Merge pull request #9 from rdvelazquez/develop

fix newlines and add more args to readme

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)
 

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";