Merge pull request #593 in HDFFV/hdf5 from hdf5_1_8_19 to 1.8/masterhdf5-1_8_19

* commit 'c15238a38fdb3692466bc1218de4c5aeb420fdcc': (153 commits)
  Commit changes to release version strings in README.txt and RELEASE.txt from release.
  Put back link targets for dynamically loaded libraries in Makefile.ams that avoid linking with libhdf5 dependencies.  Some configurations failed unnecessarily to find and link with lz and lsz when these targets were removed.
  Update URL for obtaining source inINSTALL file.
  Disable building of libdynlib* dynamically loaded plugin test libraries on CYGWIN. Added known problem entry to RELEASE.txt. Set version for 1.8.19 release. Barbara updated contents of README.txt file.
  Moved libdynlib* plugin test libraries to noist_LT_LIBRARIES with added flag '-rpath /nowhere' to stop them being installed while keeping them from linking with libhdf5, etc. Incremented version to 1.8.19-pre1 and ran bin/release to create tar and zip files for testing.
  HDF5 1.8.19-pre1 released.
  Add RELEASE.txt entry for H5Dget_chunk_size.
  Remove test entries
  Ran bin/reconfigure after so number change.
  Update hl lib .so numbers:  new function was added. Update RELEASE.txt:  move H5DOread_chunks entry to new features, clarify entry for HDFFV-10051.
  Updated notes for test fixes and added bug fix for h5diff help text.
  Update h5vers and release scripts for 1.8.19 branch, set version to 1.8.19-pre1.
  Make script name consistent across product versions
  Update version to 1.8.19-pre1.
  Propagate .so number changes to Makefile.ins with bin/reconfigure.
  Add toolset option
  Update so version numbers according to the interface compatibility report.
  Update supported Platforms section. Remove empty sub-sections of New Features and Bugs Fixed sections.
  Add entries for HDFFV-10051 and HDFFV-9934 to RELEASE.txt.
  Correct spelling
  ...

1 files changed, 356 insertions, 294 deletions

diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index 7998ae8..e1f13fd 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5tools.h"
@@ -33,7 +31,7 @@ const char *outfile = NULL;
  * Command-line options: The user can specify short or long-named
  * parameters.
  */
-static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:E";
+static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:q:z:E";
 static struct long_options l_opts[] = {
     { "help", no_arg, 'h' },
     { "version", no_arg, 'V' },
@@ -54,6 +52,8 @@ static struct long_options l_opts[] = {
     { "alignment", require_arg, 'a' },
     { "infile", require_arg, 'i' }, /* -i for backward compability */
     { "outfile", require_arg, 'o' }, /* -o for backward compability */
+    { "sort_by", require_arg, 'q' },
+    { "sort_order", require_arg, 'z' },
     { "enable-error-stack", no_arg, 'E' },
     { NULL, 0, '\0' }
 };
@@ -88,6 +88,8 @@ static void usage(const char *prog) {
     PRINTVALSTREAM(rawoutstream, "   -M A, --metadata_block_size=A  Metadata block size for H5Pset_meta_block_size\n");
     PRINTVALSTREAM(rawoutstream, "   -t T, --threshold=T     Threshold value for H5Pset_alignment\n");
     PRINTVALSTREAM(rawoutstream, "   -a A, --alignment=A     Alignment value for H5Pset_alignment\n");
+    PRINTVALSTREAM(rawoutstream, "   -q Q, --sort_by=Q       Sort groups and attributes by index Q\n");
+    PRINTVALSTREAM(rawoutstream, "   -z Z, --sort_order=Z    Sort groups and attributes by order Z\n");
     PRINTVALSTREAM(rawoutstream, "   -f FILT, --filter=FILT  Filter type\n");
     PRINTVALSTREAM(rawoutstream, "   -l LAYT, --layout=LAYT  Layout type\n");
     PRINTVALSTREAM(rawoutstream, "\n");
@@ -97,6 +99,8 @@ static void usage(const char *prog) {
     PRINTVALSTREAM(rawoutstream, "    U - is a filename.\n");
     PRINTVALSTREAM(rawoutstream, "    T - is an integer\n");
     PRINTVALSTREAM(rawoutstream, "    A - is an integer greater than zero\n");
+    PRINTVALSTREAM(rawoutstream, "    Q - is the sort index type for the input file. It can be \"name\" or \"creation_order\" (default)\n");
+    PRINTVALSTREAM(rawoutstream, "    Z - is the sort order type for the input file. It can be \"descending\" or \"ascending\" (default)\n");
     PRINTVALSTREAM(rawoutstream, "    B - is the user block size, any value that is 512 or greater and is\n");
     PRINTVALSTREAM(rawoutstream, "        a power of 2 (1024 default)\n");
     PRINTVALSTREAM(rawoutstream, "    F - is the shared object header message type, any of <dspace|dtype|fill|\n");
@@ -191,14 +195,12 @@ static void usage(const char *prog) {
  * Programmer:  Quincey Koziol
  *              Saturday, 31. January 2004
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
-static void leave(int ret) {
-	h5tools_close();
-
-	HDexit(ret);
+static void leave(int ret)
+{
+    h5tools_close();
+    HDexit(ret);
 }
 
