New upstream version 0.4.6+dfsg (b01f31be) · Commits · Debian Med / unicycler

.gitignore

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		@@ -33,6 +33,7 @@ setuptools*.zip
		.idea/

		gh-md-toc
		.coverage

		# CMake stuff (used by CLion)
		CMakeLists.txt

test/test_options.py

+4 −1

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		@@ -16,6 +16,7 @@ import unicycler.unicycler
		import sys
		import os
		import io
		import re
		from contextlib import contextmanager


		@@ -31,7 +32,9 @@ def captured_output():


		def get_default_from_help(option, help_text):
		return help_text.split(option)[1].split('default:')[1].split(')')[0].strip()
		h = help_text.split(option)[1].replace('\n', '')
		h = re.sub('\033.*?m', '', h)
		return h.split('default:')[1].split(')')[0].strip()


		class TestUnicyclerOptions(unittest.TestCase):

unicycler/assembly_graph.py

+6 −3

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		@@ -452,8 +452,8 @@ class AssemblyGraph(object):
		segment_nums_to_remove += component_nums
		self.remove_segments(segment_nums_to_remove)
		if segment_nums_to_remove:
		log.log('\nRemoved homopolymer_loops:', 2)
		log.log_number_list(segment_nums_to_remove, 2)
		log.log('Removed homopolymer loops:', 3)
		log.log_number_list(segment_nums_to_remove, 3)

		def remove_segments(self, nums_to_remove):
		"""
		@@ -939,7 +939,7 @@ class AssemblyGraph(object):
		log.log('Normalise read depths ' + get_dim_timestamp(), 3)
		self.normalise_read_depths()
		log.log('Remove zero length segments ' + get_dim_timestamp(), 3)
		self.remove_zero_length_segs()
		self.remove_zero_length_segs(suppress_log=True)
		log.log('Sort link order ' + get_dim_timestamp(), 3)
		self.sort_link_order()
		log.log('Graph cleaning finished ' + get_dim_timestamp(), 3)
		@@ -2251,6 +2251,9 @@ class AssemblyGraph(object):
		log.log('')
		log.log('Removed zero-length segments:')
		log.log_number_list(segs_to_remove)
		if suppress_log and segs_to_remove:
		log.log(' Removed zero-length segments:', 2)
		log.log_number_list(segs_to_remove, 2)
		return len(segs_to_remove)

		def merge_small_segments(self, max_merge_size):

unicycler/include/seqan/align.h

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		// ==========================================================================
		// SeqAn - The Library for Sequence Analysis
		// ==========================================================================
		// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
		// All rights reserved.
		//
		// 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 Knut Reinert or the FU Berlin 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 KNUT REINERT OR THE FU BERLIN 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.
		//
		// ==========================================================================
		// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
		// ==========================================================================

		#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_H_
		#define SEQAN_INCLUDE_SEQAN_ALIGN_H_

		// TODO(holtgrew): Usage of gapped value in align module is not consistent, need proxies in many places, reference not cleanly implemented everywhere yet.
		// TODO(holtgrew): The Author: tag at the top has to be corrected in the headers of this module.
		// TODO(holtgrew): Anchor Gaps must be integrated completely.
		// TODO(holtgrew): Local alignments & Fragments don't work nicely together at the moment, multiLocalAlignments() needs an equivalent in the new align module.
		// TODO(holtgrew): Align<>, AlignCol<> need some love and documentation.
		// TODO(holtgrew): Gaps need better documentation.
		// TODO(holtgrew): refinement should become graph_align and also host Graph<Alignment<>>
		// TODO(holtgrew): graph_msa should become align_msa, or so, see whitepaper.
		// TODO(holtgrew): The documentation and Tutorial need heavy updates, clipping alignments howto can go away.

		// ============================================================================
		// Prerequisites
		// ============================================================================

		#include <type_traits>
		#include <algorithm>

		#include <seqan/basic.h>
		#include <seqan/modifier.h> // ModifiedAlphabet<>.
		#include <seqan/align/align_metafunctions.h>
		#include <seqan/graph_align.h> // TODO(holtgrew): We should not have to depend on this.

		// TODO(holtgrew): Why not use priority queue from STL?
		#include <seqan/misc/priority_type_base.h>
		#include <seqan/misc/priority_type_heap.h>

		// ============================================================================
		// Support
		// ============================================================================

		#include <seqan/align/gapped_value_type.h>
		#include <seqan/align/align_config.h>
		#include <seqan/align/align_traceback.h>
		#include <seqan/align/matrix_base.h>

		// ============================================================================
		// Gaps & Gaps Iterator Data Structures
		// ============================================================================

		#include <seqan/align/fragment.h>

		#include <seqan/align/gaps_base.h>
		#include <seqan/align/gaps_iterator_base.h>

		#include <seqan/align/gaps_array.h>
		#include <seqan/align/gaps_iterator_array.h>

		#include <seqan/align/gap_anchor.h>
		#include <seqan/align/gaps_anchor.h>
		#include <seqan/align/gaps_iterator_anchor.h>

		// ============================================================================
		// Alignment Data Structures and Columns
		// ============================================================================

