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Update usage #4

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cf61079
update help
smsaladi Oct 2, 2017
6c6894c
fix typo in usage string
smsaladi Oct 2, 2017
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -6,7 +6,7 @@ plmc infers [undirected graphical models](https://en.wikipedia.org/wiki/Markov_r
plmc -c couplingsfile alignmentfile
plmc -o paramfile -c couplingsfile alignmentfile
plmc [-h | --help]

Required input:
alignmentfile Multiple sequence alignment in FASTA format

Expand All @@ -24,9 +24,9 @@ plmc infers [undirected graphical models](https://en.wikipedia.org/wiki/Markov_r
-lg --lambdag <value> Set group L1 lambda for couplings (e_ij)

Options, general:
-a --alphabet alphabet Alternative alphabet (default 21: -ACDEFGHIKLMNPQRSTVWY)
-a --alphabet alphabet Alternative character set to use for analysis
-f --focus identifier Select only uppercase, non-gapped sites from a focus sequence
-g --gapignore Exclude first alphabet character from potential calculations
-g --gapignore Model sequence likelihoods only by coding, non-gapped portions
-m --maxiter Maximum number of iterations
-n --ncores [<number>|max] Maximum number of threads to use in OpenMP
-h --help Usage
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10 changes: 5 additions & 5 deletions src/plm.c
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Expand Up @@ -26,10 +26,10 @@ const char *usage =
"plmc\n"
"\n"
"Usage:\n"
" plm [options] alignmentfile\n"
" plm -c couplingsfile alignmentfile\n"
" plm -o paramfile -c couplingsfile alignmentfile\n"
" plm [-h | --help]\n"
" plmc [options] alignmentfile\n"
" plmc -c couplingsfile alignmentfile\n"
" plmc -o paramfile -c couplingsfile alignmentfile\n"
" plmc [-h | --help]\n"
" \n"
" Required input:\n"
" alignmentfile Multiple sequence alignment in FASTA format\n"
Expand Down Expand Up @@ -951,4 +951,4 @@ void OutputCouplingScores(char *couplingsFile, const numeric_t *x,
fprintf(stderr, "Error writing coupling scores\n");
exit(1);
}
}
}