[.DEploid/utilities/dEploidTools.r:1:22:](https://github.com/mcveanlab/DEploid-r/blob/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.DEploid/utilities/dEploidTools.r#L82) *style:* **Variable and function names should be all lowercase.**
```r
    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:17:](https://github.com/mcveanlab/DEploid-r/blob/8550a933ae77717a1ccdda846a31b15fbd39e499/.DEploid/utilities/dEploidTools.r#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:17:](https://github.com/mcveanlab/DEploid-r/blob/8550a933ae77717a1ccdda846a31b15fbd39e499/.DEploid/utilities/dEploidTools.r#L83) *warning:* **no visible global function definition for ‘extractCoverageFromVcf’**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:83:48:](https://github.com/mcveanlab/DEploid-r/blob/8550a933ae77717a1ccdda846a31b15fbd39e499/.DEploid/utilities/dEploidTools.r#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:85:17:](https://github.com/mcveanlab/DEploid-r/blob/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.DEploid/utilities/dEploidTools.r#L193) *style:* **Variable and function names should be all lowercase.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~
```
[.DEploid/utilities/dEploidTools.r:193:41:](https://github.com/mcveanlab/DEploid-r/blob/8550a933ae77717a1ccdda846a31b15fbd39e499/.DEploid/utilities/dEploidTools.r#L193) *style:* **Put spaces around all infix operators.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~
```
[.DEploid/utilities/dEploidTools.r:198:11:](https://github.com/mcveanlab/DEploid-r/blob/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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/8550a933ae77717a1ccdda846a31b15fbd39e499/.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);
                                                                            ^
```


Thanks for reporting.  Looking now...


hvad skal jeg gøre?


Visual Regression Testing found a difference between new version and the baseline.
Check the diffs [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-pr-check/682/).
Accept the new baseline [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-update-baseline/parambuild?branch=ember).


TeamCity Selenium POM :: CI [Build 84](https://teamcity.sponte.uk/viewLog.html?buildId=1143&buildTypeId=SeleniumPom_Ci) is now running


TeamCity Selenium POM :: CI [Build 83](https://teamcity.sponte.uk/viewLog.html?buildId=1142&buildTypeId=SeleniumPom_Ci) outcome was **SUCCESS**
Summary: Tests passed: 52 Build time: 00:04:07


Ok, I do see that, but I'm not sure where that comes from.  Visual Fill Column Mode isn't even active… 😕

Maybe @joostkremers can help?


TaskCluster: https://tools.taskcluster.net/task-graph-inspector/#HhpquLq-Swi-C1YElmfz6w/


I'd call `log.Fatal` instead of `panic` directly.


.* - это от 0 до бесконечности любых символов. Стоит ли ставить после этого "?" ?


gb  vb  df df sd


Почему переменная с большой буквы? Тем более одной


TeamCity Selenium POM :: CI [Build 84](https://teamcity.sponte.uk/viewLog.html?buildId=1143&buildTypeId=SeleniumPom_Ci) outcome was **SUCCESS**
Summary: Tests passed: 52 Build time: 00:04:00


dsfdsfds  df  dfdf


spacja


Because it's cheap :trollface:


>The scripts themselves should take care of that.

So now some scripts are broken by this change? Maybe the exceptions should be implemented via flags?


Thanks for the fix @hamalMarino  and glad to see you around here ;)


Ccccmmmm Corrected typo, fixes OSIS-8


可以进行图标资源合并background: 0 0 url(/widget/common/css-base/src/icon-img/coupon_null_icon.png?__sprite);


If you do, please do somewhere `log.SetFlags(log.LstdFlags | log.Lshortfile)` to have file location info in the message.


可以进行图标资源合并，
background: 0 0 url(/widget/common/css-base/src/icon-img/coupon_null_icon.png?__sprite);


я так понимаю, 6 коммитов - это твои локальные изменения (еще не отправленные на сервер).

nothing to commit, working tree clean - означает, что на все изменения есть коммиты и не осталось изменнённых файлов.

А как у тебя получается делать вот этот "Merge" коммит?

А ты делаешь (git pull) или (git fetch -> git rebase) перед тем как отправить изменения (git push)? При этом должны подтянуться изменения (коммиты), которые были сделаны за всё время пока ты вносил изменения (локально).


@kot331107 that's called fool's luck :)))


True! It's Happier with Gretchen Rubin. I'll make that change.


Uh what is this


Test JCP


Почему для пробелов у тебя нежадный? Т.е. каким-то образом может выбрать больше пробелов чем надо?


