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fix newlines and add more args to readme #9

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Feb 20, 2018
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fix newlines and add more args to readme #9

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13 changes: 11 additions & 2 deletions README.md
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Expand Up @@ -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;
Expand All @@ -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)

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4 changes: 2 additions & 2 deletions src/argparse.cpp
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Expand Up @@ -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";

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