summary_get_organelle_output.py bug fix #281
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2. separate temporary files from different rounds
2. separate temporary files from different rounds 3. remove upper boundary for coverage-based filtering 4. remove max multiplicity boundary 5. use gekko instead of scipy for multiplicity estimation 6. limit the number of paths before generating 7. log copy info for --no-slim 8. statistical_func.py: fix a bug random.choice(np.array([0])) triggers IndexError: Cannot choose from an empty sequence
2. assembly.parse_tab_file modified largely
… to be average rather than the max 2. slim_graph.generate_baits_offsets: fix a bug generating wrong offsets: min -> max
2. fix a bug in _find_linear_tags 3. merge tagged vertices into paths before searching for linear tags
…ogpdf 2. using negative tag weights to better differentiate target and non-target but similar neighbors
… disentanglement trials
… disentanglement trials 2. skip clustering and other steps when len(vertex_info)==1 and tagged 3. bug fixes: estimate_copy_and_depth_by_cov ValueError: min() arg is an empty sequence
…er steps, which makes false statement of incomplete result
2. fix single_locus_info deletion error causing IndexError
2. make improvement by introducing heuristic searching and fix bugs in _find_linear_tags 3. modify find_target_graph 4. discard sympy
2. change the label initialization part
… the working directory
… the working directory
… to do so because either processes run into D or does not speed up
2. add contig_min_hit_percent 3. allow no depth_cutoff (depth_cutoff==-1)
…it_percent of a contig.
2. add contig_min_hit_percent 3. allow no depth_cutoff (depth_cutoff==-1)
2. add contig_min_hit_percent 3. allow no depth_cutoff (depth_cutoff==-1)
2. add contig_min_hit_percent 3. allow no depth_cutoff (depth_cutoff==-1)
…robably Bandage output issue)
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fix a bug: summary_get_organelle_output.py does not recognize degenerate/ambiguous bases #279