[R/dEploidTools.R:1:22:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                     ^
```
[R/dEploidTools.R:1:28:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                           ^
```
[R/dEploidTools.R:2:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L2) *style:* **Variable and function names should be all lowercase.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:2:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L2) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:2:48:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L2) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
                                               ^
```
[R/dEploidTools.R:3:15:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L3) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i+1
              ^
```
[R/dEploidTools.R:3:22:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L3) *style:* **Put spaces around all infix operators.**
```r
        arg_i = arg_i+1
                    ~^~
```
[R/dEploidTools.R:6:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L6) *style:* **Variable and function names should be all lowercase.**
```r
    outPrefix = "dataExplore"
    ^~~~~~~~~
```
[R/dEploidTools.R:6:15:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L6) *style:* **Use <-, not =, for assignment.**
```r
    outPrefix = "dataExplore"
              ^
```
[R/dEploidTools.R:7:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L7) *style:* **Variable and function names should be all lowercase.**
```r
    vcfFileName = ""
    ^~~~~~~~~~~
```
[R/dEploidTools.R:7:17:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L7) *style:* **Use <-, not =, for assignment.**
```r
    vcfFileName = ""
                ^
```
[R/dEploidTools.R:8:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L8) *style:* **Variable and function names should be all lowercase.**
```r
    refFileName = ""
    ^~~~~~~~~~~
```
[R/dEploidTools.R:8:17:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L8) *style:* **Use <-, not =, for assignment.**
```r
    refFileName = ""
                ^
```
[R/dEploidTools.R:9:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L9) *style:* **Variable and function names should be all lowercase.**
```r
    altFileName = ""
    ^~~~~~~~~~~
```
[R/dEploidTools.R:9:17:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L9) *style:* **Use <-, not =, for assignment.**
```r
    altFileName = ""
                ^
```
[R/dEploidTools.R:10:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L10) *style:* **Variable and function names should be all lowercase.**
```r
    plafFileName = ""
    ^~~~~~~~~~~~
```
[R/dEploidTools.R:10:18:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L10) *style:* **Use <-, not =, for assignment.**
```r
    plafFileName = ""
                 ^
```
[R/dEploidTools.R:11:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L11) *style:* **Variable and function names should be all lowercase.**
```r
    excludeFileName = ""
    ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:11:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L11) *style:* **Use <-, not =, for assignment.**
```r
    excludeFileName = ""
                    ^
```
[R/dEploidTools.R:12:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L12) *style:* **Variable and function names should be all lowercase.**
```r
    dEploidPrefix = ""
    ^~~~~~~~~~~~~
```
[R/dEploidTools.R:12:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L12) *style:* **Use <-, not =, for assignment.**
```r
    dEploidPrefix = ""
                  ^
```
[R/dEploidTools.R:13:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L13) *style:* **Variable and function names should be all lowercase.**
```r
    excludeBool = FALSE
    ^~~~~~~~~~~
```
[R/dEploidTools.R:13:17:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L13) *style:* **Use <-, not =, for assignment.**
```r
    excludeBool = FALSE
                ^
```
[R/dEploidTools.R:15:11:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L15) *style:* **Use <-, not =, for assignment.**
```r
    arg_i = 1
          ^
```
[R/dEploidTools.R:16:11:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
          ^
```
[R/dEploidTools.R:16:33:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
                                ^
```
[R/dEploidTools.R:17:14:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L17) *style:* **Use <-, not =, for assignment.**
```r
        argv = args[arg_i]
             ^
```
[R/dEploidTools.R:18:12:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
           ^
```
[R/dEploidTools.R:18:28:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
                           ^
```
[R/dEploidTools.R:19:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L19) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:19:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L19) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:19:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L19) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:19:52:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:20:13:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L20) *style:* **Variable and function names should be all lowercase.**
```r
            vcfFileName = args[arg_i]
            ^~~~~~~~~~~
```
[R/dEploidTools.R:20:25:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L20) *style:* **Use <-, not =, for assignment.**
```r
            vcfFileName = args[arg_i]
                        ^
```
[R/dEploidTools.R:21:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                  ^
```
[R/dEploidTools.R:21:36:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                                   ^
```
[R/dEploidTools.R:22:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L22) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:22:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L22) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:22:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L22) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:22:52:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:23:13:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L23) *style:* **Variable and function names should be all lowercase.**
