Index: /branches/eam_branches/ohana.20170822/src/opihi/cmd.data/uniqpair.c
===================================================================
--- /branches/eam_branches/ohana.20170822/src/opihi/cmd.data/uniqpair.c	(revision 40173)
+++ /branches/eam_branches/ohana.20170822/src/opihi/cmd.data/uniqpair.c	(revision 40173)
@@ -0,0 +1,144 @@
+# include "data.h"
+
+/* given two 32bit IDs, a 64bit joint ID and sort it, along with an index (sequence) vector */ 
+int uniqpair (int argc, char **argv) {
+
+  int N;
+  Vector *ID1vec = NULL, *ID2vec = NULL, *SEQvec = NULL, *OUTvec = NULL;
+
+  int VERBOSE = FALSE;
+  if ((N = get_argument (argc, argv, "-v"))) {
+    remove_argument (N, &argc, argv);
+    VERBOSE = TRUE;
+  }
+
+  Vector *SEQdup = NULL;
+  if ((N = get_argument (argc, argv, "-save-dups"))) {
+    remove_argument (N, &argc, argv);
+    if ((SEQdup = SelectVector (argv[N], ANYVECTOR, TRUE)) == NULL) {
+      gprint (GP_ERR, "invalid vector %s\n", "SEQdups");
+      return FALSE;
+    }
+    remove_argument (N, &argc, argv);
+  }
+
+  Vector *CNTvec = NULL;
+  if ((N = get_argument (argc, argv, "-c"))) {
+    remove_argument (N, &argc, argv);
+    if ((CNTvec = SelectVector (argv[N], ANYVECTOR, TRUE)) == NULL) {
+      gprint (GP_ERR, "invalid vector %s\n", argv[N]);
+      return FALSE;
+    }
+    remove_argument (N, &argc, argv);
+  }
+
+  if (argc != 5) {
+    gprint (GP_ERR, "USAGE: uniqpair (ID1) (ID2) (IDout) -c count\n");
+    return (FALSE);
+  }
+
+  if ((ID1vec = SelectVector (argv[1], OLDVECTOR, TRUE)) == NULL) return (FALSE);
+  if ((ID2vec = SelectVector (argv[2], OLDVECTOR, TRUE)) == NULL) return (FALSE);
+  if ((OUTvec = SelectVector (argv[3], ANYVECTOR, TRUE)) == NULL) return (FALSE);
+
+  if ((ID1vec->type == OPIHI_FLT) || (ID2vec->type == OPIHI_FLT)) {
+    gprint (GP_ERR, "ERROR: ID vectors much be int\n");
+    return (FALSE);
+  }
+  if (ID1vec->Nelements != ID2vec->Nelements) {
+    gprint (GP_ERR, "ERROR: ID vectors not all the same length\n");
+    return (FALSE);
+  }
+
+  // storage for the output and count vectors
+  int Nout = 0;
+  int NOUT = 10000;
+  ResetVector (OUTvec, OPIHI_INT, NOUT);
+  if (CNTvec) {
+    ResetVector (CNTvec, OPIHI_INT, NOUT);
+  }
+
+  // storage for the duplicate sequences
+  int NseqDup = 0;
+  int NSEQDUP = 10000;
+  if (SEQdup) {
+    ResetVector (SEQdup, OPIHI_INT, NSEQDUP);
+  }
+  
+  // incrementing pointers to the input IDs
+  opihi_int *ID1 = ID1vec->elements.Int;
+  opihi_int *ID2 = ID2vec->elements.Int;
+
+  // generate the joined and sequence vectors
+  opihi_int *IDfull = NULL;
+  opihi_int *SEQdata = NULL;
+  ALLOCATE (IDfull, opihi_int, ID1vec->Nelements);
+  ALLOCATE (SEQdata, opihi_int, SEQvec[0].Nelements);
+  for (int i = 0; i < ID1vec->Nelements; i++) {
+    IDfull[i] = ID1[i] + (ID2[i] << 32);
+    SEQdata[i] = i;
+  }
+
+  llsorttwo (IDfull, SEQdata, ID1vec->Nelements);
+
+  opihi_int *vtgt = OUTvec->elements.Int;
