1. AneuFinder
  2. Commit 7e88d111b65ba1596fe67d24ff88c1e763027a06
Browse code

bugfix usage

chakalakka authored on 23/09/2015 12:42:18
Showing 35 changed files
DESCRIPTION
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@@ -9,7 +9,7 @@ Description: This package implements functions for CNV calling, plotting, export
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 Depends: R (>= 3.1.0), GenomicRanges, ggplot2, reshape2, mclust
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 Imports: IRanges, Rsamtools, Biostrings, GenomicAlignments, grid, preseqR, ggdendro, foreach, doParallel
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 Suggests: knitr, testthat
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-License: GPL-3
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+License:
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 LazyLoad: yes
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 VignetteBuilder: knitr
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 Packaged: 2015-09-19 13:29:00 CET+1; Taudt
LICENSE
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 aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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 Copyright (C) 2015  Aaron Taudt
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-This program is free software: you can redistribute it and/or modify
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-it under the terms of the GNU General Public License as published by
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-the Free Software Foundation, either version 3 of the License, or
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-(at your option) any later version.
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-
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-This program is distributed in the hope that it will be useful,
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-but WITHOUT ANY WARRANTY; without even the implied warranty of
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-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-GNU General Public License for more details.
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-
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-You should have received a copy of the GNU General Public License
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-along with this program.  If not, see <http://www.gnu.org/licenses/>.
R/Aneufinder.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Wrapper function for the aneufinder package
R/aneufinder-package.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Copy-number detection in whole-genome single-cell sequencing data
R/binning.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Convert aligned reads from various file formats into read counts in equidistant bins
R/checkUserInput.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 check.positive.integer = function(testvar) {
R/collapseBins.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Collapse consecutive bins
R/convert2GRanges.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Read bed-file into GRanges
R/correctionMethods.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' GC correction
R/documented_objects.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Binned read counts
R/export.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Export genome browser viewable files
R/findCNVs.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Find copy number variations
R/findSCEs.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Find sister chromatid exchanges
R/getChromLengths.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Chromosome lengths for different assemblies
R/getSegments.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 # =================================================================
R/global.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' @useDynLib aneufinder
R/gtools.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 mixedorder = function (x)
R/initializeStates.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Initialize state factor levels and distributions
R/karyotypeMeasures.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Measures for Karyotype Heterogeneity
R/loadModelsFromFiles.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Load HMMs from files
R/plotting.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' @import ggplot2
R/qualityMeasures.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Quality control measures for binned read counts
R/readConfig.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' Read aneufinder configuration file
R/startup.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 .onAttach <- function(...) {
R/zinbinom.R
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-# aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-# Copyright (C) 2015  Aaron Taudt
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-#
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-# This program is free software: you can redistribute it and/or modify
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-# it under the terms of the GNU General Public License as published by
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-# the Free Software Foundation, either version 3 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-# GNU General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
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 #' The Zero-inflated Negative Binomial Distribution
src/R_interface.cpp
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-//aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-//Copyright (C) 2015  Aaron Taudt
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-//
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-//This program is free software: you can redistribute it and/or modify
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-//it under the terms of the GNU General Public License as published by
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-//the Free Software Foundation, either version 3 of the License, or
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-//(at your option) any later version.
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-//
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-//This program is distributed in the hope that it will be useful,
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-//but WITHOUT ANY WARRANTY; without even the implied warranty of
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-//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-//GNU General Public License for more details.
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-//
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-//You should have received a copy of the GNU General Public License
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-//along with this program.  If not, see <http://www.gnu.org/licenses/>.
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src/densities.cpp
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-//aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-//Copyright (C) 2015  Aaron Taudt
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-//
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-//This program is free software: you can redistribute it and/or modify
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-//it under the terms of the GNU General Public License as published by
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-//the Free Software Foundation, either version 3 of the License, or
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-//(at your option) any later version.
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-//
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-//This program is distributed in the hope that it will be useful,
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-//but WITHOUT ANY WARRANTY; without even the implied warranty of
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-//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-//GNU General Public License for more details.
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-//
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-//You should have received a copy of the GNU General Public License
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-//along with this program.  If not, see <http://www.gnu.org/licenses/>.
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src/densities.h
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-//aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-//Copyright (C) 2015  Aaron Taudt
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-//
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-//This program is free software: you can redistribute it and/or modify
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-//it under the terms of the GNU General Public License as published by
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-//the Free Software Foundation, either version 3 of the License, or
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-//(at your option) any later version.
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-//
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-//This program is distributed in the hope that it will be useful,
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-//but WITHOUT ANY WARRANTY; without even the implied warranty of
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-//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-//GNU General Public License for more details.