```r
            plafFileName = args[arg_i]
            ^~~~~~~~~~~~
```
[R/dEploidTools.R:23:26:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L23) *style:* **Use <-, not =, for assignment.**
```r
            plafFileName = args[arg_i]
                         ^
```
[R/dEploidTools.R:24:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                  ^
```
[R/dEploidTools.R:24:35:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                                  ^
```
[R/dEploidTools.R:25:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L25) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:25:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L25) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:25:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L25) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:25:52:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:26:13:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L26) *style:* **Variable and function names should be all lowercase.**
```r
            refFileName = args[arg_i]
            ^~~~~~~~~~~
```
[R/dEploidTools.R:26:25:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L26) *style:* **Use <-, not =, for assignment.**
```r
            refFileName = args[arg_i]
                        ^
```
[R/dEploidTools.R:27:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                  ^
```
[R/dEploidTools.R:27:35:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                                  ^
```
[R/dEploidTools.R:28:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L28) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:28:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L28) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:28:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L28) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:28:52:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L28) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:29:13:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L29) *style:* **Variable and function names should be all lowercase.**
```r
            altFileName = args[arg_i]
            ^~~~~~~~~~~
```
[R/dEploidTools.R:29:25:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L29) *style:* **Use <-, not =, for assignment.**
```r
            altFileName = args[arg_i]
                        ^
```
[R/dEploidTools.R:30:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                  ^
```
[R/dEploidTools.R:30:39:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                                      ^
```
[R/dEploidTools.R:31:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L31) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:31:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L31) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:31:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L31) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:31:52:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L31) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:32:13:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L32) *style:* **Variable and function names should be all lowercase.**
```r
            excludeFileName = args[arg_i]
            ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:32:29:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L32) *style:* **Use <-, not =, for assignment.**
```r
            excludeFileName = args[arg_i]
                            ^
```
[R/dEploidTools.R:33:13:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L33) *style:* **Variable and function names should be all lowercase.**
```r
            excludeBool = TRUE
            ^~~~~~~~~~~
```
[R/dEploidTools.R:33:25:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L33) *style:* **Use <-, not =, for assignment.**
```r
            excludeBool = TRUE
                        ^
```
[R/dEploidTools.R:34:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                  ^
```
[R/dEploidTools.R:34:33:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                                ^
```
[R/dEploidTools.R:35:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L35) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:35:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L35) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:35:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L35) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:35:52:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:36:13:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L36) *style:* **Variable and function names should be all lowercase.**
```r
            outPrefix = args[arg_i]
            ^~~~~~~~~
```
[R/dEploidTools.R:36:23:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L36) *style:* **Use <-, not =, for assignment.**
```r
            outPrefix = args[arg_i]
                      ^
```
[R/dEploidTools.R:37:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                  ^
```
[R/dEploidTools.R:37:40:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                                       ^
```
[R/dEploidTools.R:38:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L38) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:38:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L38) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:38:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L38) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:38:52:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:39:13:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L39) *style:* **Variable and function names should be all lowercase.**
```r
            dEploidPrefix = args[arg_i]
            ^~~~~~~~~~~~~
```
[R/dEploidTools.R:39:27:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L39) *style:* **Use <-, not =, for assignment.**
```r
            dEploidPrefix = args[arg_i]
                          ^
```
[R/dEploidTools.R:44:15:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L44) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i + 1
              ^
```
[R/dEploidTools.R:51:8:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
       ^
```
[R/dEploidTools.R:51:10:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L51) *style:* **Variable and function names should be all lowercase.**
