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@shajoezhu
shajoezhu authored Oct 13, 2016
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<img src="extra/deploid.png" width="180">
[![Build Status](https://travis-ci.org/mcveanlab/DEploid-r.svg?branch=master)](https://travis-ci.org/mcveanlab/DEploid-r)
[![Build Status](https://ci.appveyor.com/api/projects/status/hi1nq97d5l68qs4r?svg=true)](https://ci.appveyor.com/project/shajoezhu/deploid-r)



`dEploid` is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.

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R/dEploidTools.R:1:22: style: Do not place spaces around code in parentheses or square brackets.

​fun.parse <- function( args ){
                     ^

R/dEploidTools.R:1:28: style: Do not place spaces around code in parentheses or square brackets.

​fun.parse <- function( args ){
                           ^

R/dEploidTools.R:2:5: style: Variable and function names should be all lowercase.

​    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:2:5: style: Words within variable and function names should be separated by '_' rather than '.'.

​    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:2:48: style: Do not place spaces around code in parentheses or square brackets.

​    fun.local.checkAndIncreaseArgI <- function ( ){
                                               ^

R/dEploidTools.R:3:15: style: Use <-, not =, for assignment.

​        arg_i = arg_i+1
              ^

R/dEploidTools.R:3:22: style: Put spaces around all infix operators.

​        arg_i = arg_i+1
                    ~^~

R/dEploidTools.R:6:5: style: Variable and function names should be all lowercase.

​    outPrefix = "dataExplore"
    ^~~~~~~~~

R/dEploidTools.R:6:15: style: Use <-, not =, for assignment.

​    outPrefix = "dataExplore"
              ^

R/dEploidTools.R:7:5: style: Variable and function names should be all lowercase.

​    vcfFileName = ""
    ^~~~~~~~~~~

R/dEploidTools.R:7:17: style: Use <-, not =, for assignment.

​    vcfFileName = ""
                ^

R/dEploidTools.R:8:5: style: Variable and function names should be all lowercase.

​    refFileName = ""
    ^~~~~~~~~~~

R/dEploidTools.R:8:17: style: Use <-, not =, for assignment.

​    refFileName = ""
                ^

R/dEploidTools.R:9:5: style: Variable and function names should be all lowercase.

​    altFileName = ""
    ^~~~~~~~~~~

R/dEploidTools.R:9:17: style: Use <-, not =, for assignment.

​    altFileName = ""
                ^

R/dEploidTools.R:10:5: style: Variable and function names should be all lowercase.

​    plafFileName = ""
    ^~~~~~~~~~~~

R/dEploidTools.R:10:18: style: Use <-, not =, for assignment.

​    plafFileName = ""
                 ^

R/dEploidTools.R:11:5: style: Variable and function names should be all lowercase.

​    excludeFileName = ""
    ^~~~~~~~~~~~~~~

R/dEploidTools.R:11:21: style: Use <-, not =, for assignment.

​    excludeFileName = ""
                    ^

R/dEploidTools.R:12:5: style: Variable and function names should be all lowercase.

​    dEploidPrefix = ""
    ^~~~~~~~~~~~~

R/dEploidTools.R:12:19: style: Use <-, not =, for assignment.

​    dEploidPrefix = ""
                  ^

R/dEploidTools.R:13:5: style: Variable and function names should be all lowercase.

​    excludeBool = FALSE
    ^~~~~~~~~~~

R/dEploidTools.R:13:17: style: Use <-, not =, for assignment.

​    excludeBool = FALSE
                ^

R/dEploidTools.R:15:11: style: Use <-, not =, for assignment.

​    arg_i = 1
          ^

R/dEploidTools.R:16:11: style: Do not place spaces around code in parentheses or square brackets.

​    while ( arg_i < length(args) ){
          ^

R/dEploidTools.R:16:33: style: Do not place spaces around code in parentheses or square brackets.

​    while ( arg_i < length(args) ){
                                ^

R/dEploidTools.R:17:14: style: Use <-, not =, for assignment.

​        argv = args[arg_i]
             ^

R/dEploidTools.R:18:12: style: Do not place spaces around code in parentheses or square brackets.

​        if ( argv == "-vcf" ){
           ^

R/dEploidTools.R:18:28: style: Do not place spaces around code in parentheses or square brackets.

​        if ( argv == "-vcf" ){
                           ^

R/dEploidTools.R:19:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:19:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:19:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:19:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:20:13: style: Variable and function names should be all lowercase.

​            vcfFileName = args[arg_i]
            ^~~~~~~~~~~

R/dEploidTools.R:20:25: style: Use <-, not =, for assignment.

​            vcfFileName = args[arg_i]
                        ^

R/dEploidTools.R:21:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-plaf" ){
                  ^

R/dEploidTools.R:21:36: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-plaf" ){
                                   ^

R/dEploidTools.R:22:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:22:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:22:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:22:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:23:13: style: Variable and function names should be all lowercase.

​            plafFileName = args[arg_i]
            ^~~~~~~~~~~~

R/dEploidTools.R:23:26: style: Use <-, not =, for assignment.

​            plafFileName = args[arg_i]
                         ^

R/dEploidTools.R:24:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-ref" ){
                  ^

R/dEploidTools.R:24:35: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-ref" ){
                                  ^

R/dEploidTools.R:25:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:25:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:25:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:25:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:26:13: style: Variable and function names should be all lowercase.

​            refFileName = args[arg_i]
            ^~~~~~~~~~~

R/dEploidTools.R:26:25: style: Use <-, not =, for assignment.

​            refFileName = args[arg_i]
                        ^

R/dEploidTools.R:27:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-alt" ){
                  ^

R/dEploidTools.R:27:35: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-alt" ){
                                  ^

R/dEploidTools.R:28:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:28:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:28:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:28:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:29:13: style: Variable and function names should be all lowercase.

​            altFileName = args[arg_i]
            ^~~~~~~~~~~

R/dEploidTools.R:29:25: style: Use <-, not =, for assignment.

​            altFileName = args[arg_i]
                        ^

R/dEploidTools.R:30:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-exclude" ){
                  ^

R/dEploidTools.R:30:39: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-exclude" ){
                                      ^

R/dEploidTools.R:31:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:31:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:31:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:31:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:32:13: style: Variable and function names should be all lowercase.

​            excludeFileName = args[arg_i]
            ^~~~~~~~~~~~~~~

R/dEploidTools.R:32:29: style: Use <-, not =, for assignment.

​            excludeFileName = args[arg_i]
                            ^

R/dEploidTools.R:33:13: style: Variable and function names should be all lowercase.

​            excludeBool = TRUE
            ^~~~~~~~~~~

R/dEploidTools.R:33:25: style: Use <-, not =, for assignment.

​            excludeBool = TRUE
                        ^

R/dEploidTools.R:34:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-o" ){
                  ^

R/dEploidTools.R:34:33: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-o" ){
                                ^

R/dEploidTools.R:35:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:35:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:35:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:35:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:36:13: style: Variable and function names should be all lowercase.

​            outPrefix = args[arg_i]
            ^~~~~~~~~

R/dEploidTools.R:36:23: style: Use <-, not =, for assignment.

​            outPrefix = args[arg_i]
                      ^

R/dEploidTools.R:37:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-dEprefix" ){
                  ^

R/dEploidTools.R:37:40: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-dEprefix" ){
                                       ^

R/dEploidTools.R:38:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:38:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:38:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:38:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:39:13: style: Variable and function names should be all lowercase.

​            dEploidPrefix = args[arg_i]
            ^~~~~~~~~~~~~

R/dEploidTools.R:39:27: style: Use <-, not =, for assignment.

​            dEploidPrefix = args[arg_i]
                          ^

R/dEploidTools.R:44:15: style: Use <-, not =, for assignment.

​        arg_i = arg_i + 1
              ^

R/dEploidTools.R:51:8: style: Do not place spaces around code in parentheses or square brackets.

​    if ( plafFileName == "" ){
       ^

R/dEploidTools.R:51:10: style: Variable and function names should be all lowercase.

​    if ( plafFileName == "" ){
         ^~~~~~~~~~~~

R/dEploidTools.R:51:28: style: Do not place spaces around code in parentheses or square brackets.