Good point, fixed


////////////////////////////////////////////////////////////////////////////////////////////////

[#---------][10% ][DIPOLE MANAGER ROADMAP]

////////////////////////////////////////////////////////////////////////////////////////////////

[##--------][20% ][PHASE 1 - INNER WORKINGS]

[##########][100%] FIND ONE PYMOL PLUGIN TO BASE ON (GYRATION TENSOR)
[----------][0%  ] BUILD THE FUNCTION TO OPEN THE MOL2 EXTENSION
[----------][0%  ] BUILD THE FUNCTION TO GET THE MOL2 DIPOLE VALUES
[----------][0%  ] BUILD THE FUNCTION TO PLOT THE MOLECULE
[----------][0%  ] BUILD THE FUNCTION TO FIND THE GEOMETRIC CENTER OF THE DIPOLE
[#########-][90% ] BUILD THE FUNCTION TO CALCULATE DE DIPOLE VECTORS
[----------][0%  ] BUILD THE FUNCTION TO PLOT THE GEOMETRIC CENTER OF THE MOLECULE ON THE PYMOL
[----------][0%  ] BUILD THE FUNCTION TO PLOT 3 VECTORS
[----------][0%  ] BUILD THE FUNCTION TO PLOT RESULTANT VECTOR
[----------][0%  ] MAKE IT WORK FROM WITHIN PYMOL

////////////////////////////////////////////////////////////////////////////////////////////////

[----------][0%  ][PHASE 2 - GUI BUILDING]

[----------][0%  ] CREATE EXTERNAL GUI FROM PYMOL
[----------][0%  ] DISCOVER HOW TO CLOSE IT
[----------][0%  ] DEFINE GUI BASIC STRUCTURE ON PAPER
[----------][0%  ] DISCOVER HOW TO DEPLOY N INPUT FIELDS
[----------][0%  ] CREATE ALL INPUT FIELDS
[----------][0%  ] CREATE ALL BUTTONS
[----------][0%  ] BIND INPUT FIELDS TO LIST VALUES
[----------][0%  ] SAVE MOL2 FROM INPUT FIELDS
[----------][0%  ] PLOT NEW DIPOLE CALCULATIONS
[----------][0%  ] REFRESH NEW DIPOLE CALCULATIONS

////////////////////////////////////////////////////////////////////////////////////////////////

[----------][0%  ][PHASE 3 - BETA TESTING]

////////////////////////////////////////////////////////////////////////////////////////////////


poderia usar o first()


. - это любой символ в том числе пробельный
Т.е. "." включает в себя "\s"


Насколько понял это должно быть открытие тега. Зачем ".*" в начале и в конце?


‘_’ 这个形参写成model会清晰一些


Для конечного тега так же интересно зачем матчить символы пере тегом


Processing should not go on when user dismissed the openssl certificate commit confirmation. And a missing code termination.


Learning everyday. Fixed


@HoanNguyen18795 : cái function fetchUser() trong Model m viết gây ra sai id user nhé, m tự fix trong api đi.


> What's the purpose of caching single variables from a config file? They are read from the config file anyways and would only poke the cache engine each time.

:+1: same question here.


Ja.


Add two variables for LoginActivity. Save in sharedpreferences username and password


В закрытии тега не может быть пробелов между "<" и "/"


See forum at
http://jambage.com/kontakt/forum/shop-system/wuensche-neue-features-fehler/list/neues-feature.html


