GetOrganelle v1.7.7.1

1. fix a import bug of 'from scipy import stat, log, inf' issue (issue #132 #315)
2. fix a ZeroDivisionError bug when the estimated coverage is 0 (issue #311)
3. Disentangling failed -> Disentangling unsuccessful to avoid panic (issue #308)
4. fix a bug in parsing options when '-F anonym' is used (issue #319 )
5. have max_multiplicity passed to no-slim case"

GetOrganelle v1.7.7.0

1. Assembly.merge_all_possible_nodes: fix a bug which will result in bad contig names
2. add Utilities/get_annotated_regions_from_gb.py (#197 )
3. fix a bug in seq_parser.SequenceList.remove
4. Utilities/slim_graph.py: --percent and --blast-options added; exception catch
5. fix a bug in get_organelle_config.py:pipe_control_func.py:SEED_DB_HASH (#199 )
6. print slim_graph.py error (in from_assembly) and blastn error
7. fix a bug in slim_graph.py (#196 )
8. update Assembly improvement in gfa/fastg parser/writer: storing other attributes if unknown; output unequal overlaps

GetOrganelle v1.7.6.1

1. improve the target component recognition on non-circular cases (#138 & #141 )
2. assembly_graph.py & statistical_func.py: specify scipy error (#132 )
3. compatible with the newly released GetOrganelleDB v0.0.1.minima (#64 )
4. get_organelle_config.py: fix a bug when there was no available directory made before running --config-dir would be invalid; fix a bug for malfunctioning --verbose

GetOrganelle v1.7.5.3

several bug fixes.
check versions.py for details.

GetOrganelle v1.7.5.0

1. assembly_parser.py: fix a bug in estimation of the multiplicity of self-loop vertices, which were falsely forced to be at least 2. (detected in a case of Yan Zhong@SCNU)
2. other minor bug/typo fixes.

GetOrganelle v1.7.4.1

main updates: bug fixes.

see more @versions.py

GetOrganelle v1.7.4

Main updates:

1. assembly_parser.py: recording every overlap value rather than using a universal value
2. optparse -> argparse
3. output name prefix: filtered -> extended
4. other improvements
5. many bug fixes

see more @version.py

GetOrganelle v1.7.3.5

bug fixed: remove invalid --genes file check

GetOrganelle v1.7.3.4

1. fix bugs with '--config-dir',
2. customized databases (--genes/--ex-genes) passed to slim during pre-assembly & depth estimation,
3. fix a bug with get_graph_coverages_range_simple() when no contigs received

GetOrganelle v1.7.3.3

1. early termination on invalid path characters for spades
2. fix a bug introduced by activating '--max-reads inf'
3. get_organelle_config.py: fix a bug if a new organelle types was added and '--use-local' was used