​    if ( plafFileName == "" ){
                           ^

R/dEploidTools.R:58:12: style: Do not place spaces around code in parentheses or square brackets.

​    return ( list ( vcfFileName = vcfFileName,
           ^

R/dEploidTools.R:58:19: style: Do not place spaces around code in parentheses or square brackets.

​    return ( list ( vcfFileName = vcfFileName,
                  ^

R/dEploidTools.R:58:35: style: Variable and function names should be all lowercase.

​    return ( list ( vcfFileName = vcfFileName,
                                  ^~~~~~~~~~~

R/dEploidTools.R:59:35: style: Variable and function names should be all lowercase.

​                    refFileName = refFileName,
                                  ^~~~~~~~~~~

R/dEploidTools.R:60:35: style: Variable and function names should be all lowercase.

​                    altFileName = altFileName,
                                  ^~~~~~~~~~~

R/dEploidTools.R:61:36: style: Variable and function names should be all lowercase.

​                    plafFileName = plafFileName,
                                   ^~~~~~~~~~~~

R/dEploidTools.R:62:33: style: Variable and function names should be all lowercase.

​                    outPrefix = outPrefix,
                                ^~~~~~~~~

R/dEploidTools.R:63:37: style: Variable and function names should be all lowercase.

​                    dEploidPrefix = dEploidPrefix,
                                    ^~~~~~~~~~~~~

R/dEploidTools.R:64:39: style: Variable and function names should be all lowercase.

​                    excludeFileName = excludeFileName,
                                      ^~~~~~~~~~~~~~~

R/dEploidTools.R:65:35: style: Variable and function names should be all lowercase.

​                    excludeBool = excludeBool) )
                                  ^~~~~~~~~~~

R/dEploidTools.R:65:47: style: Do not place spaces around code in parentheses or square brackets.

​                    excludeBool = excludeBool) )
                                              ^

R/dEploidTools.R:69:1: style: Variable and function names should be all lowercase.

​fun.dEploidPrefix <- function ( prefix ){
^~~~~~~~~~~~~~~~~

R/dEploidTools.R:81:1: style: Words within variable and function names should be separated by '_' rather than '.'.

​fun.extract.coverage <- function ( inputs ){
^~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:82:17: style: Variable and function names should be all lowercase.

​    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~

R/dEploidTools.R:83:17: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:83:17: warning: no visible global function definition for ‘extractCoverageFromVcf’

​        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:83:48: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~

R/dEploidTools.R:85:17: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:85:17: warning: no visible global function definition for ‘extractCoverageFromTxt’

​        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:85:48: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                               ^~~~~~~~~~~

R/dEploidTools.R:85:68: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                                                   ^~~~~~~~~~~

R/dEploidTools.R:109:1: style: Variable and function names should be all lowercase.

​extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:109:38: style: Variable and function names should be all lowercase.

​extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~

R/dEploidTools.R:109:51: style: Variable and function names should be all lowercase.

​extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~

R/dEploidTools.R:110:9: style: Use <-, not =, for assignment.

​    ref = read.table(refFileName, header = TRUE, comment.char = "")
        ^

R/dEploidTools.R:110:22: style: Variable and function names should be all lowercase.

​    ref = read.table(refFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~

R/dEploidTools.R:111:9: style: Use <-, not =, for assignment.

​    alt = read.table(altFileName, header = TRUE, comment.char = "")
        ^

R/dEploidTools.R:111:22: style: Variable and function names should be all lowercase.

​    alt = read.table(altFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~

R/dEploidTools.R:112:39: style: Commas should always have a space after.

​    return ( data.frame( CHROM = ref[,1],
                                      ^

R/dEploidTools.R:113:37: style: Commas should always have a space after.

​                         POS = ref[,2],
                                    ^

R/dEploidTools.R:114:42: style: Commas should always have a space after.

​                         refCount = ref[,3],
                                         ^

R/dEploidTools.R:115:42: style: Commas should always have a space after.

​                         altCount = alt[,3] )
                                         ^

R/dEploidTools.R:120:1: style: Words within variable and function names should be separated by '_' rather than '.'.

​fun.extract.exclude <- function (excludeFileName, excludeBool){
^~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:120:34: style: Variable and function names should be all lowercase.

​fun.extract.exclude <- function (excludeFileName, excludeBool){
                                 ^~~~~~~~~~~~~~~

R/dEploidTools.R:120:51: style: Variable and function names should be all lowercase.

​fun.extract.exclude <- function (excludeFileName, excludeBool){
                                                  ^~~~~~~~~~~

R/dEploidTools.R:121:10: style: Variable and function names should be all lowercase.

​    if ( excludeBool ) {
         ^~~~~~~~~~~

R/dEploidTools.R:122:39: style: Variable and function names should be all lowercase.

​        return ( list ( excludeBool = excludeBool,
                                      ^~~~~~~~~~~

R/dEploidTools.R:123:1: style: lines should not be more than 80 characters.

​                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:123:51: style: Variable and function names should be all lowercase.

​                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
                                                  ^~~~~~~~~~~~~~~

R/dEploidTools.R:125:39: style: Variable and function names should be all lowercase.

​        return ( list ( excludeBool = excludeBool ))
                                      ^~~~~~~~~~~

R/dEploidTools.R:147:1: style: Variable and function names should be all lowercase.

​extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:147:38: style: Variable and function names should be all lowercase.

​extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                     ^~~~~~~

R/dEploidTools.R:147:47: style: Variable and function names should be all lowercase.

​extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                              ^~~~~~~~~~~~

R/dEploidTools.R:150:12: style: Place a space before left parenthesis, except in a function call.

​         if( any( grepl( "gzfile connection", w) ) )
           ^

R/dEploidTools.R:154:9: style: Use <-, not =, for assignment.

​    gzf = gzfile(vcfFile, open = "rb")
        ^

R/dEploidTools.R:154:18: style: Variable and function names should be all lowercase.

​    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~

R/dEploidTools.R:154:18: warning: no visible binding for global variable ‘vcfFile’

​    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~

R/dEploidTools.R:155:5: style: Variable and function names should be all lowercase.

​    skipNum = 0
    ^~~~~~~

R/dEploidTools.R:155:13: style: Use <-, not =, for assignment.

​    skipNum = 0
            ^

R/dEploidTools.R:156:10: style: Use <-, not =, for assignment.

​    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
         ^

R/dEploidTools.R:156:49: style: Put spaces around all infix operators.

​    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                               ~^~

R/dEploidTools.R:156:61: style: Put spaces around all infix operators.

​    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                           ~^~

R/dEploidTools.R:158:21: style: Commented code should be removed.

​        if (grepl("##", line )){
                    ^~~~~~~~~~~~

R/dEploidTools.R:159:13: style: Variable and function names should be all lowercase.

​            skipNum = skipNum+1
            ^~~~~~~

R/dEploidTools.R:159:21: style: Use <-, not =, for assignment.

​            skipNum = skipNum+1
                    ^

R/dEploidTools.R:159:23: style: Variable and function names should be all lowercase.

​            skipNum = skipNum+1
                      ^~~~~~~

R/dEploidTools.R:159:30: style: Put spaces around all infix operators.

​            skipNum = skipNum+1
                            ~^~

R/dEploidTools.R:163:14: style: Use <-, not =, for assignment.

​        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
             ^

R/dEploidTools.R:163:53: style: Put spaces around all infix operators.

​        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                   ~^~

R/dEploidTools.R:163:65: style: Put spaces around all infix operators.

​        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                               ~^~

R/dEploidTools.R:167:1: style: lines should not be more than 80 characters.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:167:10: style: Use <-, not =, for assignment.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
         ^

R/dEploidTools.R:167:31: style: Variable and function names should be all lowercase.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                              ^~~~~~~

R/dEploidTools.R:167:45: style: Put spaces around all infix operators.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                           ~^~

R/dEploidTools.R:167:46: style: Variable and function names should be all lowercase.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                             ^~~~~~~

R/dEploidTools.R:167:61: style: Put spaces around all infix operators.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                           ~^~

R/dEploidTools.R:167:77: style: Put spaces around all infix operators.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                           ~^~

R/dEploidTools.R:167:119: style: Put spaces around all infix operators.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                                                                     ~^~

R/dEploidTools.R:169:5: style: Variable and function names should be all lowercase.

