Releases: Kinggerm/GetOrganelle
Releases · Kinggerm/GetOrganelle
GetOrganelle v1.7.3.2
improve support for standard gfa format: E/L with optional fields
GetOrganelle v1.7.3.1
- bug fixed: a bug of sorting consensus vertex names using smart_trans_for_sort
- option --max-reads inf configured
GetOrganelle v1.7.3
- Add fungus_nr mode.
- Relocate default GetOrganelle databases using shell environment value GETORG_PATH or "~/.GetOrganelle" by default
- --reverse-lsc malfunction issue solved
- slim_graph.py: add --evalue
GetOrganelle v1.7.2
- slim_graph.py: fix a bug in parsing options
- automatically adding --phred-offset to avoid hammer failures
- MergingHistory and ConsensusHistory added, in replace of using the names to detect merging history
- Compatible with flye gfa format
- Scaffolding function bug fixed & improved
- get_organelle_config.py: example typo fixed
GetOrganelle v1.7.1-meta
--meta added for testing
Quickly try this version using:
conda install -c biojj -c bioconda GetOrganelle=1.7.1meta
GetOrganelle v1.7.1
- Assembly.get_all_circular_paths(): optimized for plastome order - starting from the "single copy contigs at branching points" rather than the previous "largest single copy contig"; the whole potential lsc region are now taking into account for orfs counting for output orientation.
- get_organelle_from_reads.py: 1) --ignore-k work for small k disentanglement; 2) fix a bug when input reads are very few; 3) better log info
- get_organelle_from_assembly.py: 1) do not convert gfa to fastg during sub-steps; 2) better log info
- Assembly.reduce_to_subgraph: limit_offset_current_vertex -> bait_offsets, the former was a risky setting of slim_graph.py since 1.7.0 because of --max-slim-extending-len added, now issue solved.
- Utilities/slim_fastg.py: fix a bug with anonym mode
- README.md: updated
GetOrganelle v1.7.0
- use SPAdes generated scaffolds.paths to create gap containing scaffolds (assembly_parser.py)
- get_organelle_config.py added with GetOrganelleLib/*Database removed
- slim_graph.py optimized with --max-slim-extending-len added
- fix bugs
GetOrganelle v1.6.4
Latest updates:
- conda installation
- isolate GetOrganelleDep
- log plastome structure
- --max-paths-num added
- evaluate_assembly_using_mapping.py: --stat-mode, --bowtie2-options, --plot-font added
GetOrganelle v1.6.3a
1.6.3 updates:
- --max-multiplicity added
- fix a bug when kmer-len repeats shared by two contigs; fix a bug that cause RuntimeError
- Assembly.parse_gfa(): compatibility increased
- Assembly.estimate_copy_and_depth_precisely(): fix a bug on a rare case that multiplicities res are 4,8,4
- Assembly: too many results due to palindromic repeats, problem solved
see GetOrganelleLib/versions.py for more details
GetOrganelle v1.6.2e
1.6.2e
- seq_parser.py: fix a bug for fastq format: @*****#/1
- get_organelle_from_reads.py: separate_fq_by_pair(), fix a bug when detecting pair info failed;
- evaluate_assembly_using_mapping.py: fix a bug for --plot-transparent
- GetOrganelleLib.__init__.py: __version__
- README.md: updated
1.6.2d
- get_organelle_from_reads.py: fix a bug with "-F anonym"
1.6.2c
- GetOrganelleLib/assembly_parser.py: SSC direction set according to orf
- disentangle: --reverse-lsc option added; fix a bug for disentangling contigs with no overlaps
- Utilities/plastome_arch_info.py: GC content added
- get_organelle_from_reads.py: fix a bug for --flush-step inf
1.6.2b
- fix a minor bug when raising ProcessingGraphFailed with # tags
- setup.py install modified
- open() modified
1.6.2a
- the bug with option "--genes" fixed
- the bug with "Mixing iteration and read methods" introduced by 1.6.2 fixed