noice!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Submitting the task to TaskCluster failed. You didn't give the task-graph scopes allowing it define tasks on the queue.Details:

```js
[
    {
        "message": "You do not have sufficient scopes. This request requires you\nto have one of the following sets of scopes:\n[\n  [\n    \"queue:route:index.deepspeech.tensorflow.pip.warpctc.gpu\"\n  ]\n]\n\nYou only have the scopes:\n[\n  \"assume:repo:github.com/mozilla/tensorflow:pull-request\",\n  \"queue:create-task:aws-provisioner-v1/github-worker\",\n  \"queue:route:index.garbage.*\",\n  \"secrets:get:garbage/*\",\n  \"secrets:set:garbage/*\"\n]\n\nIn other words you are missing scopes from one of the options:\n * Option 0:\n    - \"queue:route:index.deepspeech.tensorflow.pip.warpctc.gpu\"\n----\nerrorCode:  InsufficientScopes\nstatusCode: 403\nrequestInfo:\n  method:   defineTask\n  params:   {\"taskId\":\"KmO14_L0RYS8D9FN5-mVbw\"}\n  payload:  {\n  \"provisionerId\": \"aws-provisioner-v1\",\n  \"workerType\": \"github-worker\",\n  \"extra\": {\n    \"github\": {\n      \"env\": true,\n      \"events\": [\n        \"pull_request.opened\",\n        \"pull_request.synchronize\",\n        \"pull_request.reopened\",\n        \"push\"\n      ]\n    }\n  },\n  \"routes\": [\n    \"index.deepspeech.tensorflow.pip.warpctc.gpu\"\n  ],\n  \"payload\": {\n    \"maxRunTime\": 7200,\n    \"image\": \"ubuntu:14.04\",\n    \"command\": [\n      \"/bin/bash\",\n      \"--login\",\n      \"-c\",\n      \"set -xe && apt-get -qq update && apt-get -qq -y install git build-essential python-virtualenv python-dev libblas-dev liblapack-dev gfortran swig wget software-properties-common zip zlib1g-dev unzip && echo 'oracle-java8-installer shared/accepted-oracle-license-v1-1 select true' | debconf-set-selections && add-apt-repository --yes ppa:webupd8team/java && apt-get -qq update && DEBIAN_FRONTEND=noninteractive apt-get -qq -y --force-yes --no-install-recommends install oracle-java8-installer && adduser --system --home /home/build-user/ build-user && cd /home/build-user/ && echo '#!/bin/bash\\nset -xe\\nenv && id && mkdir ~/DeepSpeech/ && git clone --quiet https://github.com/lissyx/tensorflow.git ~/DeepSpeech/tf/ && cd ~/DeepSpeech/tf && git checkout --quiet dc3b4f806e2ba2c2eb5d53f59b08e58bd17ecf44 && ./setup.sh --cuda && ./build.sh --gpu' > run.sh && chmod +x run.sh && sudo -H -u build-user /bin/bash run.sh\"\n    ],\n    \"artifacts\": {\n      \"public\": {\n        \"type\": \"directory\",\n        \"path\": \"/tmp/tensorflow_gpu_pkg/\",\n        \"expires\": \"2016-11-09T12:43:30.645Z\"\n      }\n    },\n    \"env\": {\n      \"GITHUB_EVENT\": \"pull_request.synchronize\",\n      \"GITHUB_BRANCH\": \"warpctc\",\n      \"GITHUB_PULL_REQUEST\": 3,\n      \"GITHUB_BASE_REPO_URL\": \"https://github.com/mozilla/tensorflow.git\",\n      \"GITHUB_BASE_USER\": \"mozilla\",\n      \"GITHUB_BASE_SHA\": \"787ab22d490e79ea8c06511d60d6cddf1b2dd2c2\",\n      \"GITHUB_BASE_BRANCH\": \"warpctc\",\n      \"GITHUB_BASE_REF\": \"warpctc\",\n      \"GITHUB_HEAD_REPO_URL\": \"https://github.com/lissyx/tensorflow.git\",\n      \"GITHUB_HEAD_USER\": \"lissyx\",\n      \"GITHUB_HEAD_SHA\": \"dc3b4f806e2ba2c2eb5d53f59b08e58bd17ecf44\",\n      \"GITHUB_HEAD_BRANCH\": \"tc-build\",\n      \"GITHUB_HEAD_USER_EMAIL\": \"lissyx@users.noreply.github.com\"\n    }\n  },\n  \"metadata\": {\n    \"name\": \"TaskCluster TensorFlow GPU\",\n    \"description\": \"Building TensorFlow with GPU support\",\n    \"owner\": \"lissyx@users.noreply.github.com\",\n    \"source\": \"https://github.com/lissyx/tensorflow.git\"\n  },\n  \"created\": \"2016-10-10T12:43:30.646Z\",\n  \"deadline\": \"2016-10-11T12:43:30.646Z\",\n  \"schedulerId\": \"task-graph-scheduler\",\n  \"taskGroupId\": \"RXrwZtkPR2K-lnrp61rp8A\",\n  \"dependencies\": [],\n  \"requires\": \"all-completed\",\n  \"priority\": \"normal\",\n  \"retries\": 5,\n  \"scopes\": [],\n  \"tags\": {},\n  \"expires\": \"2017-10-11T12:43:30.646Z\"\n}\n  time:     2016-10-10T12:43:30.890Z\ndetails:\n{\n  \"scopesets\": [\n    [\n      \"queue:route:index.deepspeech.tensorflow.pip.warpctc.gpu\"\n    ]\n  ],\n  \"scopes\": [\n    \"assume:repo:github.com/mozilla/tensorflow:pull-request\",\n    \"queue:create-task:aws-provisioner-v1/github-worker\",\n    \"queue:route:index.garbage.*\",\n    \"secrets:get:garbage/*\",\n    \"secrets:set:garbage/*\"\n  ]\n}",
        "error": {
            "code": "InsufficientScopes",
            "message": "You do not have sufficient scopes. This request requires you\nto have one of the following sets of scopes:\n[\n  [\n    \"queue:route:index.deepspeech.tensorflow.pip.warpctc.gpu\"\n  ]\n]\n\nYou only have the scopes:\n[\n  \"assume:repo:github.com/mozilla/tensorflow:pull-request\",\n  \"queue:create-task:aws-provisioner-v1/github-worker\",\n  \"queue:route:index.garbage.