​    sampleName = names(vcf)[10]
    ^~~~~~~~~~

R/dEploidTools.R:169:16: style: Use <-, not =, for assignment.

​    sampleName = names(vcf)[10]
               ^

R/dEploidTools.R:171:9: style: Use <-, not =, for assignment.

​    tmp = vcf[[sampleName]]
        ^

R/dEploidTools.R:171:16: style: Variable and function names should be all lowercase.

​    tmp = vcf[[sampleName]]
               ^~~~~~~~~~

R/dEploidTools.R:172:11: style: Use <-, not =, for assignment.

​    field = strsplit(as.character(tmp),":")
          ^

R/dEploidTools.R:172:40: style: Commas should always have a space after.

​    field = strsplit(as.character(tmp),":")
                                       ^

R/dEploidTools.R:174:5: style: Variable and function names should be all lowercase.

​    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/dEploidTools.R:174:15: style: Use <-, not =, for assignment.

​    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
              ^

R/dEploidTools.R:174:44: style: Variable and function names should be all lowercase.

​    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
                                           ^~~~~~~~~~~~

R/dEploidTools.R:175:5: style: Variable and function names should be all lowercase.

​    tmpCov = strsplit(as.character(tmpCovStr),",")
    ^~~~~~

R/dEploidTools.R:175:12: style: Use <-, not =, for assignment.

​    tmpCov = strsplit(as.character(tmpCovStr),",")
           ^

R/dEploidTools.R:175:36: style: Variable and function names should be all lowercase.

​    tmpCov = strsplit(as.character(tmpCovStr),",")
                                   ^~~~~~~~~

R/dEploidTools.R:175:47: style: Commas should always have a space after.

​    tmpCov = strsplit(as.character(tmpCovStr),",")
                                              ^

R/dEploidTools.R:177:5: style: Variable and function names should be all lowercase.

​    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/dEploidTools.R:177:14: style: Use <-, not =, for assignment.

​    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
             ^

R/dEploidTools.R:177:41: style: Variable and function names should be all lowercase.

​    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
                                        ^~~~~~

R/dEploidTools.R:178:5: style: Variable and function names should be all lowercase.

​    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/dEploidTools.R:178:14: style: Use <-, not =, for assignment.

​    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
             ^

R/dEploidTools.R:178:41: style: Variable and function names should be all lowercase.

​    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
                                        ^~~~~~

R/dEploidTools.R:180:39: style: Commas should always have a space after.

​    return ( data.frame( CHROM = vcf[,1],
                                      ^

R/dEploidTools.R:181:37: style: Commas should always have a space after.

​                         POS = vcf[,2],
                                    ^

R/dEploidTools.R:182:37: style: Variable and function names should be all lowercase.

​                         refCount = refCount,
                                    ^~~~~~~~

R/dEploidTools.R:183:37: style: Variable and function names should be all lowercase.

​                         altCount = altCount )
                                    ^~~~~~~~

R/dEploidTools.R:204:1: style: Variable and function names should be all lowercase.

​extractPLAF<- function ( plafName ){
^~~~~~~~~~~

R/dEploidTools.R:204:12: style: Put spaces around all infix operators.

​extractPLAF<- function ( plafName ){
          ~^

R/dEploidTools.R:204:26: style: Variable and function names should be all lowercase.

​extractPLAF<- function ( plafName ){
                         ^~~~~~~~

R/dEploidTools.R:205:25: style: Variable and function names should be all lowercase.

​    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~

R/dEploidTools.R:205:41: style: Put spaces around all infix operators.

​    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~

R/dEploidTools.R:210:11: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
         ~^~~

R/dEploidTools.R:210:19: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
                 ~^~

R/dEploidTools.R:210:23: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
                     ~^~

R/dEploidTools.R:210:24: style: Place a space before left parenthesis, except in a function call.

​    f.samp<-f.samp+err*(1-2*f.samp);
                       ^

R/dEploidTools.R:210:26: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
                        ~^~

R/dEploidTools.R:210:28: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
                          ~^~

R/dEploidTools.R:211:1: style: lines should not be more than 80 characters.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Place a space before left parenthesis, except in a function call.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Commas should always have a space after.

​    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: style: Place a space before left parenthesis, except in a function call.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: lines should not be more than 80 characters.

​    #  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: style: Commented code should be removed.

​    #  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: style: Put spaces around all infix operators.

​    if (sum(is.nan(llk))>1){
                       ~^~

R/dEploidTools.R:220:1: style: Words within variable and function names should be separated by '_' rather than '.'.

​fun.dic.by.llk.var <- function ( tmpllk ){
^~~~~~~~~~~~~~~~~~

R/dEploidTools.R:221:1: style: lines should not be more than 80 characters.

​     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: style: Put spaces around all infix operators.

​     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: style: Put spaces around all infix operators.

​     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: style: Put spaces around all infix operators.

​     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: style: Words within variable and function names should be separated by '_' rather than '.'.

​fun.dic.by.theta <- function ( tmpllk, thetallk ){
^~~~~~~~~~~~~~~~

R/dEploidTools.R:226:5: style: Words within variable and function names should be separated by '_' rather than '.'.

​    DIC.WSAF.bar = -2 * sum(thetallk)
    ^~~~~~~~~~~~

R/dEploidTools.R:226:18: style: Use <-, not =, for assignment.

​    DIC.WSAF.bar = -2 * sum(thetallk)
                 ^

R/dEploidTools.R:227:1: style: lines should not be more than 80 characters.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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)
                                       ~^~

@lintr-bot
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R/dEploidTools.R:1:22: style: Do not place spaces around code in parentheses or square brackets.

​fun.parse <- function( args ){
                     ^

R/dEploidTools.R:1:28: style: Do not place spaces around code in parentheses or square brackets.

​fun.parse <- function( args ){
                           ^

R/dEploidTools.R:2:5: style: Variable and function names should be all lowercase.

​    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:2:5: style: Words within variable and function names should be separated by '_' rather than '.'.

​    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:2:48: style: Do not place spaces around code in parentheses or square brackets.

​    fun.local.checkAndIncreaseArgI <- function ( ){
                                               ^

R/dEploidTools.R:3:15: style: Use <-, not =, for assignment.

​        arg_i = arg_i+1
              ^

R/dEploidTools.R:3:22: style: Put spaces around all infix operators.

​        arg_i = arg_i+1
                    ~^~

R/dEploidTools.R:6:5: style: Variable and function names should be all lowercase.

​    outPrefix = "dataExplore"
    ^~~~~~~~~

R/dEploidTools.R:6:15: style: Use <-, not =, for assignment.

​    outPrefix = "dataExplore"
              ^

R/dEploidTools.R:7:5: style: Variable and function names should be all lowercase.

​    vcfFileName = ""
    ^~~~~~~~~~~

R/dEploidTools.R:7:17: style: Use <-, not =, for assignment.

​    vcfFileName = ""
                ^

R/dEploidTools.R:8:5: style: Variable and function names should be all lowercase.

​    refFileName = ""
    ^~~~~~~~~~~

R/dEploidTools.R:8:17: style: Use <-, not =, for assignment.

​    refFileName = ""
                ^

R/dEploidTools.R:9:5: style: Variable and function names should be all lowercase.

​    altFileName = ""
    ^~~~~~~~~~~

R/dEploidTools.R:9:17: style: Use <-, not =, for assignment.

​    altFileName = ""
                ^

R/dEploidTools.R:10:5: style: Variable and function names should be all lowercase.

​    plafFileName = ""
    ^~~~~~~~~~~~

R/dEploidTools.R:10:18: style: Use <-, not =, for assignment.

​    plafFileName = ""
                 ^

R/dEploidTools.R:11:5: style: Variable and function names should be all lowercase.

​    excludeFileName = ""
    ^~~~~~~~~~~~~~~

R/dEploidTools.R:11:21: style: Use <-, not =, for assignment.

​    excludeFileName = ""
                    ^

R/dEploidTools.R:12:5: style: Variable and function names should be all lowercase.

​    dEploidPrefix = ""
    ^~~~~~~~~~~~~

R/dEploidTools.R:12:19: style: Use <-, not =, for assignment.

