fixed batched reading on stdin input

README.md

@@ -31,7 +31,7 @@ java -jar SeqRuler.jar
 ## Help
 
 ```bash
-Usage: SeqRuler [-egGhnprsSV] [-a=<ambiguityHandling>] [-c=<cores>]
+Usage: java -jar SeqRuler.jar [-egGhnprsSV] [-a=<ambiguityHandling>] [-c=<cores>]
                 [-d=<distanceMethod>] [-f=<max_ambiguity_fraction>] [-i=FILE]
                 [-o=FILE] [-t=<edgeThresholdString>]
   -a, --ambiguity, --ambiguities=<ambiguityHandling>
@@ -47,7 +47,7 @@ Usage: SeqRuler [-egGhnprsSV] [-a=<ambiguityHandling>] [-c=<cores>]
                                mapping. Default: false
   -f, --fraction=<max_ambiguity_fraction>
                              Maximum allowable fraction of ambiguities allowed for
-                               'resolve' mode. If exceeded, use 'average' mode.
+                               'resolve' mode. If exceeded, uses 'average' mode.
   -g, --ignore-terminal-gaps Ignore terminal gaps at beginning and end of sequences
                                when calculating distances. [SNP only] Default: true
   -G, --ignore-all-gaps      Ignore all gaps when calculating distances. [SNP only]
@@ -58,7 +58,8 @@ Usage: SeqRuler [-egGhnprsSV] [-a=<ambiguityHandling>] [-c=<cores>]
                                only] Default: true
   -o, --outFile=FILE         output file with distances
   -p, --pairs                read pairs of sequences from stdin, calculate distance
-                               for each pair. format "name1, seq1, name2, seq2\n"
+                               for each pair. format "name1, seq1, name2, seq2\n".
+                               Do not include a header row
   -r, --run-server           run jetty server
   -s, --stdin                read fasta from stdin. Alternative to reading from a
                                file (-i)

modules/gui-app/src/main/java/Main.java

@@ -29,7 +29,7 @@ public class Main implements Runnable{
     private boolean use_stdin;
     @CommandLine.Option(names={"-S", "--stdout"}, description="write distances to stdout. Alternative to writing to a file (-o)", defaultValue = "false")
     private boolean use_stdout;
-    @CommandLine.Option(names={"-p", "--pairs"}, description="read pairs of sequences from stdin, calculate distance for each pair. format \"name1, seq1, name2, seq2\\n\"", defaultValue = "false")
+    @CommandLine.Option(names={"-p", "--pairs"}, description="read pairs of sequences from stdin, calculate distance for each pair. format \"name1, seq1, name2, seq2\\n\". Do not include a header row", defaultValue = "false")
     private boolean input_as_pairs;
     @CommandLine.Option(names={"-d", "--distance-method"},
             description="distance metric to use. One of [TN93, SNP]. Default: TN93", defaultValue = "TN93")
@@ -43,7 +43,7 @@ public class Main implements Runnable{
             description="How to handle ambiguous nucleotides. One of [resolve, average, gapmm, skip]", defaultValue = "resolve")
     private String ambiguityHandling;
     @CommandLine.Option(names={"-f", "--fraction"},
-            description="Maximum allowable fraction of ambiguities allowed for 'resolve' mode. If exceeded, use 'average' mode.", defaultValue = "1.0")
+            description="Maximum allowable fraction of ambiguities allowed for 'resolve' mode. If exceeded, uses 'average' mode.", defaultValue = "1.0")
     private float max_ambiguity_fraction;
     @CommandLine.Option(names={"-c", "--cores"},
             description="Number of cores to use for parallel processing. Default: 1", defaultValue = "1")

modules/gui-app/src/main/java/TN93/TN93.java

@@ -179,6 +179,10 @@ public void tn93Fasta() {
     	            	count=0;//reset counts
                 	}
             	} 
+                // process the last batch
+                if (pairs.size() > 0) {
+                    tn93_pairs(pairs);
+                }
         		return;
             } else if (use_stdin) {
                 seqs = read_fasta_stdin();