*\",\n  \"secrets:get:garbage/*\",\n  \"secrets:set:garbage/*\"\n]\n\nIn other words you are missing scopes from one of the options:\n * Option 0:\n    - \"queue:route:index.deepspeech.tensorflow.pip.warpctc.gpu\"\n----\nerrorCode:  InsufficientScopes\nstatusCode: 403\nrequestInfo:\n  method:   defineTask\n  params:   {\"taskId\":\"KmO14_L0RYS8D9FN5-mVbw\"}\n  payload:  {\n  \"provisionerId\": \"aws-provisioner-v1\",\n  \"workerType\": \"github-worker\",\n  \"extra\": {\n    \"github\": {\n      \"env\": true,\n      \"events\": [\n        \"pull_request.opened\",\n        \"pull_request.synchronize\",\n        \"pull_request.reopened\",\n        \"push\"\n      ]\n    }\n  },\n  \"routes\": [\n    \"index.deepspeech.tensorflow.pip.warpctc.gpu\"\n  ],\n  \"payload\": {\n    \"maxRunTime\": 7200,\n    \"image\": \"ubuntu:14.04\",\n    \"command\": [\n      \"/bin/bash\",\n      \"--login\",\n      \"-c\",\n      \"set -xe && apt-get -qq update && apt-get -qq -y install git build-essential python-virtualenv python-dev libblas-dev liblapack-dev gfortran swig wget software-properties-common zip zlib1g-dev unzip && echo 'oracle-java8-installer shared/accepted-oracle-license-v1-1 select true' | debconf-set-selections && add-apt-repository --yes ppa:webupd8team/java && apt-get -qq update && DEBIAN_FRONTEND=noninteractive apt-get -qq -y --force-yes --no-install-recommends install oracle-java8-installer && adduser --system --home /home/build-user/ build-user && cd /home/build-user/ && echo '#!/bin/bash\\nset -xe\\nenv && id && mkdir ~/DeepSpeech/ && git clone --quiet https://github.com/lissyx/tensorflow.git ~/DeepSpeech/tf/ && cd ~/DeepSpeech/tf && git checkout --quiet dc3b4f806e2ba2c2eb5d53f59b08e58bd17ecf44 && ./setup.sh --cuda && ./build.sh --gpu' > run.sh && chmod +x run.sh && sudo -H -u build-user /bin/bash run.sh\"\n    ],\n    \"artifacts\": {\n      \"public\": {\n        \"type\": \"directory\",\n        \"path\": \"/tmp/tensorflow_gpu_pkg/\",\n        \"expires\": \"2016-11-09T12:43:30.645Z\"\n      }\n    },\n    \"env\": {\n      \"GITHUB_EVENT\": \"pull_request.synchronize\",\n      \"GITHUB_BRANCH\": \"warpctc\",\n      \"GITHUB_PULL_REQUEST\": 3,\n      \"GITHUB_BASE_REPO_URL\": \"https://github.com/mozilla/tensorflow.git\",\n      \"GITHUB_BASE_USER\": \"mozilla\",\n      \"GITHUB_BASE_SHA\": \"787ab22d490e79ea8c06511d60d6cddf1b2dd2c2\",\n      \"GITHUB_BASE_BRANCH\": \"warpctc\",\n      \"GITHUB_BASE_REF\": \"warpctc\",\n      \"GITHUB_HEAD_REPO_URL\": \"https://github.com/lissyx/tensorflow.git\",\n      \"GITHUB_HEAD_USER\": \"lissyx\",\n      \"GITHUB_HEAD_SHA\": \"dc3b4f806e2ba2c2eb5d53f59b08e58bd17ecf44\",\n      \"GITHUB_HEAD_BRANCH\": \"tc-build\",\n      \"GITHUB_HEAD_USER_EMAIL\": \"lissyx@users.noreply.github.com\"\n    }\n  },\n  \"metadata\": {\n    \"name\": \"TaskCluster TensorFlow GPU\",\n    \"description\": \"Building TensorFlow with GPU support\",\n    \"owner\": \"lissyx@users.noreply.github.com\",\n    \"source\": \"https://github.com/lissyx/tensorflow.git\"\n  },\n  \"created\": \"2016-10-10T12:43:30.646Z\",\n  \"deadline\": \"2016-10-11T12:43:30.646Z\",\n  \"schedulerId\": \"task-graph-scheduler\",\n  \"taskGroupId\": \"RXrwZtkPR2K-lnrp61rp8A\",\n  \"dependencies\": [],\n  \"requires\": \"all-completed\",\n  \"priority\": \"normal\",\n  \"retries\": 5,\n  \"scopes\": [],\n  \"tags\": {},\n  \"expires\": \"2017-10-11T12:43:30.646Z\"\n}\n  time:     2016-10-10T12:43:30.890Z\ndetails:\n{\n  \"scopesets\": [\n    [\n      \"queue:route:index.deepspeech.tensorflow.pip.warpctc.gpu\"\n    ]\n  ],\n  \"scopes\": [\n    \"assume:repo:github.com/mozilla/tensorflow:pull-request\",\n    \"queue:create-task:aws-provisioner-v1/github-worker\",\n    \"queue:route:index.garbage.*\",\n    \"secrets:get:garbage/*\",\n    \"secrets:set:garbage/*\"\n  ]\n}",
            "requestInfo": {
                "method": "defineTask",
                "params": {
                    "taskId": "KmO14_L0RYS8D9FN5-mVbw"
                },
                "payload": {
                    "provisionerId": "aws-provisioner-v1",
                    "workerType": "github-worker",
                    "extra": {
                        "github": {
                            "env": true,
                            "events": [
                                "pull_request.opened",
                                "pull_request.synchronize",
                                "pull_request.reopened",
                                "push"
                            ]
                        }
                    },
                    "routes": [
                        "index.deepspeech.tensorflow.pip.warpctc.gpu"
                    ],
                    "payload": {
                        "maxRunTime": 7200,
                        "image": "ubuntu:14.04",
                        "command": [
                            "/bin/bash",
                            "--login",
                            "-c",
                            "set -xe && apt-get -qq update && apt-get -qq -y install git build-essential python-virtualenv python-dev libblas-dev liblapack-dev gfortran swig wget software-properties-common zip zlib1g-dev unzip && echo 'oracle-java8-installer shared/accepted-oracle-license-v1-1 select true' | debconf-set-selections && add-apt-repository --yes ppa:webupd8team/java && apt-get -qq update && DEBIAN_FRONTEND=noninteractive apt-get -qq -y --force-yes --no-install-recommends install oracle-java8-installer && adduser --system --home /home/build-user/ build-user && cd /home/build-user/ && echo '#!/bin/bash\nset -xe\nenv && id && mkdir ~/DeepSpeech/ && git clone --quiet https://github.com/lissyx/tensorflow.git ~/DeepSpeech/tf/ && cd ~/DeepSpeech/tf && git checkout --quiet dc3b4f806e2ba2c2eb5d53f59b08e58bd17ecf44 && ./setup.sh --cuda && ./build.sh --gpu' > run.sh && chmod +x run.sh && sudo -H -u build-user /bin/bash run.sh"
                        ],
                        "artifacts": {