​    dEploidPrefix = ""
                  ^

R/dEploidTools.R:13:5: style: Variable and function names should be all lowercase.

​    excludeBool = FALSE
    ^~~~~~~~~~~

R/dEploidTools.R:13:17: style: Use <-, not =, for assignment.

​    excludeBool = FALSE
                ^

R/dEploidTools.R:15:11: style: Use <-, not =, for assignment.

​    arg_i = 1
          ^

R/dEploidTools.R:16:11: style: Do not place spaces around code in parentheses or square brackets.

​    while ( arg_i < length(args) ){
          ^

R/dEploidTools.R:16:33: style: Do not place spaces around code in parentheses or square brackets.

​    while ( arg_i < length(args) ){
                                ^

R/dEploidTools.R:17:14: style: Use <-, not =, for assignment.

​        argv = args[arg_i]
             ^

R/dEploidTools.R:18:12: style: Do not place spaces around code in parentheses or square brackets.

​        if ( argv == "-vcf" ){
           ^

R/dEploidTools.R:18:28: style: Do not place spaces around code in parentheses or square brackets.

​        if ( argv == "-vcf" ){
                           ^

R/dEploidTools.R:19:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:19:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:19:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:19:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:20:13: style: Variable and function names should be all lowercase.

​            vcfFileName = args[arg_i]
            ^~~~~~~~~~~

R/dEploidTools.R:20:25: style: Use <-, not =, for assignment.

​            vcfFileName = args[arg_i]
                        ^

R/dEploidTools.R:21:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-plaf" ){
                  ^

R/dEploidTools.R:21:36: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-plaf" ){
                                   ^

R/dEploidTools.R:22:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:22:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:22:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:22:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:23:13: style: Variable and function names should be all lowercase.

​            plafFileName = args[arg_i]
            ^~~~~~~~~~~~

R/dEploidTools.R:23:26: style: Use <-, not =, for assignment.

​            plafFileName = args[arg_i]
                         ^

R/dEploidTools.R:24:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-ref" ){
                  ^

R/dEploidTools.R:24:35: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-ref" ){
                                  ^

R/dEploidTools.R:25:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:25:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:25:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:25:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:26:13: style: Variable and function names should be all lowercase.

​            refFileName = args[arg_i]
            ^~~~~~~~~~~

R/dEploidTools.R:26:25: style: Use <-, not =, for assignment.

​            refFileName = args[arg_i]
                        ^

R/dEploidTools.R:27:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-alt" ){
                  ^

R/dEploidTools.R:27:35: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-alt" ){
                                  ^

R/dEploidTools.R:28:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:28:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:28:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:28:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:29:13: style: Variable and function names should be all lowercase.

​            altFileName = args[arg_i]
            ^~~~~~~~~~~

R/dEploidTools.R:29:25: style: Use <-, not =, for assignment.

​            altFileName = args[arg_i]
                        ^

R/dEploidTools.R:30:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-exclude" ){
                  ^

R/dEploidTools.R:30:39: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-exclude" ){
                                      ^

R/dEploidTools.R:31:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:31:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:31:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:31:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:32:13: style: Variable and function names should be all lowercase.

​            excludeFileName = args[arg_i]
            ^~~~~~~~~~~~~~~

R/dEploidTools.R:32:29: style: Use <-, not =, for assignment.

​            excludeFileName = args[arg_i]
                            ^

R/dEploidTools.R:33:13: style: Variable and function names should be all lowercase.

​            excludeBool = TRUE
            ^~~~~~~~~~~

R/dEploidTools.R:33:25: style: Use <-, not =, for assignment.

​            excludeBool = TRUE
                        ^

R/dEploidTools.R:34:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-o" ){
                  ^

R/dEploidTools.R:34:33: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-o" ){
                                ^

R/dEploidTools.R:35:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:35:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:35:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:35:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:36:13: style: Variable and function names should be all lowercase.

​            outPrefix = args[arg_i]
            ^~~~~~~~~

R/dEploidTools.R:36:23: style: Use <-, not =, for assignment.

​            outPrefix = args[arg_i]
                      ^

R/dEploidTools.R:37:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-dEprefix" ){
                  ^

R/dEploidTools.R:37:40: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-dEprefix" ){
                                       ^

R/dEploidTools.R:38:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:38:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:38:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:38:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:39:13: style: Variable and function names should be all lowercase.

​            dEploidPrefix = args[arg_i]
            ^~~~~~~~~~~~~

R/dEploidTools.R:39:27: style: Use <-, not =, for assignment.

​            dEploidPrefix = args[arg_i]
                          ^

R/dEploidTools.R:44:15: style: Use <-, not =, for assignment.

​        arg_i = arg_i + 1
              ^

R/dEploidTools.R:51:8: style: Do not place spaces around code in parentheses or square brackets.

​    if ( plafFileName == "" ){
       ^

R/dEploidTools.R:51:10: style: Variable and function names should be all lowercase.

​    if ( plafFileName == "" ){
         ^~~~~~~~~~~~

R/dEploidTools.R:51:28: style: Do not place spaces around code in parentheses or square brackets.

​    if ( plafFileName == "" ){
                           ^

R/dEploidTools.R:58:12: style: Do not place spaces around code in parentheses or square brackets.

​    return ( list ( vcfFileName = vcfFileName,
           ^

R/dEploidTools.R:58:19: style: Do not place spaces around code in parentheses or square brackets.

​    return ( list ( vcfFileName = vcfFileName,
                  ^

R/dEploidTools.R:58:35: style: Variable and function names should be all lowercase.

​    return ( list ( vcfFileName = vcfFileName,
                                  ^~~~~~~~~~~

R/dEploidTools.R:59:35: style: Variable and function names should be all lowercase.

​                    refFileName = refFileName,
                                  ^~~~~~~~~~~

R/dEploidTools.R:60:35: style: Variable and function names should be all lowercase.

​                    altFileName = altFileName,
                                  ^~~~~~~~~~~

R/dEploidTools.R:61:36: style: Variable and function names should be all lowercase.

​                    plafFileName = plafFileName,
                                   ^~~~~~~~~~~~

R/dEploidTools.R:62:33: style: Variable and function names should be all lowercase.

​                    outPrefix = outPrefix,
                                ^~~~~~~~~

R/dEploidTools.R:63:37: style: Variable and function names should be all lowercase.

​                    dEploidPrefix = dEploidPrefix,
                                    ^~~~~~~~~~~~~

R/dEploidTools.R:64:39: style: Variable and function names should be all lowercase.

​                    excludeFileName = excludeFileName,
                                      ^~~~~~~~~~~~~~~

R/dEploidTools.R:65:35: style: Variable and function names should be all lowercase.

​                    excludeBool = excludeBool) )
                                  ^~~~~~~~~~~

R/dEploidTools.R:65:47: style: Do not place spaces around code in parentheses or square brackets.

​                    excludeBool = excludeBool) )
                                              ^

R/dEploidTools.R:69:1: style: Variable and function names should be all lowercase.

​fun.dEploidPrefix <- function ( prefix ){
^~~~~~~~~~~~~~~~~

R/dEploidTools.R:81:1: style: Words within variable and function names should be separated by '_' rather than '.'.

​fun.extract.coverage <- function ( inputs ){
^~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:82:17: style: Variable and function names should be all lowercase.

​    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~

R/dEploidTools.R:83:17: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:83:17: warning: no visible global function definition for ‘extractCoverageFromVcf’

​        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:83:48: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~

R/dEploidTools.R:85:17: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:85:17: warning: no visible global function definition for ‘extractCoverageFromTxt’

​        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:85:48: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                               ^~~~~~~~~~~

R/dEploidTools.R:85:68: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                                                   ^~~~~~~~~~~

R/dEploidTools.R:109:1: style: Variable and function names should be all lowercase.

​extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:109:38: style: Variable and function names should be all lowercase.

​extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~

R/dEploidTools.R:109:51: style: Variable and function names should be all lowercase.

​extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~

R/dEploidTools.R:110:9: style: Use <-, not =, for assignment.

​    ref = read.table(refFileName, header = TRUE, comment.char = "")
        ^

R/dEploidTools.R:110:22: style: Variable and function names should be all lowercase.

​    ref = read.table(refFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~

R/dEploidTools.R:111:9: style: Use <-, not =, for assignment.