+  opihi_int *vsrc = IDfull;
+
+  int onePercent = ID1vec->Nelements / 100;
+
+  struct sigaction *old_sigaction = SetInterrupt();
+  for (int i = 0; (i < ID1vec->Nelements) && !interrupt; Nout++) {
+    if (Nout >= NOUT) {
+      NOUT += 10000;
+      REALLOCATE (vtgt, opihi_int, NOUT);
+      if (CNTvec) {
+	REALLOCATE (CNTvec->elements.Int, opihi_int, NOUT);
+      }
+    }
+    vtgt[Nout] = *vsrc;
+    int Ndup = 0;
+    opihi_int lastValue = *vsrc;
+    while ((i < ID1vec->Nelements) && (*vsrc == lastValue)) {
+      i++;
+      vsrc ++;
+      Ndup ++;
+      if (VERBOSE && (i % onePercent == 0)) gprint (GP_ERR, ".");
+    }
+    if (CNTvec) {
+      CNTvec->elements.Int[Nout] = Ndup;
+    }
+    if (SEQdup && (Ndup > 1)) {
+      // we want to save SEQdata values for the duplicates
+      // SEQdata[i-Ndup] .. SEQdata[i-N
+      for (j = i - Ndup; j < i; j++) {
+	SEQdup->elements.Int[NseqDup] = SEQdata[j];
+	NseqDup ++;
+	if (NseqDup >= NSEQDUP) {
+	  NSEQDUP += 10000;
+	  REALLOCATE (SEQdup->elements.Int, opihi_int, NSEQDUP);
+	}
+      }
+    }
+  }
+  ClearInterrupt (old_sigaction);
+  if (VERBOSE) gprint (GP_ERR, "\n");
+
+  free (SEQdata);
+  free (IDfull);
+
+  if (SEQdup) {
+    SEQdup->Nelements = NseqDup;
+    REALLOCATE (SEQdup->elements.Int, opihi_int, Nseqdup);
+  }
+
+  // fix references and free up extra memory:
+  OUTvec->elements.Int = vtgt;
+  ResetVector (OUTvec, OPIHI_INT, Nout);
+  if (cvec) ResetVector (cvec, OPIHI_INT, Nout);
+
+  return (TRUE);
+}
+
+
+
+}
Index: anches/eam_branches/ohana.20170822/src/opihi/dvo/find_dups.c
===================================================================
--- /branches/eam_branches/ohana.20170822/src/opihi/dvo/find_dups.c	(revision 40172)
+++ 	(revision )
@@ -1,144 +1,0 @@
-# include "data.h"
-
-/* given two 32bit IDs, a 64bit joint ID and sort it, along with an index (sequence) vector */ 
-int uniqpair (int argc, char **argv) {
-
-  int N;
-  Vector *ID1vec = NULL, *ID2vec = NULL, *SEQvec = NULL, *OUTvec = NULL;
-
-  int VERBOSE = FALSE;
-  if ((N = get_argument (argc, argv, "-v"))) {
-    remove_argument (N, &argc, argv);
-    VERBOSE = TRUE;
-  }
-
-  Vector *SEQdup = NULL;
-  if ((N = get_argument (argc, argv, "-save-dups"))) {
-    remove_argument (N, &argc, argv);
-    if ((SEQdup = SelectVector (argv[N], ANYVECTOR, TRUE)) == NULL) {
-      gprint (GP_ERR, "invalid vector %s\n", "SEQdups");
-      return FALSE;
-    }
-    remove_argument (N, &argc, argv);
-  }
-
-  Vector *CNTvec = NULL;
-  if ((N = get_argument (argc, argv, "-c"))) {
-    remove_argument (N, &argc, argv);
-    if ((CNTvec = SelectVector (argv[N], ANYVECTOR, TRUE)) == NULL) {
-      gprint (GP_ERR, "invalid vector %s\n", argv[N]);
-      return FALSE;
-    }
-    remove_argument (N, &argc, argv);
-  }
-
-  if (argc != 5) {
-    gprint (GP_ERR, "USAGE: uniqpair (ID1) (ID2) (IDout) -c count\n");
-    return (FALSE);
-  }
-