```r
    if ( plafFileName == "" ){
         ^~~~~~~~~~~~
```
[R/dEploidTools.R:51:28:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
                           ^
```
[R/dEploidTools.R:58:12:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
           ^
```
[R/dEploidTools.R:58:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
                  ^
```
[R/dEploidTools.R:58:35:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L58) *style:* **Variable and function names should be all lowercase.**
```r
    return ( list ( vcfFileName = vcfFileName,
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:59:35:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L59) *style:* **Variable and function names should be all lowercase.**
```r
                    refFileName = refFileName,
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:60:35:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L60) *style:* **Variable and function names should be all lowercase.**
```r
                    altFileName = altFileName,
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:61:36:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L61) *style:* **Variable and function names should be all lowercase.**
```r
                    plafFileName = plafFileName,
                                   ^~~~~~~~~~~~
```
[R/dEploidTools.R:62:33:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L62) *style:* **Variable and function names should be all lowercase.**
```r
                    outPrefix = outPrefix,
                                ^~~~~~~~~
```
[R/dEploidTools.R:63:37:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L63) *style:* **Variable and function names should be all lowercase.**
```r
                    dEploidPrefix = dEploidPrefix,
                                    ^~~~~~~~~~~~~
```
[R/dEploidTools.R:64:39:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L64) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeFileName = excludeFileName,
                                      ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:65:35:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L65) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeBool = excludeBool) )
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:65:47:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L65) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    excludeBool = excludeBool) )
                                              ^
```
[R/dEploidTools.R:69:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L69) *style:* **Variable and function names should be all lowercase.**
```r
fun.dEploidPrefix <- function ( prefix ){
^~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:81:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L81) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.coverage <- function ( inputs ){
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:82:17:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L82) *style:* **Variable and function names should be all lowercase.**
```r
    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~
```
[R/dEploidTools.R:83:17:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:83:17:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L83) *warning:* **no visible global function definition for ‘extractCoverageFromVcf’**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:83:48:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~
```
[R/dEploidTools.R:85:17:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:85:17:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L85) *warning:* **no visible global function definition for ‘extractCoverageFromTxt’**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:85:48:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                               ^~~~~~~~~~~
```
[R/dEploidTools.R:85:68:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                                                   ^~~~~~~~~~~
```
[R/dEploidTools.R:109:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:109:38:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~
```
[R/dEploidTools.R:109:51:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:110:9:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L110) *style:* **Use <-, not =, for assignment.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
        ^
```
[R/dEploidTools.R:110:22:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L110) *style:* **Variable and function names should be all lowercase.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[R/dEploidTools.R:111:9:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L111) *style:* **Use <-, not =, for assignment.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
        ^
```
[R/dEploidTools.R:111:22:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L111) *style:* **Variable and function names should be all lowercase.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[R/dEploidTools.R:112:39:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L112) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = ref[,1],
                                      ^
```
[R/dEploidTools.R:113:37:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L113) *style:* **Commas should always have a space after.**
```r
                         POS = ref[,2],
                                    ^
```
[R/dEploidTools.R:114:42:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L114) *style:* **Commas should always have a space after.**
```r
                         refCount = ref[,3],
                                         ^
```
[R/dEploidTools.R:115:42:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L115) *style:* **Commas should always have a space after.**
```r
                         altCount = alt[,3] )
                                         ^
```
[R/dEploidTools.R:120:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L120) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
^~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:120:34:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                 ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:120:51:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:121:10:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L121) *style:* **Variable and function names should be all lowercase.**