                            "public": {
                                "type": "directory",
                                "path": "/tmp/tensorflow_gpu_pkg/",
                                "expires": "2016-11-09T12:43:30.645Z"
                            }
                        },
                        "env": {
                            "GITHUB_EVENT": "pull_request.synchronize",
                            "GITHUB_BRANCH": "warpctc",
                            "GITHUB_PULL_REQUEST": 3,
                            "GITHUB_BASE_REPO_URL": "https://github.com/mozilla/tensorflow.git",
                            "GITHUB_BASE_USER": "mozilla",
                            "GITHUB_BASE_SHA": "787ab22d490e79ea8c06511d60d6cddf1b2dd2c2",
                            "GITHUB_BASE_BRANCH": "warpctc",
                            "GITHUB_BASE_REF": "warpctc",
                            "GITHUB_HEAD_REPO_URL": "https://github.com/lissyx/tensorflow.git",
                            "GITHUB_HEAD_USER": "lissyx",
                            "GITHUB_HEAD_SHA": "dc3b4f806e2ba2c2eb5d53f59b08e58bd17ecf44",
                            "GITHUB_HEAD_BRANCH": "tc-build",
                            "GITHUB_HEAD_USER_EMAIL": "lissyx@users.noreply.github.com"
                        }
                    },
                    "metadata": {
                        "name": "TaskCluster TensorFlow GPU",
                        "description": "Building TensorFlow with GPU support",
                        "owner": "lissyx@users.noreply.github.com",
                        "source": "https://github.com/lissyx/tensorflow.git"
                    },
                    "created": "2016-10-10T12:43:30.646Z",
                    "deadline": "2016-10-11T12:43:30.646Z",
                    "schedulerId": "task-graph-scheduler",
                    "taskGroupId": "RXrwZtkPR2K-lnrp61rp8A",
                    "dependencies": [],
                    "requires": "all-completed",
                    "priority": "normal",
                    "retries": 5,
                    "scopes": [],
                    "tags": {},
                    "expires": "2017-10-11T12:43:30.646Z"
                },
                "time": "2016-10-10T12:43:30.890Z"
            },
            "details": {
                "scopesets": [
                    [
                        "queue:route:index.deepspeech.tensorflow.pip.warpctc.gpu"
                    ]
                ],
                "scopes": [
                    "assume:repo:github.com/mozilla/tensorflow:pull-request",
                    "queue:create-task:aws-provisioner-v1/github-worker",
                    "queue:route:index.garbage.*",
                    "secrets:get:garbage/*",
                    "secrets:set:garbage/*"
                ]
            }
        }
    },
    {
        "message": "You do not have sufficient scopes. This request requires you\nto have one of the following sets of scopes:\n[\n  [\n    \"queue:route:index.deepspeech.tensorflow.pip.warpctc.cpu\"\n  ]\n]\n\nYou only have the scopes:\n[\n  \"assume:repo:github.com/mozilla/tensorflow:pull-request\",\n  \"queue:create-task:aws-provisioner-v1/github-worker\",\n  \"queue:route:index.garbage.*\",\n  \"secrets:get:garbage/*\",\n  \"secrets:set:garbage/*\"\n]\n\nIn other words you are missing scopes from one of the options:\n * Option 0:\n    - \"queue:route:index.deepspeech.tensorflow.pip.warpctc.cpu\"\n----\nerrorCode:  InsufficientScopes\nstatusCode: 403\nrequestInfo:\n  method:   defineTask\n  params:   {\"taskId\":\"HfPNJvImStu1rmQJAFUvaQ\"}\n  payload:  {\n  \"provisionerId\": \"aws-provisioner-v1\",\n  \"workerType\": \"github-worker\",\n  \"extra\": {\n    \"github\": {\n      \"env\": true,\n      \"events\": [\n        \"pull_request.opened\",\n        \"pull_request.synchronize\",\n        \"pull_request.reopened\",\n        \"push\"\n      ]\n    }\n  },\n  \"routes\": [\n    \"index.deepspeech.tensorflow.pip.warpctc.cpu\"\n  ],\n  \"payload\": {\n    \"maxRunTime\": 7200,\n    \"image\": \"ubuntu:14.04\",\n    \"command\": [\n      \"/bin/bash\",\n      \"--login\",\n      \"-c\",\n      \"set -xe && apt-get -qq update && apt-get -qq -y install git build-essential python-virtualenv python-dev libblas-dev liblapack-dev gfortran swig wget software-properties-common zip zlib1g-dev unzip && echo 'oracle-java8-installer shared/accepted-oracle-license-v1-1 select true' | debconf-set-selections && add-apt-repository --yes ppa:webupd8team/java && apt-get -qq update && DEBIAN_FRONTEND=noninteractive apt-get -qq -y --force-yes --no-install-recommends install oracle-java8-installer && adduser --system --home /home/build-user/ build-user && cd /home/build-user/ && echo '#!