compiled files are going into the correct folders, instead of /dist/src/whatever


lllllllllllllllllllllllllllllllllllllllllllll


@Astilious Any particular reason we put this here instead of in `ROITest.py`?


ooooooooooooooooooooo


yes, that's a good catch. I'm going to allow for the weird upload-and-also-delete, but I want to ensure that we always update the manifest if we need to.


lll


Pull the master branch before you edit it. Merged Lee into Master.


The test for `p0 == NULL` is pointless.  First, it has already been dereferenced by the `strstr` on the preceding line.  Second, `p0 == NULL` implies that `a=` was found at `(void *)-2`.  I am not aware of any target operating systems that could place a user buffer at that address.

The test for `p1-p0 < 7` probably serves some purpose, but it is not clear what that purpose is.  There should be a comment explaining why `7`, or the `7` should be placed into a descriptively named `constexpr` variable, or it should be derived as a result of compile-time expressions, as was done for the fourth test in this `if`.

The test for `p1-p0 > sizeof(sIP)` is necessary, but insufficient.  When `p1-p0 == sizeof(sIP)`, this `if` will not be taken, but the resulting memcpy will overwrite all bytes in `sIP`, including the terminating null.  Any attempt to use the buffer will then overread into the next variable on the stack.


Как детектнуть куклу не знаешь?
Хочу сделать кнопки форматирования текста как у куклы вместо select option


The comments from line 5702 apply here, albeit with different numeric constants.


Although the addition of the `silent` flag suppresses the notification to the user, this still has the other problem I mentioned in e-mail: it permits a tracker to cause the client to perform `getaddrinfo` on any string that fits in the bounds of `sIP`.  Such a lookup may block, and is done in the network thread.


Test Comment


will this crash if jsonArray's length is 0?


for partials, use local variables instead of instance variables. this will make it easier to refactor/reuse partials


@flovilmart hmm okay. I think I understand, but I'm still wrapping my head around it. Can you open up a new issue with these details about your Podfile and project setup (as much info as you can the better)? That way it'll be tracked and we'll have the information somewhere more accessible, along with the info from filling out the issue template. Thanks!


don't have a space before parens. this is better rewritten as
```<%= link_to image_tag(news_item.image_url, class: 'img-responsive'), news_item_path(news_item) %>`


BRKey should be an instance wrapper around a BRKey instance - with instance methods. eg compactSign should operate on self and not an instance of []byte


No problem! Appreciate the help (it's easy to forget stuff like that)—my friend (@omibs) and I were trying to figure out how to get streaming working with this commit. I'm going to work on a "real" release by the end of the week 😎


lool.... forgot

will be fixing :)


number 9 line is nary.number.length-1;


Sorry for late review, I think it needs "toLowerCase()".
![screen shot 2016-10-11 at 7 21 16 pm](https://cloud.githubusercontent.com/assets/315275/19295676/056f0730-8feb-11e6-9081-953e4f7ea154.png)


Is this semicolon intentional? It looks dubious


@Astilious just wondering why change this here and switch the `silent=...` [out at the bottom](https://github.com/SamCB/VisionTest/commit/4fe2f23ce2363faa3fcbe4d6ca0faca2a983e090#diff-5bc02cefb3ea9e27f1a6776eabd1935dL154)?

From what I can see, it does make sense, and I guess means we don't have to change the extra line, but I felt the verbosity was worth it (for clarity sake). That said, I'm happy either way, your call on it, it's just we can't have the optional `=None` here because we're definitely treating it as a dictionary in [lines 50-51](https://github.com/SamCB/VisionTest/commit/4fe2f23ce2363faa3fcbe4d6ca0faca2a983e090#diff-5bc02cefb3ea9e27f1a6776eabd1935dR50).


How's it all feeling?


thsi should go in a utils class somewhere


but also, isn't there a way to encode byte[] with different encodings, where 'hex' is one of them?


Hm. This is again, because we have to flush our viewport before camera changeing. This souldn't be as part of the current commit, it can be hidden inside OpenGL2 SetCamera as Flush(). The problem is what we can't draw each small line in immediate mode(because of huge overhead) and have to store it until EndFrame or projection changed.


@Astilious Thanks for this. Looks like a pretty good idea. Might it be worth adding something to the filename to suggest what we tried classifying it as? For revision purposes? Again, your call.


这句是什么意思，还有待考虑。


Well it really _should_


in this case EndFrame called twice too


@Astilious Just for clarity sake, you can use:

```python
cv2.imwrite(os.path.join('cropped_ims', '{:06d}.bmp'.format(im_count)), cropped)
```

Python string formatting is fantastic, highly recommend in the future.


here


and here. And this is currently in repository


Need to revert to this version.


Oh yes. I forgot what it calls every file->new


It could be in ROITest.py. I just thought it might be better in harris as it is essentially just a different format for getting the output from that file.


*Options better use instance


@fchollet
I met an Exception: Regularizers cannot be reused
The code like this: model.add(TimeDistributed(Convolution2D(64, 3, 3, border_mode='valid',W_regularizer=l2(0.01),activity_regularizer=activity_l2(0.01))))

when I remove activity_regularizer=activity_l2(0.01),then it will be ok.


A crafted response can underflow this computation, causing `net_udp_process_game_info` to read below the buffer `data`.  One example of bad input is `":x,c=1xxxxxxxxxxxxxxxx,a=xxxxxxx:"`


<--- this pedantic cannot stop himself from commenting that there is one too many
````
EmitEmptyLine(0.4 * CurrFont()->GetSize());
````
in that pull request.

In the same breath, thank you for submitting this, a good number of users (those using bigger screens) want to see that feature implemented.  like this thread for example :http://forums.fofou.org/sumatrapdf/topic?id=3183490.  It's exactly what I was looking for.


Oh, whoops. I thought I had changed that back before committing. Yeah, I had an incompatibility and had to change it. Just change it back for now I suppose. I will create a version compatible with both when I work out creating a branch.


@Astilious Thanks for this. Though unfortunately, even though you're just returning the the ROI, it still won't load because it'll get lost at line 21 when we try to import Keras for the first time.

Implement it and push it up as it is working for you, and maybe link us to a README on how to get keras running on our machines.


OR, let's just use localeCompare, it'd be better for like Japanese character.
https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/String/localeCompare


receiver named abbreviation


Пока толком не занимался этим.
Пробовал тот пример из апи - работает, конечно, но только после того как сама кукла просрется.
А это до нескольких секунд.
В общем, пока четкого понимания нет


> This breaks compatibility to pipe chars used in strings

Not going to happen. The regex is designed to allow only the pipe char followed by an integer.