allow - to be specified for stdout fasta

src/fastaFromBed/fastaFromBed.cpp

@@ -28,7 +28,7 @@ Bed2Fa::Bed2Fa(bool useName, const string &dbFile, const string &bedFile,
     _bed = new BedFile(_bedFile);
 
     // Figure out what the output file should be.
-    if (fastaOutFile == "stdout") {
+    if (fastaOutFile == "stdout" || fastaOutFile == "-") {
         _faOut = &cout;
     }
     else {

test/fastaFromBed/test.sh

-echo $'chr1\t1\t10' | ../../bin/bedtools getfasta -fi t.fa -bed stdin -fo stdout > /dev/null
+LINES=$(echo $'chr1\t1\t10' | ../../bin/bedtools getfasta -fi t.fa -bed stdin -fo - | awk 'END{ print NR }')
+
+
+if [ "$LINES" != "2" ]; then
+    echo "BAD";
+fi
 
 LEN=$(../../bin/bedtools getfasta -split -fi t.fa -bed blocks.bed -fo stdout | awk '(NR == 2){ print length($0) }')
 
 if [ "$LEN" != "22" ]; then
-    print "BAD";
+    echo "BAD";
 fi
 
 SEQ=$(../../bin/bedtools getfasta -split -fi t.fa -bed blocks.bed -fo stdout | awk '(NR == 4){ print $0 }')
 
 if [ "$SEQ" != "cta" ]; then
-    print "BAD";
+    echo "BAD";
 fi