		#include <seqan/align/align_cols.h>
		#include <seqan/align/align_base.h>

		// ============================================================================
		// Alignment Algorithm Implementations.
		// ============================================================================

		//################################################################################
		// New module
		//################################################################################

		// The tags have to be available everywhere so we define them centrally.
		#include <seqan/align/alignment_algorithm_tags.h>

		// Defines all tags needed for the DP alignment.
		#include <seqan/align/dp_profile.h>

		// The DP Band
		#include <seqan/align/dp_band.h>

		// Stores the score value of a particular cell in the dp matrix.
		// If affine gap costs are selected one cell stores the three values
		// for all three dp matrices.
		#include <seqan/align/dp_cell.h>
		#include <seqan/align/dp_cell_linear.h>
		#include <seqan/align/dp_cell_affine.h>
		#include <seqan/align/dp_cell_dynamic.h>

		// The DP Scout
		#include <seqan/align/dp_scout.h>

		// Stores the actual trace segment that was detected during traceback.
		// The trace segments can be adapted into any alignment representation
		// form.
		#include <seqan/align/dp_trace_segment.h>
		#include <seqan/align/dp_traceback_adaptor.h>

		// Implements the different recursion formula of the alignment algorithms.
		#include <seqan/align/dp_formula.h>
		#include <seqan/align/dp_formula_linear.h>
		#include <seqan/align/dp_formula_affine.h>
		#include <seqan/align/dp_formula_dynamic.h>

		// Defines meta informations which determine how to compute a column and a
		// certain cell for different profiles.
		#include <seqan/align/dp_meta_info.h>

		// Actual matrix to store the values. Uses the matrix_base.h definitions
		// as a host.
		#include <seqan/align/dp_matrix.h>
		#include <seqan/align/dp_matrix_sparse.h>

		// The navigator that based on the selected profile and band chooses the
		// correct way to navigate through the matrix.
		#include <seqan/align/dp_matrix_navigator.h>
		#include <seqan/align/dp_matrix_navigator_score_matrix.h>
		#include <seqan/align/dp_matrix_navigator_score_matrix_sparse.h>
		#include <seqan/align/dp_matrix_navigator_trace_matrix.h>

		// Ensures the backwards compatibility for the global interfaces of the
		// alignment algorithms. Based on the called function this selects the
		// correct parameters for the new alignment module.
		#include <seqan/align/dp_context.h>
		#include <seqan/align/dp_setup.h>

		#ifdef SEQAN_SIMD_ENABLED
		#include <seqan/align/dp_scout_simd.h>
		#include <seqan/align/dp_align_simd_helper.h>
		#endif // SEQAN_SIMD_ENABLED

		// The actual implementations of the traceback and the dynamic programming that
		// is used by all different alignment algorithms.
		#include <seqan/align/dp_traceback_impl.h>
		#include <seqan/align/dp_algorithm_impl.h>

		//################################################################################
		// Old module
		//################################################################################

		// Also, we have an implementation of Hirschberg's algorithm to compute
		// alignments.
		#include <seqan/align/global_alignment_hirschberg_impl.h>

		// The implementations of Myers' bitvector algorithm for alignments can only
		// compute alignment scores. The combination of Hirschberg's and Myers'
		// algorithm is limited in the same way.
		#include <seqan/align/global_alignment_myers_impl.h>
		#include <seqan/align/global_alignment_myers_hirschberg_impl.h>

		// Implementations of the local alignment algorithms with declumping. We also
		// use them for the localAlignment() calls and return the best local alignment
		// only.
		// TODO(rmaerker): Replace this with a new implementation based on the new alignment module.
		#include <seqan/align/local_alignment_waterman_eggert_impl.h>
		#include <seqan/align/local_alignment_banded_waterman_eggert_impl.h>

		// We carry around this implementation of Smith-Waterman because it supports
		// aligning into fragment strings and alignment graphs. Eventually, it could
		// go away if Waterman-Eggert supports them.
		//#include <seqan/align/local_alignment_smith_waterman_impl.h>

		// ============================================================================
		// Alignment Algorithm Interfaces
		// ============================================================================

		#include <seqan/align/align_interface_wrapper.h>

		// The front-end functions for global alignments.
		#include <seqan/align/global_alignment_unbanded.h>
		#include <seqan/align/global_alignment_banded.h>

		// The front-end functions for local alignments.
		#include <seqan/align/local_alignment_unbanded.h>
		#include <seqan/align/local_alignment_banded.h>

		// The front-end for enumeration of local alignments.
		#include <seqan/align/local_alignment_enumeration.h> // documentation
		#include <seqan/align/local_alignment_enumeration_unbanded.h>
		#include <seqan/align/local_alignment_enumeration_banded.h>

		// The front-end functions for the more specialized alignment algorithms such as
		// Hirschberg, Myers and Myers-Hirschberg.
		#include <seqan/align/global_alignment_specialized.h>

		// ============================================================================
		// Operations On Alignments
		// ============================================================================

		#include <seqan/align/alignment_operations.h>
		#include <seqan/align/evaluate_alignment.h>

		#endif // SEQAN_INCLUDE_SEQAN_ALIGN_H_

unicycler/include/seqan/align/align_base.h

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