​    alt = read.table(altFileName, header = TRUE, comment.char = "")
        ^

R/dEploidTools.R:111:22: style: Variable and function names should be all lowercase.

​    alt = read.table(altFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~

R/dEploidTools.R:112:39: style: Commas should always have a space after.

​    return ( data.frame( CHROM = ref[,1],
                                      ^

R/dEploidTools.R:113:37: style: Commas should always have a space after.

​                         POS = ref[,2],
                                    ^

R/dEploidTools.R:114:42: style: Commas should always have a space after.

​                         refCount = ref[,3],
                                         ^

R/dEploidTools.R:115:42: style: Commas should always have a space after.

​                         altCount = alt[,3] )
                                         ^

R/dEploidTools.R:120:1: style: Words within variable and function names should be separated by '_' rather than '.'.

​fun.extract.exclude <- function (excludeFileName, excludeBool){
^~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:120:34: style: Variable and function names should be all lowercase.

​fun.extract.exclude <- function (excludeFileName, excludeBool){
                                 ^~~~~~~~~~~~~~~

R/dEploidTools.R:120:51: style: Variable and function names should be all lowercase.

​fun.extract.exclude <- function (excludeFileName, excludeBool){
                                                  ^~~~~~~~~~~

R/dEploidTools.R:121:10: style: Variable and function names should be all lowercase.

​    if ( excludeBool ) {
         ^~~~~~~~~~~

R/dEploidTools.R:122:39: style: Variable and function names should be all lowercase.

​        return ( list ( excludeBool = excludeBool,
                                      ^~~~~~~~~~~

R/dEploidTools.R:123:1: style: lines should not be more than 80 characters.

​                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:123:51: style: Variable and function names should be all lowercase.

​                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
                                                  ^~~~~~~~~~~~~~~

R/dEploidTools.R:125:39: style: Variable and function names should be all lowercase.

​        return ( list ( excludeBool = excludeBool ))
                                      ^~~~~~~~~~~

R/dEploidTools.R:147:1: style: Variable and function names should be all lowercase.

​extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:147:38: style: Variable and function names should be all lowercase.

​extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                     ^~~~~~~

R/dEploidTools.R:147:47: style: Variable and function names should be all lowercase.

​extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                              ^~~~~~~~~~~~

R/dEploidTools.R:150:12: style: Place a space before left parenthesis, except in a function call.

​         if( any( grepl( "gzfile connection", w) ) )
           ^

R/dEploidTools.R:154:9: style: Use <-, not =, for assignment.

​    gzf = gzfile(vcfFile, open = "rb")
        ^

R/dEploidTools.R:154:18: style: Variable and function names should be all lowercase.

​    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~

R/dEploidTools.R:154:18: warning: no visible binding for global variable ‘vcfFile’

​    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~

R/dEploidTools.R:155:5: style: Variable and function names should be all lowercase.

​    skipNum = 0
    ^~~~~~~

R/dEploidTools.R:155:13: style: Use <-, not =, for assignment.

​    skipNum = 0
            ^

R/dEploidTools.R:156:10: style: Use <-, not =, for assignment.

​    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
         ^

R/dEploidTools.R:156:49: style: Put spaces around all infix operators.

​    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                               ~^~

R/dEploidTools.R:156:61: style: Put spaces around all infix operators.

​    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                           ~^~

R/dEploidTools.R:158:21: style: Commented code should be removed.

​        if (grepl("##", line )){
                    ^~~~~~~~~~~~

R/dEploidTools.R:159:13: style: Variable and function names should be all lowercase.

​            skipNum = skipNum+1
            ^~~~~~~

R/dEploidTools.R:159:21: style: Use <-, not =, for assignment.

​            skipNum = skipNum+1
                    ^

R/dEploidTools.R:159:23: style: Variable and function names should be all lowercase.

​            skipNum = skipNum+1
                      ^~~~~~~

R/dEploidTools.R:159:30: style: Put spaces around all infix operators.

​            skipNum = skipNum+1
                            ~^~

R/dEploidTools.R:163:14: style: Use <-, not =, for assignment.

​        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
             ^

R/dEploidTools.R:163:53: style: Put spaces around all infix operators.

​        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                   ~^~

R/dEploidTools.R:163:65: style: Put spaces around all infix operators.

​        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                               ~^~

R/dEploidTools.R:167:1: style: lines should not be more than 80 characters.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:167:10: style: Use <-, not =, for assignment.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
         ^

R/dEploidTools.R:167:31: style: Variable and function names should be all lowercase.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                              ^~~~~~~

R/dEploidTools.R:167:45: style: Put spaces around all infix operators.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                           ~^~

R/dEploidTools.R:167:46: style: Variable and function names should be all lowercase.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                             ^~~~~~~

R/dEploidTools.R:167:61: style: Put spaces around all infix operators.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                           ~^~

R/dEploidTools.R:167:77: style: Put spaces around all infix operators.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                           ~^~

R/dEploidTools.R:167:119: style: Put spaces around all infix operators.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                                                                     ~^~

R/dEploidTools.R:169:5: style: Variable and function names should be all lowercase.

​    sampleName = names(vcf)[10]
    ^~~~~~~~~~

R/dEploidTools.R:169:16: style: Use <-, not =, for assignment.

​    sampleName = names(vcf)[10]
               ^

R/dEploidTools.R:171:9: style: Use <-, not =, for assignment.

​    tmp = vcf[[sampleName]]
        ^

R/dEploidTools.R:171:16: style: Variable and function names should be all lowercase.

​    tmp = vcf[[sampleName]]
               ^~~~~~~~~~

R/dEploidTools.R:172:11: style: Use <-, not =, for assignment.

​    field = strsplit(as.character(tmp),":")
          ^

R/dEploidTools.R:172:40: style: Commas should always have a space after.

​    field = strsplit(as.character(tmp),":")
                                       ^

R/dEploidTools.R:174:5: style: Variable and function names should be all lowercase.

​    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/dEploidTools.R:174:15: style: Use <-, not =, for assignment.

​    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
              ^

R/dEploidTools.R:174:44: style: Variable and function names should be all lowercase.

​    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
                                           ^~~~~~~~~~~~

R/dEploidTools.R:175:5: style: Variable and function names should be all lowercase.

​    tmpCov = strsplit(as.character(tmpCovStr),",")
    ^~~~~~

R/dEploidTools.R:175:12: style: Use <-, not =, for assignment.

​    tmpCov = strsplit(as.character(tmpCovStr),",")
           ^

R/dEploidTools.R:175:36: style: Variable and function names should be all lowercase.

​    tmpCov = strsplit(as.character(tmpCovStr),",")
                                   ^~~~~~~~~

R/dEploidTools.R:175:47: style: Commas should always have a space after.

​    tmpCov = strsplit(as.character(tmpCovStr),",")
                                              ^

R/dEploidTools.R:177:5: style: Variable and function names should be all lowercase.

​    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/dEploidTools.R:177:14: style: Use <-, not =, for assignment.

​    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
             ^

R/dEploidTools.R:177:41: style: Variable and function names should be all lowercase.

​    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
                                        ^~~~~~

R/dEploidTools.R:178:5: style: Variable and function names should be all lowercase.

​    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/dEploidTools.R:178:14: style: Use <-, not =, for assignment.

​    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
             ^

R/dEploidTools.R:178:41: style: Variable and function names should be all lowercase.

​    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
                                        ^~~~~~

R/dEploidTools.R:180:39: style: Commas should always have a space after.

​    return ( data.frame( CHROM = vcf[,1],
                                      ^

R/dEploidTools.R:181:37: style: Commas should always have a space after.

​                         POS = vcf[,2],
                                    ^

R/dEploidTools.R:182:37: style: Variable and function names should be all lowercase.

​                         refCount = refCount,
                                    ^~~~~~~~

R/dEploidTools.R:183:37: style: Variable and function names should be all lowercase.

​                         altCount = altCount )
                                    ^~~~~~~~

R/dEploidTools.R:204:1: style: Variable and function names should be all lowercase.

​extractPLAF<- function ( plafName ){
^~~~~~~~~~~

R/dEploidTools.R:204:12: style: Put spaces around all infix operators.