-  if ((ID1vec = SelectVector (argv[1], OLDVECTOR, TRUE)) == NULL) return (FALSE);
-  if ((ID2vec = SelectVector (argv[2], OLDVECTOR, TRUE)) == NULL) return (FALSE);
-  if ((OUTvec = SelectVector (argv[3], ANYVECTOR, TRUE)) == NULL) return (FALSE);
-
-  if ((ID1vec->type == OPIHI_FLT) || (ID2vec->type == OPIHI_FLT)) {
-    gprint (GP_ERR, "ERROR: ID vectors much be int\n");
-    return (FALSE);
-  }
-  if (ID1vec->Nelements != ID2vec->Nelements) {
-    gprint (GP_ERR, "ERROR: ID vectors not all the same length\n");
-    return (FALSE);
-  }
-
-  // storage for the output and count vectors
-  int Nout = 0;
-  int NOUT = 10000;
-  ResetVector (OUTvec, OPIHI_INT, NOUT);
-  if (CNTvec) {
-    ResetVector (CNTvec, OPIHI_INT, NOUT);
-  }
-
-  // storage for the duplicate sequences
-  int NseqDup = 0;
-  int NSEQDUP = 10000;
-  if (SEQdup) {
-    ResetVector (SEQdup, OPIHI_INT, NSEQDUP);
-  }
-  
-  // incrementing pointers to the input IDs
-  opihi_int *ID1 = ID1vec->elements.Int;
-  opihi_int *ID2 = ID2vec->elements.Int;
-
-  // generate the joined and sequence vectors
-  opihi_int *IDfull = NULL;
-  opihi_int *SEQdata = NULL;
-  ALLOCATE (IDfull, opihi_int, ID1vec->Nelements);
-  ALLOCATE (SEQdata, opihi_int, SEQvec[0].Nelements);
-  for (int i = 0; i < ID1vec->Nelements; i++) {
-    IDfull[i] = ID1[i] + (ID2[i] << 32);
-    SEQdata[i] = i;
-  }
-
-  llsorttwo (IDfull, SEQdata, ID1vec->Nelements);
-
-  opihi_int *vtgt = OUTvec->elements.Int;
-  opihi_int *vsrc = IDfull;
-
-  int onePercent = ID1vec->Nelements / 100;
-
-  struct sigaction *old_sigaction = SetInterrupt();
-  for (int i = 0; (i < ID1vec->Nelements) && !interrupt; Nout++) {
-    if (Nout >= NOUT) {
-      NOUT += 10000;
-      REALLOCATE (vtgt, opihi_int, NOUT);
-      if (CNTvec) {
-	REALLOCATE (CNTvec->elements.Int, opihi_int, NOUT);
-      }
-    }
-    vtgt[Nout] = *vsrc;
-    int Ndup = 0;
-    opihi_int lastValue = *vsrc;
-    while ((i < ID1vec->Nelements) && (*vsrc == lastValue)) {
-      i++;
-      vsrc ++;
-      Ndup ++;
-      if (VERBOSE && (i % onePercent == 0)) gprint (GP_ERR, ".");
-    }
-    if (CNTvec) {
-      CNTvec->elements.Int[Nout] = Ndup;
-    }
-    if (SEQdup && (Ndup > 1)) {
-      // we want to save SEQdata values for the duplicates
-      // SEQdata[i-Ndup] .. SEQdata[i-N
-      for (j = i - Ndup; j < i; j++) {
-	SEQdup->elements.Int[NseqDup] = SEQdata[j];
-	NseqDup ++;
-	if (NseqDup >= NSEQDUP) {
-	  NSEQDUP += 10000;
-	  REALLOCATE (SEQdup->elements.Int, opihi_int, NSEQDUP);
-	}
-      }
-    }
-  }
-  ClearInterrupt (old_sigaction);
-  if (VERBOSE) gprint (GP_ERR, "\n");
-
-  free (SEQdata);
-  free (IDfull);
-
-  if (SEQdup) {
-    SEQdup->Nelements = NseqDup;
-    REALLOCATE (SEQdup->elements.Int, opihi_int, Nseqdup);
-  }
-
-  // fix references and free up extra memory:
-  OUTvec->elements.Int = vtgt;
-  ResetVector (OUTvec, OPIHI_INT, Nout);
-  if (cvec) ResetVector (cvec, OPIHI_INT, Nout);
-
-  return (TRUE);
-}
-
-
-
-}