```r
    if ( excludeBool ) {
         ^~~~~~~~~~~
```
[R/dEploidTools.R:122:39:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L122) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool,
                                      ^~~~~~~~~~~
```
[R/dEploidTools.R:123:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L123) *style:* **lines should not be more than 80 characters.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:123:51:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L123) *style:* **Variable and function names should be all lowercase.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
                                                  ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:125:39:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L125) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool ))
                                      ^~~~~~~~~~~
```
[R/dEploidTools.R:147:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:147:38:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                     ^~~~~~~
```
[R/dEploidTools.R:147:47:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                              ^~~~~~~~~~~~
```
[R/dEploidTools.R:150:12:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L150) *style:* **Place a space before left parenthesis, except in a function call.**
```r
         if( any( grepl( "gzfile connection", w) ) )
           ^
```
[R/dEploidTools.R:154:9:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L154) *style:* **Use <-, not =, for assignment.**
```r
    gzf = gzfile(vcfFile, open = "rb")
        ^
```
[R/dEploidTools.R:154:18:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L154) *style:* **Variable and function names should be all lowercase.**
```r
    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~
```
[R/dEploidTools.R:154:18:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L154) *warning:* **no visible binding for global variable ‘vcfFile’**
```r
    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~
```
[R/dEploidTools.R:155:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L155) *style:* **Variable and function names should be all lowercase.**
```r
    skipNum = 0
    ^~~~~~~
```
[R/dEploidTools.R:155:13:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L155) *style:* **Use <-, not =, for assignment.**
```r
    skipNum = 0
            ^
```
[R/dEploidTools.R:156:10:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L156) *style:* **Use <-, not =, for assignment.**
```r
    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
         ^
```
[R/dEploidTools.R:156:49:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L156) *style:* **Put spaces around all infix operators.**
```r
    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                               ~^~
```
[R/dEploidTools.R:156:61:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L156) *style:* **Put spaces around all infix operators.**
```r
    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                           ~^~
```
[R/dEploidTools.R:158:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L158) *style:* **Commented code should be removed.**
```r
        if (grepl("##", line )){
                    ^~~~~~~~~~~~
```
[R/dEploidTools.R:159:13:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L159) *style:* **Variable and function names should be all lowercase.**
```r
            skipNum = skipNum+1
            ^~~~~~~
```
[R/dEploidTools.R:159:21:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L159) *style:* **Use <-, not =, for assignment.**
```r
            skipNum = skipNum+1
                    ^
```
[R/dEploidTools.R:159:23:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L159) *style:* **Variable and function names should be all lowercase.**
```r
            skipNum = skipNum+1
                      ^~~~~~~
```
[R/dEploidTools.R:159:30:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L159) *style:* **Put spaces around all infix operators.**
```r
            skipNum = skipNum+1
                            ~^~
```
[R/dEploidTools.R:163:14:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L163) *style:* **Use <-, not =, for assignment.**
```r
        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
             ^
```
[R/dEploidTools.R:163:53:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L163) *style:* **Put spaces around all infix operators.**
```r
        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                   ~^~
```
[R/dEploidTools.R:163:65:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L163) *style:* **Put spaces around all infix operators.**
```r
        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                               ~^~
```
[R/dEploidTools.R:167:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L167) *style:* **lines should not be more than 80 characters.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:167:10:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L167) *style:* **Use <-, not =, for assignment.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
         ^
```
[R/dEploidTools.R:167:31:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L167) *style:* **Variable and function names should be all lowercase.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                              ^~~~~~~
```
[R/dEploidTools.R:167:45:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                           ~^~
```
[R/dEploidTools.R:167:46:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L167) *style:* **Variable and function names should be all lowercase.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                             ^~~~~~~
```
[R/dEploidTools.R:167:61:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                           ~^~
```
[R/dEploidTools.R:167:77:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                           ~^~
```
[R/dEploidTools.R:167:119:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                                ~^~
```
[R/dEploidTools.R:169:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L169) *style:* **Variable and function names should be all lowercase.**