​extractPLAF<- function ( plafName ){
          ~^

R/dEploidTools.R:204:26: style: Variable and function names should be all lowercase.

​extractPLAF<- function ( plafName ){
                         ^~~~~~~~

R/dEploidTools.R:205:25: style: Variable and function names should be all lowercase.

​    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~

R/dEploidTools.R:205:41: style: Put spaces around all infix operators.

​    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~

R/dEploidTools.R:210:11: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
         ~^~~

R/dEploidTools.R:210:19: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
                 ~^~

R/dEploidTools.R:210:23: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
                     ~^~

R/dEploidTools.R:210:24: style: Place a space before left parenthesis, except in a function call.

​    f.samp<-f.samp+err*(1-2*f.samp);
                       ^

R/dEploidTools.R:210:26: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
                        ~^~

R/dEploidTools.R:210:28: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
                          ~^~

R/dEploidTools.R:211:1: style: lines should not be more than 80 characters.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Place a space before left parenthesis, except in a function call.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Commas should always have a space after.

​    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: style: Place a space before left parenthesis, except in a function call.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: lines should not be more than 80 characters.

​    #  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: style: Commented code should be removed.

​    #  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: style: Put spaces around all infix operators.

​    if (sum(is.nan(llk))>1){
                       ~^~

R/dEploidTools.R:220:1: style: Words within variable and function names should be separated by '_' rather than '.'.

​fun.dic.by.llk.var <- function ( tmpllk ){
^~~~~~~~~~~~~~~~~~

R/dEploidTools.R:221:1: style: lines should not be more than 80 characters.

​     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: style: Put spaces around all infix operators.

​     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: style: Put spaces around all infix operators.

​     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: style: Put spaces around all infix operators.

​     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: style: Words within variable and function names should be separated by '_' rather than '.'.

​fun.dic.by.theta <- function ( tmpllk, thetallk ){
^~~~~~~~~~~~~~~~

R/dEploidTools.R:226:5: style: Words within variable and function names should be separated by '_' rather than '.'.

​    DIC.WSAF.bar = -2 * sum(thetallk)
    ^~~~~~~~~~~~

R/dEploidTools.R:226:18: style: Use <-, not =, for assignment.

​    DIC.WSAF.bar = -2 * sum(thetallk)
                 ^

R/dEploidTools.R:227:1: style: lines should not be more than 80 characters.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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)
                                       ~^~

@lintr-bot
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R/dEploidTools.R:1:22: style: Do not place spaces around code in parentheses or square brackets.

​fun.parse <- function( args ){
                     ^

R/dEploidTools.R:1:28: style: Do not place spaces around code in parentheses or square brackets.

​fun.parse <- function( args ){
                           ^

R/dEploidTools.R:2:5: style: Variable and function names should be all lowercase.

​    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:2:5: style: Words within variable and function names should be separated by '_' rather than '.'.

​    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:2:48: style: Do not place spaces around code in parentheses or square brackets.

​    fun.local.checkAndIncreaseArgI <- function ( ){
                                               ^

R/dEploidTools.R:3:15: style: Use <-, not =, for assignment.

​        arg_i = arg_i+1
              ^

R/dEploidTools.R:3:22: style: Put spaces around all infix operators.

​        arg_i = arg_i+1
                    ~^~

R/dEploidTools.R:6:5: style: Variable and function names should be all lowercase.

​    outPrefix = "dataExplore"
    ^~~~~~~~~

R/dEploidTools.R:6:15: style: Use <-, not =, for assignment.

​    outPrefix = "dataExplore"
              ^

R/dEploidTools.R:7:5: style: Variable and function names should be all lowercase.

​    vcfFileName = ""
    ^~~~~~~~~~~

R/dEploidTools.R:7:17: style: Use <-, not =, for assignment.

​    vcfFileName = ""
                ^

R/dEploidTools.R:8:5: style: Variable and function names should be all lowercase.

​    refFileName = ""
    ^~~~~~~~~~~

R/dEploidTools.R:8:17: style: Use <-, not =, for assignment.

​    refFileName = ""
                ^

R/dEploidTools.R:9:5: style: Variable and function names should be all lowercase.

​    altFileName = ""
    ^~~~~~~~~~~

R/dEploidTools.R:9:17: style: Use <-, not =, for assignment.

​    altFileName = ""
                ^

R/dEploidTools.R:10:5: style: Variable and function names should be all lowercase.

​    plafFileName = ""
    ^~~~~~~~~~~~

R/dEploidTools.R:10:18: style: Use <-, not =, for assignment.

​    plafFileName = ""
                 ^

R/dEploidTools.R:11:5: style: Variable and function names should be all lowercase.

​    excludeFileName = ""
    ^~~~~~~~~~~~~~~

R/dEploidTools.R:11:21: style: Use <-, not =, for assignment.

​    excludeFileName = ""
                    ^

R/dEploidTools.R:12:5: style: Variable and function names should be all lowercase.

​    dEploidPrefix = ""
    ^~~~~~~~~~~~~

R/dEploidTools.R:12:19: style: Use <-, not =, for assignment.

​    dEploidPrefix = ""
                  ^

R/dEploidTools.R:13:5: style: Variable and function names should be all lowercase.

​    excludeBool = FALSE
    ^~~~~~~~~~~

R/dEploidTools.R:13:17: style: Use <-, not =, for assignment.

​    excludeBool = FALSE
                ^

R/dEploidTools.R:15:11: style: Use <-, not =, for assignment.

​    arg_i = 1
          ^

R/dEploidTools.R:16:11: style: Do not place spaces around code in parentheses or square brackets.

​    while ( arg_i < length(args) ){
          ^

R/dEploidTools.R:16:33: style: Do not place spaces around code in parentheses or square brackets.

​    while ( arg_i < length(args) ){
                                ^

R/dEploidTools.R:17:14: style: Use <-, not =, for assignment.

​        argv = args[arg_i]
             ^

R/dEploidTools.R:18:12: style: Do not place spaces around code in parentheses or square brackets.

​        if ( argv == "-vcf" ){
           ^

R/dEploidTools.R:18:28: style: Do not place spaces around code in parentheses or square brackets.

​        if ( argv == "-vcf" ){
                           ^

R/dEploidTools.R:19:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:19:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:19:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:19:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:20:13: style: Variable and function names should be all lowercase.

​            vcfFileName = args[arg_i]
            ^~~~~~~~~~~

R/dEploidTools.R:20:25: style: Use <-, not =, for assignment.

​            vcfFileName = args[arg_i]
                        ^

R/dEploidTools.R:21:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-plaf" ){
                  ^

R/dEploidTools.R:21:36: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-plaf" ){
                                   ^

R/dEploidTools.R:22:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:22:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:22:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:22:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:23:13: style: Variable and function names should be all lowercase.

​            plafFileName = args[arg_i]
            ^~~~~~~~~~~~

R/dEploidTools.R:23:26: style: Use <-, not =, for assignment.

​            plafFileName = args[arg_i]
                         ^

R/dEploidTools.R:24:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-ref" ){
                  ^

R/dEploidTools.R:24:35: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-ref" ){
                                  ^

R/dEploidTools.R:25:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:25:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:25:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:25:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:26:13: style: Variable and function names should be all lowercase.

​            refFileName = args[arg_i]
            ^~~~~~~~~~~

R/dEploidTools.R:26:25: style: Use <-, not =, for assignment.

​            refFileName = args[arg_i]
                        ^

R/dEploidTools.R:27:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-alt" ){
                  ^

R/dEploidTools.R:27:35: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-alt" ){
                                  ^

R/dEploidTools.R:28:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:28:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:28:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:28:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:29:13: style: Variable and function names should be all lowercase.

​            altFileName = args[arg_i]
            ^~~~~~~~~~~

R/dEploidTools.R:29:25: style: Use <-, not =, for assignment.

​            altFileName = args[arg_i]
                        ^

R/dEploidTools.R:30:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-exclude" ){
                  ^

R/dEploidTools.R:30:39: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-exclude" ){
                                      ^

R/dEploidTools.R:31:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:31:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:31:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:31:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:32:13: style: Variable and function names should be all lowercase.

​            excludeFileName = args[arg_i]
            ^~~~~~~~~~~~~~~

R/dEploidTools.R:32:29: style: Use <-, not =, for assignment.

