Version 1.4.0

Added options --fixstart_mincluster/--mincluster to change promer option -c|mincluster during fixstart stage.

Version 1.3.1

• bug fix with regex not matching, so sequences lost, when running get_dnaa
• Update the built-in dna FASTA file from uniprot (issue #73)

Version 1.3.0

• add --debug option to progcheck
• bug fix running spades (used to assume python2 was in path, but not any longer)
• drop dependency on bio_assembly_refinement python package
• add --verbose option to fixstart (see issue #57)
• bug fix handling whitespace in fasta headers with fixstart (see issue #64)
• bug fix incorrect break point coordinates in fixstart log

Version 1.2.1

No changes to algorithm or final fasta. Cosmetic changes related to logging:

• bug fix reporting spades version (issue #56)
• more verbose reporting of version numbers (particularly python package dependencies)
• verbose added to bam2reads (issue #57)
• When verbose, output final summary of contig numbers and circularizations (issue #55)
• New option circlator all --unchanged_code, to let user choose return code when contigs unchanged (issue #55)

Version 1.2.0

• options to not use the spades flags --careful (thanks again @gedankenstuecke) or not use --only-assembler.
• new command "test", which does a complete run of "circlator all" on a small built-in test data set.

Version 1.1.5

• Supports samtools 1.2+ (thanks @gedankenstuecke)
• Require pysam version 0.8.1-0.8.3 (latest 0.9.0 does not install with Travis)
• Added unit tests for the mapping code

Version 1.1.4

Bug fix where circularization sometimes failed (thanks to Jia-Xing Yue for reporting)

Version 1.1.3

Fixes bug when running the 'merge' task without --reads option (see issue #44).

Version 1.1.2

• Add support for SPAdes version 3.6.2.
• Remove support for SPAdes 3.6.1 (but older versions are OK) because it does not output graph information.

Version 1.1.1

Bug fixes to handle Spades version 3.6.1:

• Circlator will work with it, but with less functionality
• If spades version >3.6.0 is detected, lots of warning messages are output suggesting that 3.6.0 would be better instead.

Also bug fix using --no_pair_merge (it was making the pipeline die).