```r
    sampleName = names(vcf)[10]
    ^~~~~~~~~~
```
[R/dEploidTools.R:169:16:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L169) *style:* **Use <-, not =, for assignment.**
```r
    sampleName = names(vcf)[10]
               ^
```
[R/dEploidTools.R:171:9:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L171) *style:* **Use <-, not =, for assignment.**
```r
    tmp = vcf[[sampleName]]
        ^
```
[R/dEploidTools.R:171:16:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L171) *style:* **Variable and function names should be all lowercase.**
```r
    tmp = vcf[[sampleName]]
               ^~~~~~~~~~
```
[R/dEploidTools.R:172:11:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L172) *style:* **Use <-, not =, for assignment.**
```r
    field = strsplit(as.character(tmp),":")
          ^
```
[R/dEploidTools.R:172:40:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L172) *style:* **Commas should always have a space after.**
```r
    field = strsplit(as.character(tmp),":")
                                       ^
```
[R/dEploidTools.R:174:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L174) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/dEploidTools.R:174:15:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L174) *style:* **Use <-, not =, for assignment.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
              ^
```
[R/dEploidTools.R:174:44:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L174) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
                                           ^~~~~~~~~~~~
```
[R/dEploidTools.R:175:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L175) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
    ^~~~~~
```
[R/dEploidTools.R:175:12:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L175) *style:* **Use <-, not =, for assignment.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
           ^
```
[R/dEploidTools.R:175:36:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L175) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                   ^~~~~~~~~
```
[R/dEploidTools.R:175:47:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L175) *style:* **Commas should always have a space after.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                              ^
```
[R/dEploidTools.R:177:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L177) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/dEploidTools.R:177:14:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L177) *style:* **Use <-, not =, for assignment.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
             ^
```
[R/dEploidTools.R:177:41:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L177) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
                                        ^~~~~~
```
[R/dEploidTools.R:178:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L178) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/dEploidTools.R:178:14:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L178) *style:* **Use <-, not =, for assignment.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
             ^
```
[R/dEploidTools.R:178:41:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L178) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
                                        ^~~~~~
```
[R/dEploidTools.R:180:39:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L180) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = vcf[,1],
                                      ^
```
[R/dEploidTools.R:181:37:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L181) *style:* **Commas should always have a space after.**
```r
                         POS = vcf[,2],
                                    ^
```
[R/dEploidTools.R:182:37:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L182) *style:* **Variable and function names should be all lowercase.**
```r
                         refCount = refCount,
                                    ^~~~~~~~
```
[R/dEploidTools.R:183:37:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L183) *style:* **Variable and function names should be all lowercase.**
```r
                         altCount = altCount )
                                    ^~~~~~~~
```
[R/dEploidTools.R:204:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L204) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
^~~~~~~~~~~
```
[R/dEploidTools.R:204:12:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L204) *style:* **Put spaces around all infix operators.**
```r
extractPLAF<- function ( plafName ){
          ~^
```
[R/dEploidTools.R:204:26:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L204) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
                         ^~~~~~~~
```
[R/dEploidTools.R:205:25:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L205) *style:* **Variable and function names should be all lowercase.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~
```
[R/dEploidTools.R:205:41:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L205) *style:* **Put spaces around all infix operators.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~
```
[R/dEploidTools.R:210:11:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
         ~^~~
```
[R/dEploidTools.R:210:19:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                 ~^~
```
[R/dEploidTools.R:210:23:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                     ~^~
```
[R/dEploidTools.R:210:24:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L210) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                       ^
```
[R/dEploidTools.R:210:26:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                        ~^~
```
[R/dEploidTools.R:210:28:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                          ~^~
```
[R/dEploidTools.R:211:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **lines should not be more than 80 characters.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:211:8:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
      ~^~~
```
[R/dEploidTools.R:211:23:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                     ~^~
```
[R/dEploidTools.R:211:30:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                            ~^~
