diff --git a/htsutils.c b/htsutils.c
index fc055a0..a8ebdc6 100644
--- a/htsutils.c
+++ b/htsutils.c
@@ -14,6 +14,10 @@ int parseBAM(Settings *props)
     bam_hdr_t *header = sam_hdr_read(fh_in);
     bam1_t *bam = bam_init1();
     
+    int absent;
+    khiter_t k;
+    khash_t(pass_hash) *hptr = kh_init(pass_hash);
+    
     uint32_t lines = 0;
     uint32_t poly = 0;
     
@@ -47,23 +51,48 @@ int parseBAM(Settings *props)
         if ((polyTailSize >= props->sizepoly) && (polyReadSize <= (bam->core.l_qseq - props->sizepoly)))
         {
             poly++;
+            
+            // add polyBasePosition to hash
+            k = kh_put(pass_hash, hptr, polyBasePosition, &absent);
+            if (absent)
+                kh_value(hptr, k) = 1;
+            else
+                kh_value(hptr, k)++;
+            
         }
         
+        
+        
         //printf("Tail: %d|%d\tHead: %d|%d\tSeq:: ", polyTailA,polyTailT,polyHeadA,polyHeadT);
         //dumpBamSeq(bam);
         //printf("\n");
         
         lines++;
-        //if (lines == 10)
+        //if (lines == 1)
         //    break;
         
     }
     
+    fprintf(stderr, "BAM Lines: %d / %d\n", poly, lines);
+    
+    // loop through hash and print values
+    fprintf(stderr, "HASH Size: %d\n", kh_size(hptr));
+    for (k = kh_begin(hptr); k != kh_end(hptr); ++k)
+    {
+        if (kh_exist(hptr, k))
+        {
+            int key = kh_key(hptr, k);
+            int val = kh_val(hptr, k);
+            printf("%d\t%d\n", key, val);
+        }
+    }
+    
+    kh_destroy(pass_hash, hptr);
     bam_destroy1(bam);
     bam_hdr_destroy(header);
     sam_close(fh_in);
     
-    printf("BAM Lines: %d / %d\n", poly, lines);
+    
     
     return 0;
 }
diff --git a/htsutils.h b/htsutils.h
index 9dd989d..7a7a3f3 100644
--- a/htsutils.h
+++ b/htsutils.h
@@ -12,12 +12,17 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <ctype.h>
+
 #include <htslib/sam.h>
+#include <htslib/khash.h>
+
 #include "config.h"
 
 #define POLY_HEAD 0
 #define POLY_TAIL 1
 
+KHASH_MAP_INIT_INT(pass_hash, int);
+
 int parseBAM(Settings *);
 void dumpBamSeq(bam1_t *);
 
diff --git a/main.c b/main.c
index b2c0225..956f523 100644
--- a/main.c
+++ b/main.c
@@ -31,7 +31,7 @@ int main(int argc, const char * argv[])
     
     double time_spent = (double)(end - begin) / CLOCKS_PER_SEC;
     
-    printf("Time: %.4f sec\n", time_spent);
+    fprintf(stderr, "Time: %.4f sec\n", time_spent);
     
     return 0;
 }