 /*-------------------------------------------------------------------------
@@ -214,134 +216,179 @@ static void leave(int ret) {
  *
  *-------------------------------------------------------------------------
  */
-
 static
-int read_info(const char *filename, pack_opt_t *options) {
-
-	char stype[10];
-	char comp_info[1024];
-	FILE *fp = NULL;
-	char c;
-	int i, rc = 1;
-	int ret_value = EXIT_SUCCESS;
-
-	if ((fp = HDfopen(filename, "r")) == (FILE *) NULL) {
-		error_msg("cannot open options file %s\n", filename);
-		h5tools_setstatus(EXIT_FAILURE);
-		ret_value = EXIT_FAILURE;
-		goto done;
-	}
-
-	/* cycle until end of file reached */
-	while (1) {
-		rc = fscanf(fp, "%s", stype);
-		if (rc == -1)
-			break;
-
-		/*-------------------------------------------------------------------------
-		 * filter
-		 *-------------------------------------------------------------------------
-		 */
-		if (HDstrcmp(stype,"-f") == 0) {
-			/* find begining of info */
-			i = 0;
-			c = '0';
-			while (c != ' ') {
-				if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+int read_info(const char *filename, pack_opt_t *options)
+{
+    char stype[10] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
+    char comp_info[1024];
+    FILE *fp = NULL;
+    char c;
+    int i, rc = 1;
+    int ret_value = EXIT_SUCCESS;
+
+    if ((fp = HDfopen(filename, "r")) == (FILE *) NULL) {
+        error_msg("cannot open options file %s\n", filename);
+        h5tools_setstatus(EXIT_FAILURE);
+        ret_value = EXIT_FAILURE;
+        goto done;
+    }
+
+    /* cycle until end of file reached */
+    while (1) {
+        rc = fscanf(fp, "%s", stype);
+        if (rc == -1)
+            break;
+
+        /*-------------------------------------------------------------------------
+         * filter
+         *-------------------------------------------------------------------------
+         */
+        if (HDstrcmp(stype,"-f") == 0) {
+            /* find begining of info */
+            i = 0;
+            c = '0';
+            while (c != ' ') {
+                if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
                     error_msg("fscanf error\n");
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = EXIT_FAILURE;
                     goto done;
                 } /* end if */
-				if (HDfeof(fp))
-					break;
-			}
-			c = '0';
-			/* go until end */
-			while (c != ' ') {
-				if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+                if (HDfeof(fp))
+                    break;
+            }
+            c = '0';
+            /* go until end */
+            while (c != ' ') {
+                if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
                     error_msg("fscanf error\n");
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = EXIT_FAILURE;
                     goto done;
                 } /* end if */
-				comp_info[i] = c;
-				i++;
-				if (HDfeof(fp))
-					break;
-				if (c == 10 /*eol*/)
-					break;
-			}
-			comp_info[i - 1] = '\0'; /*cut the last " */
-
-			if (h5repack_addfilter(comp_info, options) == -1) {
-				error_msg("could not add compression option\n");
-				h5tools_setstatus(EXIT_FAILURE);
-				ret_value = EXIT_FAILURE;
-				goto done;
-			}
-		}
-		/*-------------------------------------------------------------------------
-		 * layout
-		 *-------------------------------------------------------------------------
-		 */
-		else if (HDstrcmp(stype,"-l") == 0) {
-
-			/* find begining of info */
-			i = 0;
-			c = '0';
-			while (c != ' ') {
-				if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+                comp_info[i] = c;
+                i++;
+                if (HDfeof(fp))
+                    break;
+                if (c == 10 /*eol*/)
+                    break;
+            }
+            comp_info[i - 1] = '\0'; /*cut the last " */
+
+            if (h5repack_addfilter(comp_info, options) == -1) {
+                error_msg("could not add compression option\n");
+                h5tools_setstatus(EXIT_FAILURE);
+                ret_value = EXIT_FAILURE;
+                goto done;
+            }
+        }
+        /*-------------------------------------------------------------------------
+         * layout
+         *-------------------------------------------------------------------------
+         */
+        else if (HDstrcmp(stype,"-l") == 0) {
+
+            /* find begining of info */
+            i = 0;
+            c = '0';
+            while (c != ' ') {
+                if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
                     error_msg("fscanf error\n");
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = EXIT_FAILURE;
                     goto done;
                 } /* end if */
-				if (HDfeof(fp))
-					break;
-			}
-			c = '0';
-			/* go until end */
-			while (c != ' ') {
-				if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+                if (HDfeof(fp))
+                    break;
+            }
+            c = '0';
+            /* go until end */
+            while (c != ' ') {
+                if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
                     error_msg("fscanf error\n");
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = EXIT_FAILURE;
                     goto done;
                 } /* end if */
-				comp_info[i] = c;
-				i++;
-				if (HDfeof(fp))
-					break;
-				if (c == 10 /*eol*/)
-					break;
-			}
-			comp_info[i - 1] = '\0'; /*cut the last " */
-
-			if (h5repack_addlayout(comp_info, options) == -1) {
-				error_msg("could not add chunck option\n");
-				h5tools_setstatus(EXIT_FAILURE);
-				ret_value = EXIT_FAILURE;
-				goto done;
-			}
-		}
-		/*-------------------------------------------------------------------------
-		 * not valid
-		 *-------------------------------------------------------------------------
-		 */
-		else {
-			error_msg("bad file format for %s", filename);
-			h5tools_setstatus(EXIT_FAILURE);
-			ret_value = EXIT_FAILURE;
-			goto done;
-		}
-	}
+                comp_info[i] = c;
+                i++;
+                if (HDfeof(fp))
+                    break;
+                if (c == 10 /*eol*/)
+                    break;
+            }
+            comp_info[i - 1] = '\0'; /*cut the last " */
+
+            if (h5repack_addlayout(comp_info, options) == -1) {
+                error_msg("could not add chunck option\n");
+                h5tools_setstatus(EXIT_FAILURE);
+                ret_value = EXIT_FAILURE;
+                goto done;
+            }
+        }
+        /*-------------------------------------------------------------------------
+         * not valid
+         *-------------------------------------------------------------------------
+         */
+        else {
+            error_msg("bad file format for %s", filename);
+            h5tools_setstatus(EXIT_FAILURE);
+            ret_value = EXIT_FAILURE;
+            goto done;
+        }
+    }
 
