fix read.table() skipping many rows

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: tcR
 Type: Package
 Title: Advanced Data Analysis of T Cell Receptor Repertoires
-Version: 2.1
+Version: 2.1.1
 Date: 2015-07-28
 Author: Vadim Nazarov
 Maintainer: Vadim Nazarov <vdm.nazarov@gmail.com>
 Description: Platform for the advanced analysis of T cell receptor repertoires data and visualisation of the analysis results.
 License: Apache License 2.0
-Depends: R (>= 2.15.1), ggplot2 (>= 1.0.0), dplyr (>= 0.4.0), gridExtra (>= 0.9.0), reshape2 (>= 1.2.0), igraph (>= 0.7.1)
-Imports: utils (>= 3.1.0), Rcpp (>= 0.11.1), grid (>= 3.0.0), data.table (>= 1.9.0), gtable (>= 0.1.2), roxygen2 (>= 3.0.0), stringdist (>= 0.7.3)
+Depends: R (>= 2.15.1), ggplot2 (>= 1.0.0), dplyr (>= 0.4.0), gridExtra (>= 2.0.0), reshape2 (>= 1.2.0), igraph (>= 0.7.1)
+Imports: utils (>= 3.1.0), Rcpp (>= 0.11.1), grid (>= 3.1.2), data.table (>= 1.9.0), gtable (>= 0.1.2), roxygen2 (>= 3.0.0), stringdist (>= 0.7.3)
 Suggests: knitr (>= 1.8)
 LinkingTo: Rcpp
 URL: http://imminfo.github.io/tcr/

R/input.R

@@ -87,7 +87,7 @@ parse.cloneset <- function (.filename,
   }
   close(f)
 
-  table.colnames <- make.names(read.table(gzfile(.filename), sep = .sep, skip = .skip, nrows = 1, stringsAsFactors = F, strip.white = T, comment.char = "")[1,])
+  table.colnames <- make.names(read.table(gzfile(.filename), sep = .sep, skip = .skip, nrows = 1, stringsAsFactors = F, strip.white = T, comment.char = "", fill = T, quote = '')[1,])
 
   swlist <- list('character', 'character',
                  'integer', 'integer',
@@ -105,7 +105,7 @@ parse.cloneset <- function (.filename,
     do.call(switch, c(x, swlist))
   }, USE.NAMES = F))
 
-  suppressWarnings(df <- read.table(file = gzfile(.filename), header = T, colClasses = col.classes, sep = .sep, skip = .skip, strip.white = T, comment.char = ""))
+  suppressWarnings(df <- read.table(file = gzfile(.filename), header = T, colClasses = col.classes, sep = .sep, skip = .skip, strip.white = T, fill = T, comment.char = "", quote = ''))
 
   df$Read.proportion <- df[, make.names(.reads)] / sum(df[, make.names(.reads)])
   .read.prop <- 'Read.proportion'
@@ -565,7 +565,7 @@ parse.mixcr <- function (.filename) {
   .dj.insertions <- "DJ.insertions"
   .total.insertions <- "Total.insertions"
 
-  table.colnames <- tolower(make.names(read.table(gzfile(.filename), sep = .sep, skip = 0, nrows = 1, stringsAsFactors = F, strip.white = T, comment.char = "")[1,]))
+  table.colnames <- tolower(make.names(read.table(gzfile(.filename), sep = .sep, skip = 0, nrows = 1, stringsAsFactors = F, strip.white = T, comment.char = "", quote = '')[1,]))
 
   if ('all.v.hits' %in% table.colnames) {
     .vgenes <- 'all.v.hits'
@@ -607,7 +607,7 @@ parse.mixcr <- function (.filename) {
     do.call(switch, c(x, swlist))
   }, USE.NAMES = F))
 
-  suppressWarnings(df <- read.table(file = gzfile(.filename), header = T, colClasses = col.classes, sep = .sep, skip = 0, strip.white = T, comment.char = "", fill = T))
+  suppressWarnings(df <- read.table(file = gzfile(.filename), header = T, colClasses = col.classes, sep = .sep, skip = 0, strip.white = T, comment.char = "", fill = T, quote = ''))
   names(df) <- tolower(names(df))
 
   df$Read.proportion <- df[, make.names(.reads)] / sum(df[, make.names(.reads)])