/bin/bash\\nset -xe\\nenv && id && mkdir ~/DeepSpeech/ && git clone --quiet https://github.com/lissyx/tensorflow.git ~/DeepSpeech/tf/ && cd ~/DeepSpeech/tf && git checkout --quiet dc3b4f806e2ba2c2eb5d53f59b08e58bd17ecf44 && ./setup.sh && ./build.sh' > run.sh && chmod +x run.sh && sudo -H -u build-user /bin/bash run.sh\"\n    ],\n    \"artifacts\": {\n      \"public\": {\n        \"type\": \"directory\",\n        \"path\": \"/tmp/tensorflow_pkg/\",\n        \"expires\": \"2016-11-09T12:43:30.646Z\"\n      }\n    },\n    \"env\": {\n      \"GITHUB_EVENT\": \"pull_request.synchronize\",\n      \"GITHUB_BRANCH\": \"warpctc\",\n      \"GITHUB_PULL_REQUEST\": 3,\n      \"GITHUB_BASE_REPO_URL\": \"https://github.com/mozilla/tensorflow.git\",\n      \"GITHUB_BASE_USER\": \"mozilla\",\n      \"GITHUB_BASE_SHA\": \"787ab22d490e79ea8c06511d60d6cddf1b2dd2c2\",\n      \"GITHUB_BASE_BRANCH\": \"warpctc\",\n      \"GITHUB_BASE_REF\": \"warpctc\",\n      \"GITHUB_HEAD_REPO_URL\": \"https://github.com/lissyx/tensorflow.git\",\n      \"GITHUB_HEAD_USER\": \"lissyx\",\n      \"GITHUB_HEAD_SHA\": \"dc3b4f806e2ba2c2eb5d53f59b08e58bd17ecf44\",\n      \"GITHUB_HEAD_BRANCH\": \"tc-build\",\n      \"GITHUB_HEAD_USER_EMAIL\": \"lissyx@users.noreply.github.com\"\n    }\n  },\n  \"metadata\": {\n    \"name\": \"TaskCluster TensorFlow CPU only\",\n    \"description\": \"Building TensorFlow with CPU only support\",\n    \"owner\": \"lissyx@users.noreply.github.com\",\n    \"source\": \"https://github.com/lissyx/tensorflow.git\"\n  },\n  \"created\": \"2016-10-10T12:43:30.646Z\",\n  \"deadline\": \"2016-10-11T12:43:30.646Z\",\n  \"schedulerId\": \"task-graph-scheduler\",\n  \"taskGroupId\": \"RXrwZtkPR2K-lnrp61rp8A\",\n  \"dependencies\": [],\n  \"requires\": \"all-completed\",\n  \"priority\": \"normal\",\n  \"retries\": 5,\n  \"scopes\": [],\n  \"tags\": {},\n  \"expires\": \"2017-10-11T12:43:30.646Z\"\n}\n  time:     2016-10-10T12:43:30.885Z\ndetails:\n{\n  \"scopesets\": [\n    [\n      \"queue:route:index.deepspeech.tensorflow.pip.warpctc.cpu\"\n    ]\n  ],\n  \"scopes\": [\n    \"assume:repo:github.com/mozilla/tensorflow:pull-request\",\n    \"queue:create-task:aws-provisioner-v1/github-worker\",\n    \"queue:route:index.garbage.*\",\n    \"secrets:get:garbage/*\",\n    \"secrets:set:garbage/*\"\n  ]\n}",
        "error": {
            "code": "InsufficientScopes",
            "message": "You do not have sufficient scopes. This request requires you\nto have one of the following sets of scopes:\n[\n  [\n    \"queue:route:index.deepspeech.tensorflow.pip.warpctc.cpu\"\n  ]\n]\n\nYou only have the scopes:\n[\n  \"assume:repo:github.com/mozilla/tensorflow:pull-request\",\n  \"queue:create-task:aws-provisioner-v1/github-worker\",\n  \"queue:route:index.garbage.*\",\n  \"secrets:get:garbage/*\",\n  \"secrets:set:garbage/*\"\n]\n\nIn other words you are missing scopes from one of the options:\n * Option 0:\n    - \"queue:route:index.deepspeech.tensorflow.pip.warpctc.cpu\"\n----\nerrorCode:  InsufficientScopes\nstatusCode: 403\nrequestInfo:\n  method:   defineTask\n  params:   {\"taskId\":\"HfPNJvImStu1rmQJAFUvaQ\"}\n  payload:  {\n  \"provisionerId\": \"aws-provisioner-v1\",\n  \"workerType\": \"github-worker\",\n  \"extra\": {\n    \"github\": {\n      \"env\": true,\n      \"events\": [\n        \"pull_request.opened\",\n        \"pull_request.synchronize\",\n        \"pull_request.reopened\",\n        \"push\"\n      ]\n    }\n  },\n  \"routes\": [\n    \"index.deepspeech.tensorflow.pip.warpctc.cpu\"\n  ],\n  \"payload\": {\n    \"maxRunTime\": 7200,\n    \"image\": \"ubuntu:14.04\",\n    \"command\": [\n      \"/bin/bash\",\n      \"--login\",\n      \"-c\",\n      \"set -xe && apt-get -qq update && apt-get -qq -y install git build-essential python-virtualenv python-dev libblas-dev liblapack-dev gfortran swig wget software-properties-common zip zlib1g-dev unzip && echo 'oracle-java8-installer shared/accepted-oracle-license-v1-1 select true' | debconf-set-selections && add-apt-repository --yes ppa:webupd8team/java && apt-get -qq update && DEBIAN_FRONTEND=noninteractive apt-get -qq -y --force-yes --no-install-recommends install oracle-java8-installer && adduser --system --home /home/build-user/ build-user && cd /home/build-user/ && echo '#!/bin/bash\\nset -xe\\nenv && id && mkdir ~/DeepSpeech/ && git clone --quiet https://github.com/lissyx/tensorflow.git ~/DeepSpeech/tf/ && cd ~/DeepSpeech/tf && git checkout --quiet dc3b4f806e2ba2c2eb5d53f59b08e58bd17ecf44 && ./setup.sh && ./build.sh' > run.sh && chmod +x run.sh && sudo -H -u build-user /bin/bash run.sh\"\n    ],\n    \"artifacts\": {\n      \"public\": {\n        \"type\": \"directory\",\n        \"path\": \"/tmp/tensorflow_pkg/\",\n        \"expires\": \"2016-11-09T12:43:30.646Z\"\n      }\n    },\n    \"env\": {\n      \"GITHUB_EVENT\": \"pull_request.synchronize\",\n      \"GITHUB_BRANCH\": \"warpctc\",\n      \"GITHUB_PULL_REQUEST\": 3,\n      \"GITHUB_BASE_REPO_URL\": \"https://github.com/mozilla/tensorflow.git\",\n      \"GITHUB_BASE_USER\": \"mozilla\",\n      \"GITHUB_BASE_SHA\": \"787ab22d490e79ea8c06511d60d6cddf1b2dd2c2\",\n      \"GITHUB_BASE_BRANCH\": \"warpctc\",\n      \"GITHUB_BASE_REF\": \"warpctc\",\n      \"GITHUB_HEAD_REPO_URL\": \"https://github.com/lissyx/tensorflow.git\",\n      \"GITHUB_HEAD_USER\": \"lissyx\",\n      \"GITHUB_HEAD_SHA\": \"dc3b4f806e2ba2c2eb5d53f59b08e58bd17ecf44\",\n      \"GITHUB_HEAD_BRANCH\": \"tc-build\",\n      \"GITHUB_HEAD_USER_EMAIL\": \"lissyx@users.noreply.github.com\"\n    }\n  },\n  \"metadata\": {\n    \"name\": \"TaskCluster TensorFlow CPU only\",\n    \"description\": \"Building TensorFlow with CPU only support\",\n    \"owner\": \"lissyx@users.noreply.github.com\",\n    \"source\": \"https://github.com/lissyx/tensorflow.git\"\n  },\n  \"created\": \"2016-10-10T12:43:30.646Z\",\n  \"deadline\": \"2016-10-11T12:43:30.646Z\",\n  \"schedulerId\": \"task-graph-scheduler\",\n  \"taskGroupId\": \"RXrwZtkPR2K-lnrp61rp8A\",\n  \"dependencies\": [],\n  \"requires\": \"all-completed\",\n  \"priority\": \"normal\",\n  \"retries\": 5,\n  \"scopes\": [],\n  \"tags\": {},\n  \"expires\": \"2017-10-11T12:43:30.646Z\"\n}\n  time:     2016-10-10T12:43:30.885Z\ndetails:\n{\n  \"scopesets\": [\n    [\n      \"queue:route:index.deepspeech.tensorflow.pip.warpctc.cpu\"\n    ]\n  ],\n  \"scopes\": [\n    \"assume:repo:github.com/mozilla/tensorflow:pull-request\",\n    \"queue:create-task:aws-provisioner-v1/github-worker\",\n    \"queue:route:index.garbage.*\",\n    \"secrets:get:garbage/*\",\n    \"secrets:set:garbage/*\"\n  ]\n}",
