From cf610798e6b6a6c45e27cc8d7e61e3ade292562a Mon Sep 17 00:00:00 2001 From: Shyam Saladi Date: Mon, 2 Oct 2017 00:22:39 -0700 Subject: [PATCH 1/2] update help --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 43245b8..bf07634 100644 --- a/README.md +++ b/README.md @@ -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 @@ -24,9 +24,9 @@ plmc infers [undirected graphical models](https://en.wikipedia.org/wiki/Markov_r -lg --lambdag 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 [|max] Maximum number of threads to use in OpenMP -h --help Usage From 6c6894cad68a2a7ad0d169de909402acf6a8de32 Mon Sep 17 00:00:00 2001 From: Shyam Saladi Date: Mon, 2 Oct 2017 00:23:58 -0700 Subject: [PATCH 2/2] fix typo in usage string --- src/plm.c | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/plm.c b/src/plm.c index d7eddec..c0103a7 100644 --- a/src/plm.c +++ b/src/plm.c @@ -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" @@ -951,4 +951,4 @@ void OutputCouplingScores(char *couplingsFile, const numeric_t *x, fprintf(stderr, "Error writing coupling scores\n"); exit(1); } -} \ No newline at end of file +}