​            excludeFileName = args[arg_i]
                            ^

R/dEploidTools.R:33:13: style: Variable and function names should be all lowercase.

​            excludeBool = TRUE
            ^~~~~~~~~~~

R/dEploidTools.R:33:25: style: Use <-, not =, for assignment.

​            excludeBool = TRUE
                        ^

R/dEploidTools.R:34:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-o" ){
                  ^

R/dEploidTools.R:34:33: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-o" ){
                                ^

R/dEploidTools.R:35:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:35:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:35:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:35:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:36:13: style: Variable and function names should be all lowercase.

​            outPrefix = args[arg_i]
            ^~~~~~~~~

R/dEploidTools.R:36:23: style: Use <-, not =, for assignment.

​            outPrefix = args[arg_i]
                      ^

R/dEploidTools.R:37:19: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-dEprefix" ){
                  ^

R/dEploidTools.R:37:40: style: Do not place spaces around code in parentheses or square brackets.

​        } else if ( argv == "-dEprefix" ){
                                       ^

R/dEploidTools.R:38:19: style: Use <-, not =, for assignment.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^

R/dEploidTools.R:38:21: style: Variable and function names should be all lowercase.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:38:21: style: Words within variable and function names should be separated by '_' rather than '.'.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:38:52: style: Do not place spaces around code in parentheses or square brackets.

​            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^

R/dEploidTools.R:39:13: style: Variable and function names should be all lowercase.

​            dEploidPrefix = args[arg_i]
            ^~~~~~~~~~~~~

R/dEploidTools.R:39:27: style: Use <-, not =, for assignment.

​            dEploidPrefix = args[arg_i]
                          ^

R/dEploidTools.R:44:15: style: Use <-, not =, for assignment.

​        arg_i = arg_i + 1
              ^

R/dEploidTools.R:51:8: style: Do not place spaces around code in parentheses or square brackets.

​    if ( plafFileName == "" ){
       ^

R/dEploidTools.R:51:10: style: Variable and function names should be all lowercase.

​    if ( plafFileName == "" ){
         ^~~~~~~~~~~~

R/dEploidTools.R:51:28: style: Do not place spaces around code in parentheses or square brackets.

​    if ( plafFileName == "" ){
                           ^

R/dEploidTools.R:58:12: style: Do not place spaces around code in parentheses or square brackets.

​    return ( list ( vcfFileName = vcfFileName,
           ^

R/dEploidTools.R:58:19: style: Do not place spaces around code in parentheses or square brackets.

​    return ( list ( vcfFileName = vcfFileName,
                  ^

R/dEploidTools.R:58:35: style: Variable and function names should be all lowercase.

​    return ( list ( vcfFileName = vcfFileName,
                                  ^~~~~~~~~~~

R/dEploidTools.R:59:35: style: Variable and function names should be all lowercase.

​                    refFileName = refFileName,
                                  ^~~~~~~~~~~

R/dEploidTools.R:60:35: style: Variable and function names should be all lowercase.

​                    altFileName = altFileName,
                                  ^~~~~~~~~~~

R/dEploidTools.R:61:36: style: Variable and function names should be all lowercase.

​                    plafFileName = plafFileName,
                                   ^~~~~~~~~~~~

R/dEploidTools.R:62:33: style: Variable and function names should be all lowercase.

​                    outPrefix = outPrefix,
                                ^~~~~~~~~

R/dEploidTools.R:63:37: style: Variable and function names should be all lowercase.

​                    dEploidPrefix = dEploidPrefix,
                                    ^~~~~~~~~~~~~

R/dEploidTools.R:64:39: style: Variable and function names should be all lowercase.

​                    excludeFileName = excludeFileName,
                                      ^~~~~~~~~~~~~~~

R/dEploidTools.R:65:35: style: Variable and function names should be all lowercase.

​                    excludeBool = excludeBool) )
                                  ^~~~~~~~~~~

R/dEploidTools.R:65:47: style: Do not place spaces around code in parentheses or square brackets.

​                    excludeBool = excludeBool) )
                                              ^

R/dEploidTools.R:69:1: style: Variable and function names should be all lowercase.

​fun.dEploidPrefix <- function ( prefix ){
^~~~~~~~~~~~~~~~~

R/dEploidTools.R:81:1: style: Words within variable and function names should be separated by '_' rather than '.'.

​fun.extract.coverage <- function ( inputs ){
^~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:82:17: style: Variable and function names should be all lowercase.

​    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~

R/dEploidTools.R:83:17: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:83:17: warning: no visible global function definition for ‘extractCoverageFromVcf’

​        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:83:48: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~

R/dEploidTools.R:85:17: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:85:17: warning: no visible global function definition for ‘extractCoverageFromTxt’

​        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:85:48: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                               ^~~~~~~~~~~

R/dEploidTools.R:85:68: style: Variable and function names should be all lowercase.

​        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                                                   ^~~~~~~~~~~

R/dEploidTools.R:109:1: style: Variable and function names should be all lowercase.

​extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:109:38: style: Variable and function names should be all lowercase.

​extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~

R/dEploidTools.R:109:51: style: Variable and function names should be all lowercase.

​extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~

R/dEploidTools.R:110:9: style: Use <-, not =, for assignment.

​    ref = read.table(refFileName, header = TRUE, comment.char = "")
        ^

R/dEploidTools.R:110:22: style: Variable and function names should be all lowercase.

​    ref = read.table(refFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~

R/dEploidTools.R:111:9: style: Use <-, not =, for assignment.

​    alt = read.table(altFileName, header = TRUE, comment.char = "")
        ^

R/dEploidTools.R:111:22: style: Variable and function names should be all lowercase.

​    alt = read.table(altFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~

R/dEploidTools.R:112:39: style: Commas should always have a space after.

​    return ( data.frame( CHROM = ref[,1],
                                      ^

R/dEploidTools.R:113:37: style: Commas should always have a space after.

​                         POS = ref[,2],
                                    ^

R/dEploidTools.R:114:42: style: Commas should always have a space after.

​                         refCount = ref[,3],
                                         ^

R/dEploidTools.R:115:42: style: Commas should always have a space after.

​                         altCount = alt[,3] )
                                         ^

R/dEploidTools.R:120:1: style: Words within variable and function names should be separated by '_' rather than '.'.

​fun.extract.exclude <- function (excludeFileName, excludeBool){
^~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:120:34: style: Variable and function names should be all lowercase.

​fun.extract.exclude <- function (excludeFileName, excludeBool){
                                 ^~~~~~~~~~~~~~~

R/dEploidTools.R:120:51: style: Variable and function names should be all lowercase.

​fun.extract.exclude <- function (excludeFileName, excludeBool){
                                                  ^~~~~~~~~~~

R/dEploidTools.R:121:10: style: Variable and function names should be all lowercase.

​    if ( excludeBool ) {
         ^~~~~~~~~~~

R/dEploidTools.R:122:39: style: Variable and function names should be all lowercase.

​        return ( list ( excludeBool = excludeBool,
                                      ^~~~~~~~~~~

R/dEploidTools.R:123:1: style: lines should not be more than 80 characters.

​                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:123:51: style: Variable and function names should be all lowercase.

​                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
                                                  ^~~~~~~~~~~~~~~

R/dEploidTools.R:125:39: style: Variable and function names should be all lowercase.

​        return ( list ( excludeBool = excludeBool ))
                                      ^~~~~~~~~~~

R/dEploidTools.R:147:1: style: Variable and function names should be all lowercase.

​extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:147:38: style: Variable and function names should be all lowercase.

​extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                     ^~~~~~~

R/dEploidTools.R:147:47: style: Variable and function names should be all lowercase.

​extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                              ^~~~~~~~~~~~

R/dEploidTools.R:150:12: style: Place a space before left parenthesis, except in a function call.

​         if( any( grepl( "gzfile connection", w) ) )
           ^

R/dEploidTools.R:154:9: style: Use <-, not =, for assignment.

​    gzf = gzfile(vcfFile, open = "rb")
        ^

R/dEploidTools.R:154:18: style: Variable and function names should be all lowercase.

​    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~

R/dEploidTools.R:154:18: warning: no visible binding for global variable ‘vcfFile’

​    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~

R/dEploidTools.R:155:5: style: Variable and function names should be all lowercase.