```
[R/dEploidTools.R:211:43:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                         ~^~
```
[R/dEploidTools.R:211:44:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                           ^
```
[R/dEploidTools.R:211:46:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                            ~^~
```
[R/dEploidTools.R:211:54:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                    ~^~
```
[R/dEploidTools.R:211:59:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                         ~^~
```
[R/dEploidTools.R:211:72:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                      ~^~
```
[R/dEploidTools.R:211:77:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **Commas should always have a space after.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                            ^
```
[R/dEploidTools.R:211:77:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                            ^
```
[R/dEploidTools.R:211:79:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                             ~^~
```
[R/dEploidTools.R:211:87:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                                ~^~
```
[R/dEploidTools.R:212:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L212) *style:* **lines should not be more than 80 characters.**
```r
    #  llk<-lgamma(fac*f.samp+cov.alt)+lgamma(fac*(1-f.samp)+cov.ref)-lgamma(fac*f.samp)-lgamma(fac*(1-f.samp));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:212:8:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L212) *style:* **Commented code should be removed.**
```r
    #  llk<-lgamma(fac*f.samp+cov.alt)+lgamma(fac*(1-f.samp)+cov.ref)-lgamma(fac*f.samp)-lgamma(fac*(1-f.samp));
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:213:25:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L213) *style:* **Put spaces around all infix operators.**
```r
    if (sum(is.nan(llk))>1){
                       ~^~
```
[R/dEploidTools.R:220:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L220) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.dic.by.llk.var <- function ( tmpllk ){
^~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:221:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L221) *style:* **lines should not be more than 80 characters.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:221:23:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L221) *style:* **Put spaces around all infix operators.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
                     ~^~
```
[R/dEploidTools.R:221:40:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L221) *style:* **Put spaces around all infix operators.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
                                      ~^~
```
[R/dEploidTools.R:221:48:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L221) *style:* **Put spaces around all infix operators.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
                                              ~^~
```
[R/dEploidTools.R:225:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L225) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.dic.by.theta <- function ( tmpllk, thetallk ){
^~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:226:5:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L226) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    DIC.WSAF.bar = -2 * sum(thetallk)
    ^~~~~~~~~~~~
```
[R/dEploidTools.R:226:18:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L226) *style:* **Use <-, not =, for assignment.**
```r
    DIC.WSAF.bar = -2 * sum(thetallk)
                 ^
```
[R/dEploidTools.R:227:1:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L227) *style:* **lines should not be more than 80 characters.**
```r
    return (  mean(-2*tmpllk) + (mean(-2*tmpllk) - DIC.WSAF.bar) ) # D_bar + pD, where pD = D_bar - D_theta, and D_bar = mean(D_theta)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:227:22:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L227) *style:* **Put spaces around all infix operators.**
```r
    return (  mean(-2*tmpllk) + (mean(-2*tmpllk) - DIC.WSAF.bar) ) # D_bar + pD, where pD = D_bar - D_theta, and D_bar = mean(D_theta)
                    ~^~
```
[R/dEploidTools.R:227:41:](https://github.com/mcveanlab/DEploid-r/blob/16c3481dce5bb0bcf50c42b0d50a31a989709387/R/dEploidTools.R#L227) *style:* **Put spaces around all infix operators.**
```r
    return (  mean(-2*tmpllk) + (mean(-2*tmpllk) - DIC.WSAF.bar) ) # D_bar + pD, where pD = D_bar - D_theta, and D_bar = mean(D_theta)
                                       ~^~
```


oh my.. I made a mistake in there, the file should be onlp-platform-any.yml and it was named onlp-platform-any.ym .. sorry :( give me a second to fix


## Wordpress Theme by Underscores


о


I manually run 'brew install coreutils' and 'upgrade_oh_my_zsh',however,the color becomes very strange,do I need to do something else?


@rtoal would be proud of the beauty that is the one liner, as brought to you by jQuery


Humm, normally not... but if you throw a really messed up (previously long term used 2.1 version map it can take a while to clean it up! I think the Debian packager guy (over on the Gitter channel) said the first time he used a recent version with the auditing "feature" it took _a while_ - IIRC it is actually a hang-over from moving a `qDebug()` bit of information into the main-line code...


If you git stash > git pull > git stash pop before a commit or used rebase we'd not have that many merges and conflicts.


i seem to recall a discussion about this some time ago

as i recall, '/usr/bin/env python' is the more robust approach

i think the argument revolved around python being install in a location other than /usr/bin/python, and being able to invoke weewx scripts with different versions of python on a single host.


should be `color?: number[] | string | dojo._base.Color;` I think.
or `color?: [number, number, number] | [number, number, number, number] | string | dojo._base.Color;` I think.


Exclude the files you don't want to track in `.gitignore`.


HEY DUMMY!

You better VOID that API key and secret, it is now PUBLIC KNOWLEDGE.

Hope I saw it before anyone malicious did.