 done:
-	if (fp)
-		HDfclose(fp);
+    if (fp)
+        HDfclose(fp);
+
+    return ret_value;
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    set_sort_by
+ *
+ * Purpose: set the "by" form of sorting by translating from a string input
+ *          parameter to a H5_index_t return value
+ *          current sort values are [creation_order | name]
+ *
+ * Return: H5_index_t form of sort or H5_INDEX_UNKNOWN if none found
+ *-------------------------------------------------------------------------
+ */
+static H5_index_t
+set_sort_by(const char *form)
+{
+    H5_index_t idx_type = H5_INDEX_UNKNOWN;
+
+    if (HDstrcmp(form,"name")==0) /* H5_INDEX_NAME */
+        idx_type = H5_INDEX_NAME;
+    else if (HDstrcmp(form,"creation_order")==0) /* H5_INDEX_CRT_ORDER */
+        idx_type = H5_INDEX_CRT_ORDER;
+
+    return idx_type;
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    set_sort_order
+ *
+ * Purpose: set the order of sorting by translating from a string input
+ *          parameter to a H5_iter_order_t return value
+ *          current order values are [ascending | descending ]
+ *
+ * Return: H5_iter_order_t form of order or H5_ITER_UNKNOWN if none found
+ *-------------------------------------------------------------------------
+ */
+static H5_iter_order_t
+set_sort_order(const char *form)
+{
+    H5_iter_order_t iter_order = H5_ITER_UNKNOWN;
 
