Index: trunk/Ohana/src/opihi/cmd.data/reindex.c
===================================================================
--- trunk/Ohana/src/opihi/cmd.data/reindex.c	(revision 33662)
+++ trunk/Ohana/src/opihi/cmd.data/reindex.c	(revision 34461)
@@ -5,9 +5,15 @@
 int reindex (int argc, char **argv) {
   
-  int  i, Npts, Nmax;
+  int  i, Nmax, N;
   Vector *ivec, *ovec, *xvec;
 
   ivec = ovec = xvec = NULL;
-  Npts = 0;
+  int Npts = 0;
+
+  int KEEP_UNMATCH = FALSE;
+  if ((N = get_argument (argc, argv, "-keep-unmatched"))) {
+    remove_argument (N, &argc, argv);
+    KEEP_UNMATCH = TRUE;
+  }
 
   if (argc != 6) goto usage;
@@ -22,4 +28,5 @@
 
   // ovec matches ivec in type and xvec in size (xvec need not have all ivec elements, and may have duplicates
+  int NPTS = xvec[0].Nelements;
   ResetVector (ovec, ivec->type, xvec[0].Nelements);
 
@@ -31,6 +38,15 @@
     opihi_int *vx = xvec[0].elements.Int;
     for (Npts = i = 0; i < xvec[0].Nelements; i++, vx++) {
-      if (*vx == -1) continue;
-      if (*vx < 0) ESCAPE("unexpected value in index: %d (%d)\n", *vx, i);
+      if (Npts >= NPTS) {
+	NPTS += 2000;
+	REALLOCATE (ovec[0].elements.Flt, opihi_flt, NPTS);
+      }
+      if (*vx < 0) {
+	if (KEEP_UNMATCH) {
+	  ovec[0].elements.Flt[Npts] = NAN;
+	  Npts++;
+	} 
+	continue;
+      }
       if (*vx > Nmax) ESCAPE("unexpected value in index: %d (%d)\n", *vx, i);
       ovec[0].elements.Flt[Npts] = vi[*vx];
@@ -42,6 +58,15 @@
     opihi_int *vx = xvec[0].elements.Int;
     for (Npts = i = 0; i < xvec[0].Nelements; i++, vx++) {
-      if (*vx == -1) continue;
-      if (*vx < 0) ESCAPE("unexpected value in index: %d (%d)\n", *vx, i);
+      if (Npts >= NPTS) {
+	NPTS += 2000;
+	REALLOCATE (ovec[0].elements.Int, opihi_int, NPTS);
+      }
+      if (*vx < 0) {
+	if (KEEP_UNMATCH) {
+	  ovec[0].elements.Flt[Npts] = -1;
+	  Npts++;
+	} 
+	continue;
+      }
       if (*vx > Nmax) ESCAPE("unexpected value in index: %d (%d)\n", *vx, i);
       ovec[0].elements.Int[Npts] = vi[*vx];
@@ -60,5 +85,10 @@
 usage:
     gprint (GP_ERR, "USAGE: reindex (out) = (in) using (index)\n");
-    gprint (GP_ERR, "  creates a new vectors (out) from (in) based on sequence in (index)\n");
+    gprint (GP_ERR, "  Creates a new vector (out) from (in) based on sequence in (index)\n");
+    gprint (GP_ERR, "  output[i] = input[index[i]]\n");
+    gprint (GP_ERR, "  If -keep-unmatched is provided, elements of index with negative values will be set to NaN / -1,\n");
+    gprint (GP_ERR, "    otherwise they will be skipped in the output.\n");
+    gprint (GP_ERR, "  The output vector has the type of the input vector and the length of the index (if -keep-unmatched).\n");
+    gprint (GP_ERR, "  The index vector may have duplicates\n");
     return (FALSE);
 }