# Path: loom/util.py
# def cp_ns(source, destin):
#     'like cp -ns, link destin to source if destin does not exist'
#     if not os.path.exists(destin):
#         assert os.path.exists(source), source
#         dirname = os.path.dirname(destin)
#         if dirname:
#             mkdir_p(dirname)
#         try:
#             os.symlink(source, destin)
#         except OSError as e:
#             if not os.path.exists(destin):
#                 raise e


from loom.util import cp_ns
import loom.store
import loom.documented
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# - Redistributions of source code must retain the above copyright
#   notice, this list of conditions and the following disclaimer.
# - Redistributions in binary form must reproduce the above copyright
#   notice, this list of conditions and the following disclaimer in the
#   documentation and/or other materials provided with the distribution.
# - Neither the name of Salesforce.com nor the names of its contributors
#   may be used to endorse or promote products derived from this
#   software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
# FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE
# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
# OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
# TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
# USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.



def make_fake_consensus(paths, debug=False):
    for key, destin in loom.store.iter_paths('samples.0', paths['consensus']):
        source = loom.store.get_path(paths, key)

# Path: loom/util.py
# def cp_ns(source, destin):
#     'like cp -ns, link destin to source if destin does not exist'
#     if not os.path.exists(destin):
#         assert os.path.exists(source), source
#         dirname = os.path.dirname(destin)
#         if dirname:
#             mkdir_p(dirname)
#         try:
#             os.symlink(source, destin)
#         except OSError as e:
#             if not os.path.exists(destin):
#                 raise e


# Path: loom/consensus.py
from loom.util import cp_ns
import loom.store
import loom.documented

# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# - Redistributions of source code must retain the above copyright
#   notice, this list of conditions and the following disclaimer.
# - Redistributions in binary form must reproduce the above copyright
#   notice, this list of conditions and the following disclaimer in the
#   documentation and/or other materials provided with the distribution.
# - Neither the name of Salesforce.com nor the names of its contributors
#   may be used to endorse or promote products derived from this
#   software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
# FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE
# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
# OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
# TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
# USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.



def make_fake_consensus(paths, debug=False):
    for key, destin in loom.store.iter_paths('samples.0', paths['consensus']):
        source = loom.store.get_path(paths, key)

        cp_ns(source, destin)