The correlation of two vectors with zero s.d. should be NaN, I think?

It's a division by zero case


My bad, guys! I just reverted this merge https://github.com/gjaldon/heroku-buildpack-phoenix-static/pull/41 and will reintroduce the changes in a backwards-compatible way @ericmj.


lol


@alexiusacademia I started working on adding irregular sections in the [sections module](https://github.com/benjiyamin/pyflo/blob/master/pyflo/sections.py) for open channel flow. I have yet to add unit tests and focus on making the code efficient. Do you have experience with irregular sections? I've opened it in Issue #1.

I've also thought about adding infiltration calculations as a module as well.

Do you have any feature ideas? we can brainstorm.


This is undefined behaviour.  Earlier in this commit, array `UDP_Socket` was reduced to be exactly 2 elements long, so accessing `[2]` is undefined.  In `_GLIBCXX_DEBUG` builds, it triggers an exception from the checked implementation of `array`.  In ASan builds, it kills the program.  In release builds, it causes memory corruption by writing beyond the end of the array.


It looks like someone already made a fix,

https://github.com/GDSSecurity/Windows-Exploit-Suggester/commit/67ed73aa0018073c639bd8ea877422c81202fc5a


Boom. Captchas work.


add qidian MM


The above is correct, but incomplete.  Due to the way tracker IDs are assigned, there appears not to be any protection against receiving a message with a tracker ID from a peer other than the tracker.  Such a message could still be processed through this function, so anyone who can send datagrams to the client can trigger this problem.  It is not restricted to malicious trackers.


@william-gr I hope this time I got it right. Please correct if I messed up again.

Thanks.


Hey @bjskistad What has been done. It has been a while since I've kept up


As in terms of features that is


Yes, that was what I found

On 13/10/2016 12:11 PM, "Matthew Wall" <notifications@github.com> wrote:
>
> i seem to recall a discussion about this some time ago
>
> as i recall, '/usr/bin/env python' is the more robust approach
>
> i think the argument revolved around python being install in a location
other than /usr/bin/python, and being able to invoke weewx scripts with
different versions of python on a single host.
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub, or mute the thread.


ref #46


Not much. We're creating some docs, and getting back into the swing of things.


Has login and project creation been added?


Thêm dialog box trong profile master để xem bình luận của phản biện.
Thêm 1 page send-post-to-tester để chuyển bài viết cho phản biện.
Sử dụng 1 dialog box chung cho 3 page vừa edit .


Ok, so I was in the middle of experiments with it. Nothing had finished.

For reference: https://gist.github.com/hawkrives/9ffcf27347c08520542c33cd3a42fdd2

I'm going to try and summarize what I was working on in #aao.


@bjskistad


ddddd


eeeeee


项目第一次初始化数据库脚本


同步


I'm unsure if I'm using the correct syntax to request multiple parameters to run the rake task. I have defined set_current_week in the application_helper.rb file. Can I use that here so I don't need to pass any parameters?


@whitequark,
The way you wrote all the style->stroke conversion (by hand) introduces to same amount of bugs (some forgotten things (like width for error messages), not all style parameters copied (styles configuration lost it's meaning) etc).


Yes.


Ok what else?


Login isn't really working yet though.


Hmmm


Yeah.


Can you use VoIP


What?


Voice Over IP


I'm not sure how to do this. Also, does it make sense to do this here? My thinking is one rake task can not only update scores but also update pick.losses with the pulled score information


idk


@juanmottesi yo tmb arregle ese bug y meti varios cambios mas, mañana hacemos sync en clase a ver que onda :P


Prbly.


Here let me find the one I use


I think we need to check what's happening with the POST request.


Ok Ill check in just a sec


kk


Here is what I use for VoIP (also known as pretty much Skype) https://discordapp.com


it makes deving so much easier and faster


@wonderwoman13, I'm having issues with the API and am hoping it's just syntax-related. Wanted to get this to you ASAP in hopes we can discuss on our call tomorrow


@whitequark,
How can I reproduce this?


