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Commits (2)
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__copyright__ = "Copyright (C) 2020 Blaise Li"
__licence__ = "GNU GPLv3"
__version__ = 0.2 __version__ = 0.2
from .libhts import ( from .libhts import (
aligner2min_mapq, aligner2min_mapq,
......
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
from math import floor, ceil, sqrt, log from math import floor, ceil, sqrt, log
from functools import reduce from functools import reduce
from re import sub from re import sub
......
...@@ -9,6 +9,22 @@ ...@@ -9,6 +9,22 @@
# If it is a file, it should contain at least two columns, # If it is a file, it should contain at least two columns,
# the first one with library names and the second with size factors. # the first one with library names and the second with size factors.
# If it is a value, it shoud be the size factor. # If it is a value, it shoud be the size factor.
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
# Requires: # Requires:
# * bedops (for bedmap) -> module load bedops/2.4.36 # * bedops (for bedmap) -> module load bedops/2.4.36
# * python3 -> module load Python/3.6.0 # * python3 -> module load Python/3.6.0
......
...@@ -5,6 +5,21 @@ ...@@ -5,6 +5,21 @@
# Works if either <mapping.sam>, <mapping.sam.gz> or <mapping.sam.bz2> exists. # Works if either <mapping.sam>, <mapping.sam.gz> or <mapping.sam.bz2> exists.
# Generates two files: <mapping_sorted.bam> and <mapping_sorted.bam.bai>. # Generates two files: <mapping_sorted.bam> and <mapping_sorted.bam.bai>.
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
# http://linuxcommand.org/wss0150.php # http://linuxcommand.org/wss0150.php
PROGNAME=$(basename $0) PROGNAME=$(basename $0)
......
# Copyright (C) 2020 Blaise Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
from setuptools import setup, find_packages from setuptools import setup, find_packages
#from Cython.Build import cythonize #from Cython.Build import cythonize
......