            "requestInfo": {
                "method": "defineTask",
                "params": {
                    "taskId": "HfPNJvImStu1rmQJAFUvaQ"
                },
                "payload": {
                    "provisionerId": "aws-provisioner-v1",
                    "workerType": "github-worker",
                    "extra": {
                        "github": {
                            "env": true,
                            "events": [
                                "pull_request.opened",
                                "pull_request.synchronize",
                                "pull_request.reopened",
                                "push"
                            ]
                        }
                    },
                    "routes": [
                        "index.deepspeech.tensorflow.pip.warpctc.cpu"
                    ],
                    "payload": {
                        "maxRunTime": 7200,
                        "image": "ubuntu:14.04",
                        "command": [
                            "/bin/bash",
                            "--login",
                            "-c",
                            "set -xe && apt-get -qq update && apt-get -qq -y install git build-essential python-virtualenv python-dev libblas-dev liblapack-dev gfortran swig wget software-properties-common zip zlib1g-dev unzip && echo 'oracle-java8-installer shared/accepted-oracle-license-v1-1 select true' | debconf-set-selections && add-apt-repository --yes ppa:webupd8team/java && apt-get -qq update && DEBIAN_FRONTEND=noninteractive apt-get -qq -y --force-yes --no-install-recommends install oracle-java8-installer && adduser --system --home /home/build-user/ build-user && cd /home/build-user/ && echo '#!/bin/bash\nset -xe\nenv && id && mkdir ~/DeepSpeech/ && git clone --quiet https://github.com/lissyx/tensorflow.git ~/DeepSpeech/tf/ && cd ~/DeepSpeech/tf && git checkout --quiet dc3b4f806e2ba2c2eb5d53f59b08e58bd17ecf44 && ./setup.sh && ./build.sh' > run.sh && chmod +x run.sh && sudo -H -u build-user /bin/bash run.sh"
                        ],
                        "artifacts": {
                            "public": {
                                "type": "directory",
                                "path": "/tmp/tensorflow_pkg/",
                                "expires": "2016-11-09T12:43:30.646Z"
                            }
                        },
                        "env": {
                            "GITHUB_EVENT": "pull_request.synchronize",
                            "GITHUB_BRANCH": "warpctc",
                            "GITHUB_PULL_REQUEST": 3,
                            "GITHUB_BASE_REPO_URL": "https://github.com/mozilla/tensorflow.git",
                            "GITHUB_BASE_USER": "mozilla",
                            "GITHUB_BASE_SHA": "787ab22d490e79ea8c06511d60d6cddf1b2dd2c2",
                            "GITHUB_BASE_BRANCH": "warpctc",
                            "GITHUB_BASE_REF": "warpctc",
                            "GITHUB_HEAD_REPO_URL": "https://github.com/lissyx/tensorflow.git",
                            "GITHUB_HEAD_USER": "lissyx",
                            "GITHUB_HEAD_SHA": "dc3b4f806e2ba2c2eb5d53f59b08e58bd17ecf44",
                            "GITHUB_HEAD_BRANCH": "tc-build",
                            "GITHUB_HEAD_USER_EMAIL": "lissyx@users.noreply.github.com"
                        }
                    },
                    "metadata": {
                        "name": "TaskCluster TensorFlow CPU only",
                        "description": "Building TensorFlow with CPU only support",
                        "owner": "lissyx@users.noreply.github.com",
                        "source": "https://github.com/lissyx/tensorflow.git"
                    },
                    "created": "2016-10-10T12:43:30.646Z",
                    "deadline": "2016-10-11T12:43:30.646Z",
                    "schedulerId": "task-graph-scheduler",
                    "taskGroupId": "RXrwZtkPR2K-lnrp61rp8A",
                    "dependencies": [],
                    "requires": "all-completed",
                    "priority": "normal",
                    "retries": 5,
                    "scopes": [],
                    "tags": {},
                    "expires": "2017-10-11T12:43:30.646Z"
                },
                "time": "2016-10-10T12:43:30.885Z"
            },
            "details": {
                "scopesets": [
                    [
                        "queue:route:index.deepspeech.tensorflow.pip.warpctc.cpu"
                    ]
                ],
                "scopes": [
                    "assume:repo:github.com/mozilla/tensorflow:pull-request",
                    "queue:create-task:aws-provisioner-v1/github-worker",
                    "queue:route:index.garbage.*",
                    "secrets:get:garbage/*",
                    "secrets:set:garbage/*"
                ]
            }
        }
    }
]
```