@bhancock8: awesome. pushing a commit with the current one removed and switched the notebook to the generalized one.


@bjskistad tell me once you login and stuff


Hello


@HittmanA Btw we created https://newawe-test.herokuapp.com for live testing


Doesn't take me anywhere except my dashboard and yah!


Hold on let me make a room real quick


Hi: One question, where is de the simple web server in python that run on port 3000?


Try that


This will house all the database crapola we're going to create in 2016!


@jdcasey
I'm not sure what expiration time is suitable here, just set it to be 2 days.


@Innectic >.>


No need for a `MessagePacket` here - just returning a string will be fine. :smile:


Same here!


Manager textView textField Position in order to keyBoard not cover extView textField


1231 TESTANDO


Did this work for you?


Good Job


That'll happen once in a blue moon... I'd say we should take it out, no need to throw (most of the time) useless information at a user.


Duel.SwapControl will check it


Is that style still required?


UQLibrary has style guide for text-field (it has a specific colour for text-field underline)
please use a variable for the border style


why does github desktop add 2 emoji at the beginning of the initial commit


SSSSHHH, I'm in the midst of fixing that command still >.>


Oh, ok


@whitequark,
My main issue with styles was adding units for strokes. This, in fact, must be done in one place instead of searching all the places where it can be inserted. It potentially cause the same number of bugs.
* After this commit code becomes better and cleaner.
* The further changes with this code is simplier.
* Risks with bugs is the same as massive changing to Stroke::units, all of bugs is trivial and solveable.
I still don't see any problems with this sort of "refactoring". Every code needs more and more control, and this is cost of its existence.


another commit comment ~1m


I took it to be a debugging/testing option.  But I can add it to the man page as well.


Changed color of background


Yeah !!!


test duplicate commit ~1m


hey.. try harder dick


that's what she said


Where is your TODO?


It's ok :)


Please, rename newURL to outputUrlDisplay (it's more specific)

In camel case naming convention abbreviations are capitalized (not UPPERCASED), eg outputUrl (not outputURL)


下面


kkkkkkkkkkkkk


can you also cherry-pick into riscv-binutils-2.27 branch?


actually, it looks right in my branch, did we lose part in the patch?


Awesome, one of the nicest specs I have seen in a while! 👍  🎉


Why is not just 'id'?


I agree with @wcalebgray  on this point.  Since resubscribe only has any actionable contact with MailChimp in the event that the subscribe flag was changed, it shouldn't be all that chatty.

This line prevents the call to subscribe unless they are in the act of subscribing:
https://github.com/DynamoMTL/spree_chimpy/blob/master/lib/spree/chimpy/subscription.rb#L26

This is the bit that prevents unnecessary calls:
```
def subscribing?
  @model.subscribed && (@model.subscribed_changed? || @model.id_changed? || @model.new_record?)
end
```

It could trigger when a merge var value is changed too, though.  Do you have experience with that being the part that was overly chatty?

I'd be up for implementing another rake task that does batch updating of the users' subscribed status to mailchimp if you guys think that would be a smarter way to keep the list in sync.


There IS an account repo. It's just that @JaanJanno put it in some weird place.


```
make: *** No rule to make target `/var/android/out/target/product/fp2/obj/STATIC_LIBRARIES/librecovery_updater_msm_intermediates/export_includes', needed by `/var/android/out/target/product/fp2/obj/EXECUTABLES/updater_intermediates/import_includes'.  Stop.
```
`brunch fp2` still doesn't work :( (but it's too late right now)


Not compiling on my side, though, :/

Inspect your `out` folder. You should see `boot.img`, `recovery.img`, `system.img`, _et al._