--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/test/test-regidx.c	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,116 @@
+/*  test/test-regidx.c -- Regions index test harness.
+
+    Copyright (C) 2014 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+#include <stdarg.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <string.h>
+#include <htslib/regidx.h>
+
+void error(const char *format, ...)
+{
+    va_list ap;
+    va_start(ap, format);
+    vfprintf(stderr, format, ap);
+    va_end(ap);
+    exit(-1);
+}
+
+int custom_parse(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr)
+{
+    // Use the standard parser for CHROM,FROM,TO
+    int i, ret = regidx_parse_tab(line,chr_beg,chr_end,reg,NULL,NULL);
+    if ( ret!=0 ) return ret;
+
+    // Skip the fields that were parsed above
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    for (i=0; i<3; i++)
+    {
+        while ( *ss && !isspace(*ss) ) ss++;
+        if ( !*ss ) return -2;  // wrong number of fields
+        while ( *ss && isspace(*ss) ) ss++;
+    }
+    if ( !*ss ) return -2;
+
+    // Parse the payload
+    char *se = ss;
+    while ( *se && !isspace(*se) ) se++;
+    char **dat = (char**) payload;
+    *dat = (char*) malloc(se-ss+1);
+    memcpy(*dat,ss,se-ss+1);
+    (*dat)[se-ss] = 0;
+    return 0;
+}
+void custom_free(void *payload)
+{
+    char **dat = (char**)payload;
+    free(*dat);
+}
+
+int main(int argc, char **argv)
+{
+    // Init index with no file name, we will insert the regions manually
+    regidx_t *idx = regidx_init(NULL,custom_parse,custom_free,sizeof(char*),NULL);
+    if ( !idx ) error("init failed\n");
+
+    // Insert regions
+    char *line;
+    line = "1 10000000 10000000 1:10000000-10000000"; if ( regidx_insert(idx,line)!=0 ) error("insert failed: %s\n", line);
+    line = "1 20000000 20000001 1:20000000-20000001"; if ( regidx_insert(idx,line)!=0 ) error("insert failed: %s\n", line);
+    line = "1 20000002 20000002 1:20000002-20000002"; if ( regidx_insert(idx,line)!=0 ) error("insert failed: %s\n", line);
+    line = "1 30000000 30000000 1:30000000-30000000"; if ( regidx_insert(idx,line)!=0 ) error("insert failed: %s\n", line);
+
+    // Finish initialization
+    regidx_insert(idx,NULL);
+
+    // Test 
+    regitr_t itr;
+    int from, to;
+
+    from = to = 10000000;
+    if ( !regidx_overlap(idx,"1",from-1,to-1,&itr) ) error("query failed: 1:%d-%d\n",from,to);
+    if ( strcmp("1:10000000-10000000",REGITR_PAYLOAD(itr,char*)) ) error("query failed: 1:%d-%d vs %s\n", from,to,REGITR_PAYLOAD(itr,char*));
+    if ( !regidx_overlap(idx,"1",from-2,to-1,&itr) ) error("query failed: 1:%d-%d\n",from-1,to);
+    if ( !regidx_overlap(idx,"1",from-2,to+3,&itr) ) error("query failed: 1:%d-%d\n",from-1,to+2);
+    if ( regidx_overlap(idx,"1",from-2,to-2,&itr) ) error("query failed: 1:%d-%d\n",from-1,to-1);
+
+    from = to = 20000000;
+    if ( !regidx_overlap(idx,"1",from-1,to-1,&itr) ) error("query failed: 1:%d-%d\n",from,to);
+
+    from = to = 20000002;
+    if ( !regidx_overlap(idx,"1",from-1,to-1,&itr) ) error("query failed: 1:%d-%d\n",from,to);
+
+    from = to = 30000000;
+    if ( !regidx_overlap(idx,"1",from-1,to-1,&itr) ) error("query failed: 1:%d-%d\n",from,to);
+
+    // Clean up
+    regidx_destroy(idx);
+    
+    return 0;
+}
+
+