See forum at
http://jambage.com/kontakt/forum/shop-system/wuensche-neue-features-fehler/list/neues-feature.html

It requires the commit for the table extension

https://github.com/franzholz/table/commit/142131d7a33e7354690839915930c8b942c5a34b


TaskCluster: https://tools.taskcluster.net/task-graph-inspector/#ed7LoxNXTYetsucSVzTwog/


TaskCluster: https://tools.taskcluster.net/task-graph-inspector/#OAaPzFjPTnChuUF6xhR5oA/


TaskCluster: https://tools.taskcluster.net/task-graph-inspector/#G4k9bMEgQqCkYj1Tt1pGLA/


Нейминг поправлю, забыл откорректировать перед заливкой.


Visual Regression Testing found a difference between new version and the baseline.
Check the diffs [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-pr-check/683/).
Accept the new baseline [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-update-baseline/parambuild?branch=ember).


primer commit de ejemplo


Visual Regression Testing found a difference between new version and the baseline.
Check the diffs [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-pr-check/684/).
Accept the new baseline [here](http://jenkins.wikia-prod:8080/job/design-system-reference-page-update-baseline/parambuild?branch=ember).


![azzpcvy 1](https://cloud.githubusercontent.com/assets/22616589/19236581/c4309c76-8ebd-11e6-9359-176cfdf09560.png)


Is this right? The store logo is not showing at all with this commented out.


What is this psychic broccoli


Lol Sorry wrong commit


pruebas git, github y bucket


和 #672 一样的么


TeamCity OTA+ :: rvi_sota_server :: ci [Build 1303](http://teamcity.prod01.internal.advancedtelematic.com:8111/viewLog.html?buildId=15243&buildTypeId=ota_plus_RviSotaServer_Ci) is now running


Bien reçu ton envoi.
Jean Lionel


you could make two `const int`, one for 7 and the other for 20 - BIT_DEPTH. it is unlikely to make a big difference but could make the compiler more aware.