Issues in help output

[sjackman]

Error: no input or process files specified
Usage 1 (direct execution): MHAP -s<fasta/dat from/self file> [-q<fasta/dat to file>] [-f<kmer filter list, must be sorted>]
Usage 2 (generate precomputed binaries): MHAP -p<directory of fasta files> -q <output directory> [-f<kmer filter list, must be sorted>]
Options: 
     -k [int merSize], default: 16
      --memory [do not store kmers in memory]
      --num-hashes [int # hashes], default: 1024
      --min-store-length [int # of minimum sequence length that is hashed], default: 0
      --threshold [int threshold for % matching minimums], default: 0.05

The type is int but the default is double 0.05.

      --max-shift [double fraction of the overlap size where shift in k-mer match is still considered valid], default: 0.2
      --num-min-matches [int # hashes that maches before performing local alignment], default: 3

maches should be matches.

      --num-threads [int # threads to use for computation], default (2 x #cores): 8
      --subsequence-size [depricated, int size of maximum minhashed sequence], default: 100000

depricated should be deprecated

      --no-self [do not compute results to self], default: false
      --store-full-id [use full sequence id rather than order in file], default: false

      --threshold [int threshold for % matching minimums], default: 0.05
      --max-shift [int # max sequence shift allowed for a valid kmer relative to median value], default: 0.2

These two options are duplicated above. The types are int but the default values are double.

[konstantinberlin]

Addressed in the upcoming version.