Some options have default listed twice in --help

[tseemann]

eg. "default 10000 (default: 10000)" is this because of long and short options?

  --tree_builder TREE_BUILDER, -t TREE_BUILDER
                        Application to use for tree building
                        [raxml|fasttree|hybrid], default RAxML (default:
                        raxml)
  --iterations ITERATIONS, -i ITERATIONS
                        Maximum No. of iterations, default is 5 (default: 5)
  --min_snps MIN_SNPS, -m MIN_SNPS
                        Min SNPs to identify a recombination block, default is
                        3 (default: 3)
  --filter_percentage FILTER_PERCENTAGE, -f FILTER_PERCENTAGE
                        Filter out taxa with more than this percentage of
                        gaps, default is 25 (default: 25)
  --min_window_size MIN_WINDOW_SIZE, -a MIN_WINDOW_SIZE
                        Minimum window size, default 100 (default: 100)
  --max_window_size MAX_WINDOW_SIZE, -b MAX_WINDOW_SIZE
                        Maximum window size, default 10000 (default: 10000)
  --raxml_model RAXML_MODEL, -r RAXML_MODEL
                        RAxML model [GTRGAMMA|GTRCAT], default GTRCAT
                        (default: GTRCAT)

[andrewjpage]

In my version of python (3.6.0) the default brackets are missing. What version are you running?

optional arguments:
  -h, --help            show this help message and exit
  --outgroup OUTGROUP, -o OUTGROUP
                        Outgroup name for rerooting. A list of comma separated
                        names can be used if they form a clade
  --starting_tree STARTING_TREE, -s STARTING_TREE
                        Starting tree
  --use_time_stamp, -u  Use a time stamp in file names
  --verbose, -v         Turn on debugging
  --no_cleanup, -n      Dont cleanup intermediate files
  --tree_builder TREE_BUILDER, -t TREE_BUILDER
                        Application to use for tree building
                        [raxml|fasttree|hybrid], default RAxML
  --iterations ITERATIONS, -i ITERATIONS
                        Maximum No. of iterations, default is 5
  --min_snps MIN_SNPS, -m MIN_SNPS
                        Min SNPs to identify a recombination block, default is
                        3
  --filter_percentage FILTER_PERCENTAGE, -f FILTER_PERCENTAGE
                        Filter out taxa with more than this percentage of
                        gaps, default is 25
  --prefix PREFIX, -p PREFIX
                        Add a prefix to the final output filenames
  --threads THREADS, -c THREADS
                        Number of threads to run with RAXML, but only if a
                        PTHREADS version is available
  --converge_method CONVERGE_METHOD, -z CONVERGE_METHOD
                        Criteria to use to know when to halt iterations [weigh
                        ted_robinson_foulds|robinson_foulds|recombination]
  --version             show program's version number and exit
  --min_window_size MIN_WINDOW_SIZE, -a MIN_WINDOW_SIZE
                        Minimum window size, default 100
  --max_window_size MAX_WINDOW_SIZE, -b MAX_WINDOW_SIZE
                        Maximum window size, default 10000
  --remove_identical_sequences, -d
                        Remove identical sequences

[andrewjpage]

I've figured out how to force the defaults and its in PR #200
Thanks for highlighting the bug.

[tseemann]

Python 3.6.2