-	return ret_value;
+    if (HDstrcmp(form,"ascending")==0) /* H5_ITER_INC */
+        iter_order = H5_ITER_INC;
+    else if (HDstrcmp(form,"descending")==0) /* H5_ITER_DEC */
+        iter_order = H5_ITER_DEC;
+
+    return iter_order;
 }
 
 /*-------------------------------------------------------------------------
@@ -351,184 +398,196 @@ done:
  *
  *-------------------------------------------------------------------------
  */
-
 static
-int parse_command_line(int argc, const char **argv, pack_opt_t* options) {
-
-	int opt;
-	int ret_value = 0;
-
-	/* parse command line options */
-	while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
-		switch ((char) opt) {
-
-		/* -i for backward compability */
-		case 'i':
-			infile = opt_arg;
-			has_i_o = 1;
-			break;
-
-		/* -o for backward compability */
-		case 'o':
-			outfile = opt_arg;
-			has_i_o = 1;
-			break;
-
-		case 'h':
-			usage(h5tools_getprogname());
-			h5tools_setstatus(EXIT_SUCCESS);
-			ret_value = -1;
-			goto done;
-
-		case 'V':
-			print_version(h5tools_getprogname());
-			h5tools_setstatus(EXIT_SUCCESS);
-			ret_value = -1;
-			goto done;
-
-		case 'v':
-			options->verbose = 1;
-			break;
-
-		case 'f':
-			/* parse the -f filter option */
-			if (h5repack_addfilter(opt_arg, options) < 0) {
-				error_msg("in parsing filter\n");
-				h5tools_setstatus(EXIT_FAILURE);
-				ret_value = -1;
-				goto done;
-			}
-			break;
-
-		case 'l':
-			/* parse the -l layout option */
-			if (h5repack_addlayout(opt_arg, options) < 0) {
-				error_msg("in parsing layout\n");
-				h5tools_setstatus(EXIT_FAILURE);
-				ret_value = -1;
-				goto done;
-			}
-			break;
-
-		case 'm':
-			options->min_comp = HDstrtoull(opt_arg , NULL, 0);
-			if ((int) options->min_comp <= 0) {
-				error_msg("invalid minimum compress size <%s>\n", opt_arg);
-				h5tools_setstatus(EXIT_FAILURE);
-				ret_value = -1;
-				goto done;
-			}
-			break;
-
-		case 'e':
-			ret_value = read_info(opt_arg, options);
-			if (ret_value < 0)
-				goto done;
-			break;
-
-		case 'n':
-			options->use_native = 1;
-			break;
-
-		case 'L':
-			options->latest = 1;
-			break;
-
-		case 'c':
-			options->grp_compact = HDatoi( opt_arg );
-			if (options->grp_compact > 0)
-				options->latest = 1; /* must use latest format */
-			break;
-
-		case 'd':
-			options->grp_indexed = HDatoi( opt_arg );
-			if (options->grp_indexed > 0)
-				options->latest = 1; /* must use latest format */
-			break;
-
-		case 's':
-			{
-				int idx = 0;
-				int ssize = 0;
-				char *msgPtr = HDstrchr( opt_arg, ':');
-				options->latest = 1; /* must use latest format */
-				if (msgPtr == NULL) {
-					ssize = HDatoi( opt_arg );
-					for (idx = 0; idx < 5; idx++)
-						options->msg_size[idx] = ssize;
-				}
-				else {
-					char msgType[10];
-					HDstrcpy(msgType, msgPtr + 1);
-					msgPtr[0] = '\0';
-					ssize = HDatoi( opt_arg );
-					if (HDstrncmp(msgType, "dspace",6) == 0) {
-						options->msg_size[0] = ssize;
-					}
-					else if (HDstrncmp(msgType, "dtype", 5) == 0) {
-						options->msg_size[1] = ssize;
-					}
-					else if (HDstrncmp(msgType, "fill", 4) == 0) {
-						options->msg_size[2] = ssize;
-					}
-					else if (HDstrncmp(msgType, "pline", 5) == 0) {
-						options->msg_size[3] = ssize;
-					}
-					else if (HDstrncmp(msgType, "attr", 4) == 0) {
-						options->msg_size[4] = ssize;
-					}
-				}
-			}
-			break;
-
-		case 'u':
-			options->ublock_filename = opt_arg;
-			break;
-
-		case 'b':
-			options->ublock_size = (hsize_t) HDatol( opt_arg );
-			break;
-
-		case 'M':
-			options->meta_block_size = (hsize_t) HDatol( opt_arg );
-			break;
-
-		case 't':
-			options->threshold = (hsize_t) HDatol( opt_arg );
-			break;
-
-		case 'a':
-			options->alignment = HDstrtoull(opt_arg , NULL, 0);
-			if (options->alignment < 1) {
-				error_msg("invalid alignment size\n", opt_arg);
-				h5tools_setstatus(EXIT_FAILURE);
-				ret_value = -1;
-				goto done;
-			}
-			break;
-
-        case 'E':
+int parse_command_line(int argc, const char **argv, pack_opt_t* options)
+{
+    int opt;
+    int ret_value = 0;
+
+    /* parse command line options */
+    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+        switch ((char) opt) {
+
+            /* -i for backward compability */
+            case 'i':
+                infile = opt_arg;
+                has_i_o = 1;
+                break;
+
+            /* -o for backward compability */
+            case 'o':
+                outfile = opt_arg;
+                has_i_o = 1;
+                break;
+
+            case 'h':
+                usage(h5tools_getprogname());
+                h5tools_setstatus(EXIT_SUCCESS);
+                ret_value = -1;
+                goto done;
+
+            case 'V':
+                print_version(h5tools_getprogname());
+                h5tools_setstatus(EXIT_SUCCESS);
+                ret_value = -1;
+                goto done;
+
+            case 'v':
+                options->verbose = 1;
