diff --git a/src/trim_primer_quality.cpp b/src/trim_primer_quality.cpp
index 899c5d67..37d53e6d 100755
--- a/src/trim_primer_quality.cpp
+++ b/src/trim_primer_quality.cpp
@@ -187,6 +187,7 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r
   int32_t n, start_pos = 0, ref_add = 0;
   bool pos_start = false;
   del_len = max_del_len;
+   
   while(i < r->core.n_cigar){
     if (del_len == 0 && pos_start){ // No more bases on query to soft clip
       ncigar[j] = cigar[i];
@@ -200,7 +201,18 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r
       pos_start = true;
       continue;
     }
+    
+    //add the condition that we have a leading deletion
+    if(cig == 2 && del_len == 0){
+        ncigar[j] = cigar[i];
+        pos_start = true;
+        i++;
+        j++;
+        continue;    
+    }
+
     ref_add = n;
+    
     if ((bam_cigar_type(cig) & 1)){ // Consumes Query
       if(del_len >= n ){
 	ncigar[j] = bam_cigar_gen(n, BAM_CSOFT_CLIP);
@@ -221,18 +233,38 @@ cigar_ primer_trim(bam1_t *r, bool &isize_flag, int32_t new_pos, bool unpaired_r
 	ncigar[j] = bam_cigar_gen(n, cig);
 	j++;
       }
+     //add the condition that we have a leading deletion
+    if(cig == 2 && del_len == 0){
+        ncigar[j] = cigar[i];
+        pos_start = true;
+        i++;
+        j++;
+     }
+   
       if(del_len ==0 && (bam_cigar_type(ncigar[j-1]) & 1) && (bam_cigar_type(ncigar[j-1]) & 2)){ // After soft clipping of query complete, keep incrementing start_pos until first base that consumes both query and ref
-      	pos_start = true;
+        pos_start = true;
       }
     }
+
+    //deletions consume the reference but not the query,
+    //insertions consume the query but not the reference
     if((bam_cigar_type(cig) & 2)) { // Consumes reference but not query
+      //std::cout << "ref add " << ref_add << " " << start_pos << " " << cig << "\n";
       start_pos += ref_add;
     }
     i++;
   }
+
+  /*uint32_t p=0;
+  while(p < j){
+    std::cout << bam_cigar_op(ncigar[p]) << " " << bam_cigar_oplen(ncigar[p]) <<"\n";
+    p++;
+  }*/
+  //std::cout << "start pos " << start_pos << "\n";
   if(reverse){
     reverse_cigar(ncigar, j);
   }
+  
   return {
     ncigar,
     true,
diff --git a/tests/test_primer_trim.cpp b/tests/test_primer_trim.cpp
index 4bede7cf..21179603 100755
--- a/tests/test_primer_trim.cpp
+++ b/tests/test_primer_trim.cpp
@@ -37,29 +37,29 @@ int main(){
   int primer_indices[] = {0, 0, 7, 7, 6};
   uint8_t cigar_flag[5][11] = {
     {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CMATCH},
-    {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CMATCH},
-    {BAM_CMATCH, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP},
+    {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CDEL, BAM_CPAD, BAM_CDEL, BAM_CMATCH},
+    {BAM_CMATCH, BAM_CPAD, BAM_CDEL, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP},
     {BAM_CMATCH, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP},
     {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH}
   };
   uint32_t cigar_len[5][11] = {
     {6, 5, 1, 139},
-    {24, 3, 1, 1, 4, 114},
-    {121, 4, 1, 1, 11, 6},
+    {24, 3, 1, 1, 4, 1, 1, 1,114}, //change this
+    {121, 1, 4, 4, 1, 1, 11, 6}, //change this
     {103, 1, 10,1,13, 24},
     {23, 18, 3, 57, 1, 10, 1, 39}
   };
   uint32_t read_start_pos[5] = {
-    30, 31, 231, 249, 274
+    30, 29, 231, 249, 274 //also change
   };
   uint8_t condense_cigar_flag[5][8] = {
     {BAM_CSOFT_CLIP, BAM_CMATCH},
-    {BAM_CSOFT_CLIP, BAM_CMATCH},
-    {BAM_CMATCH, BAM_CSOFT_CLIP},
+    {BAM_CSOFT_CLIP, BAM_CDEL, BAM_CPAD, BAM_CDEL, BAM_CMATCH}, //change this
+    {BAM_CMATCH, BAM_CPAD, BAM_CDEL, BAM_CSOFT_CLIP}, //change this
     {BAM_CMATCH, BAM_CSOFT_CLIP},
     {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH}
   };
-  uint32_t condense_cigar_len[5][8] = {{12, 139}, {33, 114}, {121, 23}, {103, 49}, {23, 18,3, 57, 1, 10, 1, 39}};
+  uint32_t condense_cigar_len[5][8] = {{12, 139}, {33, 1,1,1,114}, {121, 1, 4, 23}, {103, 49}, {23, 18,3, 57, 1, 10, 1, 39}};
   unsigned int overlapping_primer_sizes[] = {0, 2, 2, 0, 0, 0, 0, 2, 2, 1};
   int ctr = 0;
   std::vector<primer> overlapping_primers;
@@ -100,11 +100,12 @@ int main(){
       cigar = bam_get_cigar(aln);
       for (uint i = 0; i < t.nlength; ++i){