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-//
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-//You should have received a copy of the GNU General Public License
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-//along with this program.  If not, see <http://www.gnu.org/licenses/>.
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src/logging.h
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-//aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-//Copyright (C) 2015  Aaron Taudt
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-//
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-//This program is free software: you can redistribute it and/or modify
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-//it under the terms of the GNU General Public License as published by
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-//the Free Software Foundation, either version 3 of the License, or
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-//(at your option) any later version.
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-//
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-//This program is distributed in the hope that it will be useful,
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-//but WITHOUT ANY WARRANTY; without even the implied warranty of
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-//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-//GNU General Public License for more details.
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-//
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-//You should have received a copy of the GNU General Public License
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-//along with this program.  If not, see <http://www.gnu.org/licenses/>.
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src/loghmm.cpp
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-//aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-//Copyright (C) 2015  Aaron Taudt
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-//
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-//This program is free software: you can redistribute it and/or modify
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-//it under the terms of the GNU General Public License as published by
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-//the Free Software Foundation, either version 3 of the License, or
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-//(at your option) any later version.
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-//
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-//This program is distributed in the hope that it will be useful,
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-//but WITHOUT ANY WARRANTY; without even the implied warranty of
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-//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-//GNU General Public License for more details.
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-//
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-//You should have received a copy of the GNU General Public License
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-//along with this program.  If not, see <http://www.gnu.org/licenses/>.
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src/loghmm.h
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-//aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-//Copyright (C) 2015  Aaron Taudt
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-//
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-//This program is free software: you can redistribute it and/or modify
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-//it under the terms of the GNU General Public License as published by
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-//the Free Software Foundation, either version 3 of the License, or
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-//(at your option) any later version.
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-//
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-//This program is distributed in the hope that it will be useful,
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-//but WITHOUT ANY WARRANTY; without even the implied warranty of
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-//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-//GNU General Public License for more details.
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-//
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-//You should have received a copy of the GNU General Public License
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-//along with this program.  If not, see <http://www.gnu.org/licenses/>.
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src/scalehmm.cpp
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-//aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-//Copyright (C) 2015  Aaron Taudt
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-//
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-//This program is free software: you can redistribute it and/or modify
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-//it under the terms of the GNU General Public License as published by
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-//the Free Software Foundation, either version 3 of the License, or
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-//(at your option) any later version.
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-//
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-//This program is distributed in the hope that it will be useful,
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-//but WITHOUT ANY WARRANTY; without even the implied warranty of
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-//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-//GNU General Public License for more details.
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-//
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-//You should have received a copy of the GNU General Public License
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-//along with this program.  If not, see <http://www.gnu.org/licenses/>.
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src/scalehmm.h
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-//aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-//Copyright (C) 2015  Aaron Taudt
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-//
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-//This program is free software: you can redistribute it and/or modify
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-//it under the terms of the GNU General Public License as published by
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-//the Free Software Foundation, either version 3 of the License, or
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-//(at your option) any later version.
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-//
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-//This program is distributed in the hope that it will be useful,
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-//but WITHOUT ANY WARRANTY; without even the implied warranty of
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-//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-//GNU General Public License for more details.
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-//
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-//You should have received a copy of the GNU General Public License
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-//along with this program.  If not, see <http://www.gnu.org/licenses/>.
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src/utility.cpp
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-//aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-//Copyright (C) 2015  Aaron Taudt
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-//
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-//This program is free software: you can redistribute it and/or modify
5 
-//it under the terms of the GNU General Public License as published by
6 
-//the Free Software Foundation, either version 3 of the License, or
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-//(at your option) any later version.
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-//
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-//This program is distributed in the hope that it will be useful,
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-//but WITHOUT ANY WARRANTY; without even the implied warranty of
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-//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-//GNU General Public License for more details.
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-//
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-//You should have received a copy of the GNU General Public License
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-//along with this program.  If not, see <http://www.gnu.org/licenses/>.
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src/utility.h
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-//aneufinder - An R-package for CNV detection in whole-genome single cell sequencing data
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-//Copyright (C) 2015  Aaron Taudt
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-//
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-//This program is free software: you can redistribute it and/or modify
5 
-//it under the terms of the GNU General Public License as published by
6 
-//the Free Software Foundation, either version 3 of the License, or
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-//(at your option) any later version.
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-//
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-//This program is distributed in the hope that it will be useful,
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-//but WITHOUT ANY WARRANTY; without even the implied warranty of
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-//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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-//GNU General Public License for more details.
13 
-//
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-//You should have received a copy of the GNU General Public License
15 
-//along with this program.  If not, see <http://www.gnu.org/licenses/>.
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