+                break;
+
+            case 'f':
+                /* parse the -f filter option */
+                if (h5repack_addfilter(opt_arg, options) < 0) {
+                    error_msg("in parsing filter\n");
+                    h5tools_setstatus(EXIT_FAILURE);
+                    ret_value = -1;
+                    goto done;
+                }
+                break;
+
+            case 'l':
+                /* parse the -l layout option */
+                if (h5repack_addlayout(opt_arg, options) < 0) {
+                    error_msg("in parsing layout\n");
+                    h5tools_setstatus(EXIT_FAILURE);
+                    ret_value = -1;
+                    goto done;
+                }
+                break;
+
+            case 'm':
+                options->min_comp = HDstrtoull(opt_arg , NULL, 0);
+                if ((int) options->min_comp <= 0) {
+                    error_msg("invalid minimum compress size <%s>\n", opt_arg);
+                    h5tools_setstatus(EXIT_FAILURE);
+                    ret_value = -1;
+                    goto done;
+                }
+                break;
+
+            case 'e':
+                ret_value = read_info(opt_arg, options);
+                if (ret_value < 0)
+                    goto done;
+                break;
+
+            case 'n':
+                options->use_native = 1;
+                break;
+
+            case 'L':
+                options->latest = TRUE;
+                break;
+
+            case 'c':
+                options->grp_compact = HDatoi( opt_arg );
+                if (options->grp_compact > 0)
+                    options->latest = TRUE; /* must use latest format */
+                break;
+
+            case 'd':
+                options->grp_indexed = HDatoi( opt_arg );
+                if (options->grp_indexed > 0)
+                    options->latest = TRUE; /* must use latest format */
+                break;
+
+            case 's':
+                {
+                    int idx = 0;
+                    int ssize = 0;
+                    char *msgPtr = HDstrchr( opt_arg, ':');
+                    options->latest = TRUE; /* must use latest format */
+                    if (msgPtr == NULL) {
+                        ssize = HDatoi( opt_arg );
+                        for (idx = 0; idx < 5; idx++)
+                            options->msg_size[idx] = ssize;
+                    }
+                    else {
+                        char msgType[10];
+
+                        HDstrcpy(msgType, msgPtr + 1);
+                        msgPtr[0] = '\0';
+                        ssize = HDatoi( opt_arg );
+                        if (HDstrncmp(msgType, "dspace",6) == 0)
+                            options->msg_size[0] = ssize;
+                        else if (HDstrncmp(msgType, "dtype", 5) == 0)
+                            options->msg_size[1] = ssize;
+                        else if (HDstrncmp(msgType, "fill", 4) == 0)
+                            options->msg_size[2] = ssize;
+                        else if (HDstrncmp(msgType, "pline", 5) == 0)
+                            options->msg_size[3] = ssize;
+                        else if (HDstrncmp(msgType, "attr", 4) == 0)
+                            options->msg_size[4] = ssize;
+                    }
+                }
+                break;
+
+            case 'u':
+                options->ublock_filename = opt_arg;
+                break;
+
+            case 'b':
+                options->ublock_size = (hsize_t) HDatol( opt_arg );
+                break;
+
+            case 'M':
+                options->meta_block_size = (hsize_t) HDatol( opt_arg );
+                break;
+
+            case 't':
+                options->threshold = (hsize_t) HDatol( opt_arg );
+                break;
+
+            case 'a':
+                options->alignment = HDstrtoull(opt_arg , NULL, 0);
+                if (options->alignment < 1) {
+                    error_msg("invalid alignment size\n", opt_arg);
+                    h5tools_setstatus(EXIT_FAILURE);
+                    ret_value = -1;
+                    goto done;
+                }
+                break;
+
+            case 'q':
+                if((sort_by = set_sort_by(opt_arg)) < 0) {
+                    error_msg(" failed to set sort by form <%s>\n", opt_arg);
+                    h5tools_setstatus(EXIT_FAILURE);
+                    ret_value = -1;
+                    goto done;
+                }
+                break;
+
+            case 'z':
+                if((sort_order = set_sort_order(opt_arg)) < 0) {
+                    error_msg(" failed to set sort order form <%s>\n", opt_arg);
+                    h5tools_setstatus(EXIT_FAILURE);
+                    ret_value = -1;
+                    goto done;
+                }
+                break;
+
+            case 'E':
             enable_error_stack = TRUE;
             break;
 
