From 74add4230f68b08f041ba9433491f21921cd6a1c Mon Sep 17 00:00:00 2001 From: Ryan Velazquez Date: Tue, 20 Feb 2018 13:34:50 -0500 Subject: [PATCH] fix newlines and add more args to readme --- README.md | 13 +++++++++++-- src/argparse.cpp | 4 ++-- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index cae6ea2..71722aa 100644 --- a/README.md +++ b/README.md @@ -58,6 +58,10 @@ ARGUMENTS skip: do not include sites with ambiguous nucleotides in distance calculations; gapmm: a gap ('-') matched to anything other than another gap is like matching an N (4-fold ambig) to it; a string (e.g. RY): any ambiguity in the list is RESOLVED; any ambiguitiy NOT in the list is averaged (LIST-NOT LIST will also be averaged); + -g FRACTION in combination with AMBIGS, works to limit (for resolve and string options to AMBIG) + the maximum tolerated FRACTION of ambiguous characters; sequences whose pairwise comparisons + include no more than FRACTION [0,1] of sites with resolvable ambiguities will be resolved + while all others will be AVERAGED (default=1.0) -f FORMAT controls the format of the output unless -c is set (default=csv) csv: seqname1, seqname2, distance; csvn: 1, 2, distance; @@ -67,10 +71,15 @@ ARGUMENTS when computing distance histograms (a character, default=':'): -s SECOND_FASTA if specified, read another FASTA file from SECOND_FASTA and perform pairwise comparison BETWEEN the files (default=NULL) -b bootstrap alignment columns before computing distances (default = false) - when -s is supplied, permutes the assigment of sequences to files + when -s is supplied, permutes the assigment of sequences to file + -r if -b is specified AND -s is supplied, using -r will bootstrap across sites + instead of allocating sequences to 'compartments' randomly -c only count the pairs below a threshold, do not write out all the pairs -m compute inter- and intra-population means suitable for FST caclulations - only applied when -s is used to provide a second file -u PROBABILITY subsample sequences with specified probability (a value between 0 and 1, default = 1.0) + only applied when -s is used to provide a second file + -u PROBABILITY subsample sequences with specified probability (a value between 0 and 1, default = 1.0) + -0 report distances between each sequence and itself (as 0); this is useful to ensure every sequence + in the input file appears in the output, e.g. for network construction to contrast clustered/unclustered -q do not report progress updates and other diagnostics to stderr FASTA read sequences to compare from this file (default=stdin) diff --git a/src/argparse.cpp b/src/argparse.cpp index 0cbeacf..a01d07e 100644 --- a/src/argparse.cpp +++ b/src/argparse.cpp @@ -68,8 +68,8 @@ namespace argparse " -m compute inter- and intra-population means suitable for FST caclulations\n" " only applied when -s is used to provide a second file\n" " -u PROBABILITY subsample sequences with specified probability (a value between 0 and 1, default = " TO_STR ( DEFAULT_INCLUDE_PROB) ")\n" - " -0 report distances between each sequence and itself (as 0); this is useful to ensure every sequence" - " in the input file appears in the output, e.g. for network construction to contrast clustered/unclustered" + " -0 report distances between each sequence and itself (as 0); this is useful to ensure every sequence\n" + " in the input file appears in the output, e.g. for network construction to contrast clustered/unclustered\n" " -q do not report progress updates and other diagnostics to stderr \n" " FASTA read sequences to compare from this file (default=stdin)\n";