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Commits (2)
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__copyright__ = "Copyright (C) 2020 Blaise Li"
__licence__ = "GNU GPLv3"
__version__ = 0.2
from .libhts import (
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 functools import reduce
from re import sub
......
......@@ -9,6 +9,22 @@
# If it is a file, it should contain at least two columns,
# the first one with library names and the second with size factors.
# 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:
# * bedops (for bedmap) -> module load bedops/2.4.36
# * python3 -> module load Python/3.6.0
......
......@@ -5,6 +5,21 @@
# Works if either <mapping.sam>, <mapping.sam.gz> or <mapping.sam.bz2> exists.
# 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
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 Cython.Build import cythonize
......