diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
index 408271e71..8f377cae3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
@@ -8,16 +8,20 @@ import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 // create a fasta sequence file from a reference and intervals
 
 @WalkerName("FastaReferenceMaker")
 public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
+    @Argument(fullName="lineWidth", shortName="lw", doc="Maximum length of sequence to write per line", required=false) public int fastaLineWidth=60;
+    @Argument(fullName="rawOnelineSeq", shortName="raw", doc="Print sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity) - CAUTION: adjacent intervals will automatically be merged", required=false) public boolean fastaRawSeqs=false;
 
     protected FastaSequence fasta;
 
     public void initialize() {
-        fasta = new FastaSequence(out);
+        if (fastaRawSeqs) fastaLineWidth = Integer.MAX_VALUE;
+        fasta = new FastaSequence(out, fastaLineWidth, fastaRawSeqs);
     }
 
 	public Pair<GenomeLoc, String> map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
index ae7c859cb..8bb8d6a72 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
@@ -13,9 +13,13 @@ public class FastaSequence {
     private long sequenceCounter = 1;
     private boolean printedHeader = false;
     private String name = null;
+    private int lineWidth = -1;
+    private boolean noHeader = false;
 
-	public FastaSequence(PrintStream out) {
+	public FastaSequence(PrintStream out, int lineWidth, boolean noHeader) {
         this.out = out;
+        this.lineWidth = lineWidth;
+        this.noHeader = noHeader;
     }
 
     public void setName(String name) {
@@ -45,18 +49,18 @@ public class FastaSequence {
     }
 
     private void printFasta(boolean printAll) {
-        if ( sb.length() == 0 || (!printAll && sb.length() < 60) )
+        if ( sb.length() == 0 || (!printAll && sb.length() < lineWidth) )
             return;
-        if ( !printedHeader ) {
+        if ( !printedHeader && !noHeader) {
             if ( name == null ) out.println(">" + sequenceCounter);
-            else  out.println(">" + name);
+            else out.println(">" + name);
             printedHeader = true;
         }
-        int lines = sb.length() / 60;
+        int lines = sb.length() / lineWidth;
         int currentStart = 0;
         for (int i=0; i < lines; i++) {
-            out.println(sb.substring(currentStart, currentStart+60));
-            currentStart += 60;
+            out.println(sb.substring(currentStart, currentStart+lineWidth));
+            currentStart += lineWidth;
         }
         if ( printAll ) {
             out.println(sb.substring(currentStart));