 	if(((cigar[i]) & BAM_CIGAR_MASK) != cigar_flag[primer_ctr][i]){
+      std::cout << bam_cigar_op(cigar[i]) << " " << bam_cigar_oplen(cigar[i]) << " i " << i << "\n";	
 	  success = -1;
 	  std::cout << "Cigar flag didn't match for " << cand_primer.get_indice()  <<  " ! Expected " <<  (uint) cigar_flag[primer_ctr][i]  << " " << "Got " << ((cigar[i]) & BAM_CIGAR_MASK) << std::endl;
 	}
 	if((((cigar[i]) >> BAM_CIGAR_SHIFT)) != cigar_len[primer_ctr][i]){
-	  success = -1;
+      success = -1;
 	  std::cout << "Cigar length didn't match for " << bam_get_qname(aln)  <<  " ! Expected " << (uint) cigar_len[primer_ctr][i]  << " " << "Got " << ((cigar[i]) >> BAM_CIGAR_SHIFT) << std::endl;
 	}
       }
@@ -117,10 +118,10 @@ int main(){
       for (uint i = 0; i < t.nlength; ++i){
 	if(((cigar[i]) & BAM_CIGAR_MASK) != condense_cigar_flag[primer_ctr][i]){
 	  success = -1;
-	  std::cout << "Cigar flag didn't match! Expected " << condense_cigar_flag[primer_ctr][i]  << " " << "Got " << ((cigar[i]) & BAM_CIGAR_MASK) << std::endl;
+      std::cout << "Cigar flag didn't match! Expected " << condense_cigar_flag[primer_ctr][i]  << " " << "Got " << ((cigar[i]) & BAM_CIGAR_MASK) << std::endl;
 	}
 	if((((cigar[i]) >> BAM_CIGAR_SHIFT)) != condense_cigar_len[primer_ctr][i]){
-	  success = -1;
+      success = -1;
 	  std::cout << "Cigar length didn't match after condense! Expected " << condense_cigar_len[primer_ctr][i]  << " " << "Got " << ((cigar[i]) >> BAM_CIGAR_SHIFT) << std::endl;
 	}
       }
diff --git a/tests/test_unpaired_trim.cpp b/tests/test_unpaired_trim.cpp
index c4451167..a07b39df 100755
--- a/tests/test_unpaired_trim.cpp
+++ b/tests/test_unpaired_trim.cpp
@@ -41,35 +41,35 @@ int main(){
   int primer_ctr = 0;
   int forward_primer_indices[] = {1, 1, 5, 5, 6};
   int rev_primer_indices[] = {3, -1, -1, -1, 4};
-  uint8_t cigar_flag[5][16] = {
-    {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CINS, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP}, // 3S15M5D2M1D14M1I56M1P6M3P93M2D4M2I8M
+  uint8_t cigar_flag[5][17] = {
+    {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CDEL, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CINS, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP}, // 3S15M5D2M1D14M1I56M1P6M3P93M2D4M2I8M
     {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH},
     {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CSOFT_CLIP},
-    {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH},
+    {BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CSOFT_CLIP, BAM_CDEL, BAM_CPAD, BAM_CDEL, BAM_CMATCH, BAM_CPAD, BAM_CMATCH},
     {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CSOFT_CLIP}
   };
-  uint32_t cigar_len[5][16] = {
-    {3, 15, 2, 1, 14, 1, 56, 1, 6, 3, 93, 2, 1, 3, 2, 8},
+  uint32_t cigar_len[5][17] = {
+    {3, 15, 5, 2, 1, 14, 1, 56, 1, 6, 3, 93, 2, 1, 3, 2, 8}, //change here
     {1, 19, 1, 56, 1, 6, 3, 99, 2, 65},
     {8, 13, 1, 6, 3, 99, 2, 62, 3},
-    {9, 10, 3, 97, 2, 26},
+    {9, 10, 3, 3, 3, 2, 97, 2, 26}, //change here
     {18, 71, 2, 89, 18}
   };
   uint32_t read_start_pos[5] = {
-    94, 92, 173, 175, 201
+    89, 92, 173, 170, 201
   };
   uint8_t condense_cigar_flag[5][14] = {
-    {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CINS, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CSOFT_CLIP},
+    {BAM_CSOFT_CLIP, BAM_CDEL, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CINS, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CDEL, BAM_CMATCH, BAM_CSOFT_CLIP},
     {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CPAD, BAM_CMATCH},
     {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CSOFT_CLIP},
-    {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH},
+    {BAM_CSOFT_CLIP, BAM_CDEL, BAM_CPAD, BAM_CDEL, BAM_CMATCH, BAM_CPAD, BAM_CMATCH}, //change here
     {BAM_CSOFT_CLIP, BAM_CMATCH, BAM_CPAD, BAM_CMATCH, BAM_CSOFT_CLIP}
   };
-  uint32_t condense_cigar_len[5][13] = {
-    {18, 2, 1, 14,1, 56, 1, 6, 3, 93, 2, 1, 13},
+  uint32_t condense_cigar_len[5][14] = {
+    {18, 5, 2, 1, 14,1, 56, 1, 6, 3, 93, 2, 1, 13}, //change here
     {1, 19, 1, 56, 1, 6, 3, 99, 2, 65},
     {31, 99, 2, 62, 3},
-    {22, 97, 2, 26},
+    {22, 3, 3, 2, 97, 2, 26}, //change here
     {18, 71, 2, 89, 18}
   };
   unsigned int fwd_overlapping_primer_sizes[] = {2, 1, 1, 1, 1};