little change in -p option description; added little example with m…

…ultiple PAF files

README.md

@@ -169,17 +169,29 @@ It writes [GFA1](https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md#the-gf
 
 #### wfmash
 
+#### single PAF file
+
+```
+wfmash x.fa x.fa -X > x.paf
+seqwish -s x.fa -p x.paf -g x.gfa
+```
+
+#### multiple PAF file
+
 ```
-wfmash x.fa.gz x.fa.gz -X > x.paf
-seqwish -s x.fa.gz -p x.paf -g x.gfa
+wfmash c.fa a.fa > a.paf
+wfmash c.fa b.fa > b.paf
+cat a.fa b.fa c.fa > abc.fa
+seqwish -s abc.fa -p a.paf,b.paf -g abc.gfa
 ```
 
 #### minimap2
 
 [minimap2](https://github.com/lh3/minimap2) does not emit the CIGAR string in PAF output by default. To do this, specify the `-c` flag:
+
 ```
-minimap2 x.fa.gz x.fa.gz -c -X > x.paf
-seqwish -s x.fa.gz -p x.paf -g x.gfa
+minimap2 x.fa x.fa -c -X > x.paf
+seqwish -s x.fa -p x.paf -g x.gfa
 ```
 
 ## TODO

src/main.cpp

@@ -28,7 +28,7 @@ using namespace seqwish;
 int main(int argc, char** argv) {
     args::ArgumentParser parser("seqwish: a variation graph inducer\n" + seqwish::Version::get_version() + ": " + seqwish::Version::get_codename());
     args::HelpFlag help(parser, "help", "display this help menu", {'h', "help"});
-    args::ValueFlag<std::string> paf_alns(parser, "FILE", "Induce the graph from these PAF formatted alignments. Optionally, a list of filenames and minimum match lengths: [file_1]:[min_match_length_1],... This allows the differential filtering of short matches from some but not all inputs, in effect allowing `-k` to be specified differently for each input.", {'p', "paf-alns"});
+    args::ValueFlag<std::string> paf_alns(parser, "FILE", "Induce the graph from these PAF formatted alignments. Optionally, a list of filenames and minimum match lengths: [file_1][:min_match_length_1],... This allows the differential filtering of short matches from some but not all inputs, in effect allowing `-k` to be specified differently for each input.", {'p', "paf-alns"});
     args::ValueFlag<std::string> seqs(parser, "FILE", "The sequences used to generate the alignments (FASTA, FASTQ, .seq)", {'s', "seqs"});
     args::ValueFlag<std::string> base(parser, "BASE", "Build graph using this basename", {'b', "base"});
     args::ValueFlag<std::string> gfa_out(parser, "FILE", "Write the graph in GFA to FILE", {'g', "gfa"});