-        default:
-            break;
+            default:
+                break;
         } /* switch */
-
     } /* while */
 
     if (has_i_o == 0) {
-		/* check for file names to be processed */
-		if (argc <= opt_ind || argv[opt_ind + 1] == NULL) {
-			error_msg("missing file names\n");
-			usage(h5tools_getprogname());
-			h5tools_setstatus(EXIT_FAILURE);
-			ret_value = -1;
-		}
-	}
+        /* check for file names to be processed */
+        if (argc <= opt_ind || argv[opt_ind + 1] == NULL) {
+            error_msg("missing file names\n");
+            usage(h5tools_getprogname());
+            h5tools_setstatus(EXIT_FAILURE);
+            ret_value = -1;
+        }
+    }
 
 done:
-	return ret_value;
+    return ret_value;
 }
 
 /*-------------------------------------------------------------------------
@@ -548,16 +607,16 @@ done:
  *
  *-------------------------------------------------------------------------
  */
-int main(int argc, const char **argv) {
+int main(int argc, const char **argv)
+{
+    pack_opt_t options; /*the global options */
     H5E_auto2_t         func;
     H5E_auto2_t         tools_func;
     void               *edata;
     void               *tools_edata;
 
-	pack_opt_t options; /*the global options */
-
-	h5tools_setprogname(PROGRAMNAME);
-	h5tools_setstatus(EXIT_SUCCESS);
+    h5tools_setprogname(PROGRAMNAME);
+    h5tools_setstatus(EXIT_SUCCESS);
 
     /* Disable error reporting */
     H5Eget_auto2(H5E_DEFAULT, &func, &edata);
@@ -579,6 +638,9 @@ int main(int argc, const char **argv) {
     /* initialize options  */
     h5repack_init(&options, 0);
 
+    /* Initialize default indexing options */
+    sort_by = H5_INDEX_CRT_ORDER;
+
     if (parse_command_line(argc, argv, &options) < 0)
         goto done;
 
@@ -610,12 +672,12 @@ int main(int argc, const char **argv) {
     }
 
     /* pack it */
-	h5tools_setstatus(h5repack(infile, outfile, &options));
+    h5tools_setstatus(h5repack(infile, outfile, &options));
 
 done:
-	/* free tables */
-	h5repack_end(&options);
+    /* free tables */
+    h5repack_end(&options);
 
-	leave(h5tools_getstatus());
+    leave(h5tools_getstatus());
 }