​    skipNum = 0
    ^~~~~~~

R/dEploidTools.R:155:13: style: Use <-, not =, for assignment.

​    skipNum = 0
            ^

R/dEploidTools.R:156:10: style: Use <-, not =, for assignment.

​    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
         ^

R/dEploidTools.R:156:49: style: Put spaces around all infix operators.

​    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                               ~^~

R/dEploidTools.R:156:61: style: Put spaces around all infix operators.

​    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                           ~^~

R/dEploidTools.R:158:21: style: Commented code should be removed.

​        if (grepl("##", line )){
                    ^~~~~~~~~~~~

R/dEploidTools.R:159:13: style: Variable and function names should be all lowercase.

​            skipNum = skipNum+1
            ^~~~~~~

R/dEploidTools.R:159:21: style: Use <-, not =, for assignment.

​            skipNum = skipNum+1
                    ^

R/dEploidTools.R:159:23: style: Variable and function names should be all lowercase.

​            skipNum = skipNum+1
                      ^~~~~~~

R/dEploidTools.R:159:30: style: Put spaces around all infix operators.

​            skipNum = skipNum+1
                            ~^~

R/dEploidTools.R:163:14: style: Use <-, not =, for assignment.

​        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
             ^

R/dEploidTools.R:163:53: style: Put spaces around all infix operators.

​        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                   ~^~

R/dEploidTools.R:163:65: style: Put spaces around all infix operators.

​        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                               ~^~

R/dEploidTools.R:167:1: style: lines should not be more than 80 characters.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/dEploidTools.R:167:10: style: Use <-, not =, for assignment.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
         ^

R/dEploidTools.R:167:31: style: Variable and function names should be all lowercase.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                              ^~~~~~~

R/dEploidTools.R:167:45: style: Put spaces around all infix operators.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                           ~^~

R/dEploidTools.R:167:46: style: Variable and function names should be all lowercase.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                             ^~~~~~~

R/dEploidTools.R:167:61: style: Put spaces around all infix operators.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                           ~^~

R/dEploidTools.R:167:77: style: Put spaces around all infix operators.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                           ~^~

R/dEploidTools.R:167:119: style: Put spaces around all infix operators.

​    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                                                                     ~^~

R/dEploidTools.R:169:5: style: Variable and function names should be all lowercase.

​    sampleName = names(vcf)[10]
    ^~~~~~~~~~

R/dEploidTools.R:169:16: style: Use <-, not =, for assignment.

​    sampleName = names(vcf)[10]
               ^

R/dEploidTools.R:171:9: style: Use <-, not =, for assignment.

​    tmp = vcf[[sampleName]]
        ^

R/dEploidTools.R:171:16: style: Variable and function names should be all lowercase.

​    tmp = vcf[[sampleName]]
               ^~~~~~~~~~

R/dEploidTools.R:172:11: style: Use <-, not =, for assignment.

​    field = strsplit(as.character(tmp),":")
          ^

R/dEploidTools.R:172:40: style: Commas should always have a space after.

​    field = strsplit(as.character(tmp),":")
                                       ^

R/dEploidTools.R:174:5: style: Variable and function names should be all lowercase.

​    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/dEploidTools.R:174:15: style: Use <-, not =, for assignment.

​    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
              ^

R/dEploidTools.R:174:44: style: Variable and function names should be all lowercase.

​    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
                                           ^~~~~~~~~~~~

R/dEploidTools.R:175:5: style: Variable and function names should be all lowercase.

​    tmpCov = strsplit(as.character(tmpCovStr),",")
    ^~~~~~

R/dEploidTools.R:175:12: style: Use <-, not =, for assignment.

​    tmpCov = strsplit(as.character(tmpCovStr),",")
           ^

R/dEploidTools.R:175:36: style: Variable and function names should be all lowercase.

​    tmpCov = strsplit(as.character(tmpCovStr),",")
                                   ^~~~~~~~~

R/dEploidTools.R:175:47: style: Commas should always have a space after.

​    tmpCov = strsplit(as.character(tmpCovStr),",")
                                              ^

R/dEploidTools.R:177:5: style: Variable and function names should be all lowercase.

​    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/dEploidTools.R:177:14: style: Use <-, not =, for assignment.

​    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
             ^

R/dEploidTools.R:177:41: style: Variable and function names should be all lowercase.

​    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
                                        ^~~~~~

R/dEploidTools.R:178:5: style: Variable and function names should be all lowercase.

​    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/dEploidTools.R:178:14: style: Use <-, not =, for assignment.

​    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
             ^

R/dEploidTools.R:178:41: style: Variable and function names should be all lowercase.

​    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
                                        ^~~~~~

R/dEploidTools.R:180:39: style: Commas should always have a space after.

​    return ( data.frame( CHROM = vcf[,1],
                                      ^

R/dEploidTools.R:181:37: style: Commas should always have a space after.

​                         POS = vcf[,2],
                                    ^

R/dEploidTools.R:182:37: style: Variable and function names should be all lowercase.

​                         refCount = refCount,
                                    ^~~~~~~~

R/dEploidTools.R:183:37: style: Variable and function names should be all lowercase.

​                         altCount = altCount )
                                    ^~~~~~~~

R/dEploidTools.R:204:1: style: Variable and function names should be all lowercase.

​extractPLAF<- function ( plafName ){
^~~~~~~~~~~

R/dEploidTools.R:204:12: style: Put spaces around all infix operators.

​extractPLAF<- function ( plafName ){
          ~^

R/dEploidTools.R:204:26: style: Variable and function names should be all lowercase.

​extractPLAF<- function ( plafName ){
                         ^~~~~~~~

R/dEploidTools.R:205:25: style: Variable and function names should be all lowercase.

​    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~

R/dEploidTools.R:205:41: style: Put spaces around all infix operators.

​    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~

R/dEploidTools.R:210:11: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
         ~^~~

R/dEploidTools.R:210:19: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
                 ~^~

R/dEploidTools.R:210:23: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
                     ~^~

R/dEploidTools.R:210:24: style: Place a space before left parenthesis, except in a function call.

​    f.samp<-f.samp+err*(1-2*f.samp);
                       ^

R/dEploidTools.R:210:26: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
                        ~^~

R/dEploidTools.R:210:28: style: Put spaces around all infix operators.

​    f.samp<-f.samp+err*(1-2*f.samp);
                          ~^~

R/dEploidTools.R:211:1: style: lines should not be more than 80 characters.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Place a space before left parenthesis, except in a function call.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: Commas should always have a space after.

​    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: style: Place a space before left parenthesis, except in a function call.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    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: style: lines should not be more than 80 characters.

​    #  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: style: Commented code should be removed.

​    #  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: style: Put spaces around all infix operators.

​    if (sum(is.nan(llk))>1){
                       ~^~

R/dEploidTools.R:220:1: style: Words within variable and function names should be separated by '_' rather than '.'.

​fun.dic.by.llk.var <- function ( tmpllk ){
^~~~~~~~~~~~~~~~~~

R/dEploidTools.R:221:1: style: lines should not be more than 80 characters.

​     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: style: Put spaces around all infix operators.

​     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: style: Put spaces around all infix operators.

​     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: style: Put spaces around all infix operators.

​     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: style: Words within variable and function names should be separated by '_' rather than '.'.

​fun.dic.by.theta <- function ( tmpllk, thetallk ){
^~~~~~~~~~~~~~~~

R/dEploidTools.R:226:5: style: Words within variable and function names should be separated by '_' rather than '.'.

​    DIC.WSAF.bar = -2 * sum(thetallk)
    ^~~~~~~~~~~~

R/dEploidTools.R:226:18: style: Use <-, not =, for assignment.

​    DIC.WSAF.bar = -2 * sum(thetallk)
                 ^

R/dEploidTools.R:227:1: style: lines should not be more than 80 characters.

​    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: style: Put spaces around all infix operators.

​    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: style: Put spaces around all infix operators.

​    return (  mean(-2*tmpllk) + (mean(-2*tmpllk) - DIC.WSAF.bar) ) # D_bar + pD, where pD = D_bar - D_theta, and D_bar = mean(D_theta)
                                       ~^~

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