diff --git a/data/test.gff b/data/test.gff
index ee33aabc..9a5f0d9f 100644
--- a/data/test.gff
+++ b/data/test.gff
@@ -1,7 +1,7 @@
 ## GFF3 file format
-test	Genbank	primer_binding_site	2	290	.	+	.	ID=id-test1;Note=daft punk
-test	Genbank	long_terminal_repeat	1	55	.	+	.	ID=id-test2;Note=random access memories
-test	Genbank	CDS	2	292	.	+	.	ID=id-test3;Note=eluvite
-test	Genbank	CDS	1	55	.	+	.	ID=id-test4;Note=ategnato
-test	Genbank	CDS	2	292	.	+	.	ID=id-testedit1;Note=PinkFloyd;EditPosition=100;EditSequence=A
-test	Genbank	CDS	2	292	.	+	.	ID=id-testedit2;Note=AnotherBrickInTheWall;EditPosition=102;EditSequence=AA
\ No newline at end of file
+test	Genbank	primer_binding_site	2	290	.	+	.	ID=id-test1;Note=daft punk;Parent=geneFragmentsOfTime;
+test	Genbank	long_terminal_repeat	1	55	.	+	.	ID=id-test2;Note=random access memories;Parent=geneGetLucky;
+test	Genbank	CDS	2	292	.	+	.	ID=id-test3;Note=eluvite;gene=geneKatyPerry;
+test	Genbank	CDS	1	55	.	+	.	ID=id-test4;Note=ategnato;gene=geneKatyPerry;
+test	Genbank	CDS	2	292	.	+	.	ID=id-testedit1;Note=PinkFloyd;EditPosition=100;EditSequence=A;
+test	Genbank	CDS	2	292	.	+	.	ID=id-testedit2;Note=AnotherBrickInTheWall;EditPosition=102;EditSequence=AA;gene=geneTaylorSwift;
diff --git a/src/call_variants.cpp b/src/call_variants.cpp
index 46d10555..4f7ab4d6 100644
--- a/src/call_variants.cpp
+++ b/src/call_variants.cpp
@@ -28,6 +28,7 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min
   ref_antd refantd(ref_path, gff_path);
   std::ostringstream out_str;
   std::ofstream fout((out_file+".tsv").c_str());
+  //make columns in the file
   fout << "REGION"
     "\tPOS"
     "\tREF"
@@ -47,6 +48,7 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min
     "\tREF_AA"
     "\tALT_CODON"
     "\tALT_AA"
+    "\tPOS_AA"
        << std::endl;
   int ctr = 0;
   int64_t pos = 0;
@@ -118,6 +120,7 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min
       freq_depth = get_frequency_depth(*it, pdepth, mdepth);
       if(freq_depth[0] < min_threshold)
 	continue;
+      //this only adds the first bit of the information to the tsv
       out_str << region << "\t";
       out_str << pos << "\t";
       out_str << ref << "\t";
@@ -135,6 +138,7 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min
 	Exp | Error | Err free |
 	Obs | AD    | RD       |
        */
+      //adding pvalue related info
       err = pow(10, ( -1 * (it->mean_qual)/10));
       kt_fisher_exact((err * mdepth), (1-err) * mdepth, it->depth, ref_it->depth, &pval_left, &pval_right, &pval_twotailed);
       out_str << pval_left << "\t";
@@ -143,10 +147,11 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min
       } else {
 	out_str << "FALSE" << "\t";
       }
+      //adding codon related info, can add gene info here too
       if(it->nuc[0] != '+' && it->nuc[0] != '-'){
 	refantd.codon_aa_stream(region, out_str, fout, pos, it->nuc[0]);
       } else {
-	fout << out_str.str() << "NA\tNA\tNA\tNA\tNA" << std::endl;
+	fout << out_str.str() << "NA\tNA\tNA\tNA\tNA\tNA" << std::endl;
       }
       out_str.str("");
       out_str.clear();
diff --git a/src/ref_seq.cpp b/src/ref_seq.cpp
index 1b3d22a4..d52ef05c 100644
--- a/src/ref_seq.cpp
+++ b/src/ref_seq.cpp
@@ -109,23 +109,35 @@ ref_antd::~ref_antd()
   if (this->fai) fai_destroy(this->fai);
 }
 
+//used to add codon info to variants output
 int ref_antd::codon_aa_stream(std::string region, std::ostringstream &line_stream, std::ofstream &fout, int64_t pos, char alt){
   std::vector<gff3_feature> features = gff.query_features(pos, "CDS");
   if(features.size() == 0){	// No matching CDS
-    fout << line_stream.str() << "NA\tNA\tNA\tNA\tNA" << std::endl;
+    fout << line_stream.str() << "NA\tNA\tNA\tNA\tNA\tNA" << std::endl;
     return 0;
   }
   std::vector<gff3_feature>::iterator it;
   char *ref_codon, *alt_codon;
   for(it = features.begin(); it != features.end(); it++){
     fout << line_stream.str();
-    fout << it->get_attribute("ID") << "\t";
+    //add in gene level info, control for case it's not present
+    std::string gene = it->get_attribute("gene");
+    if (gene.empty()){
+        fout << it->get_attribute("ID") << "\t";
+    } else {
+        fout << gene + ":" + it->get_attribute("ID") << "\t";
+    }
     ref_codon = this->get_codon(pos, region, *it);
     fout << ref_codon[0] << ref_codon[1] << ref_codon[2] << "\t";
     fout << codon2aa(ref_codon[0], ref_codon[1], ref_codon[2]) << "\t";
     alt_codon = this->get_codon(pos, region, *it, alt);
     fout << alt_codon[0] << alt_codon[1] << alt_codon[2] << "\t";
-    fout << codon2aa(alt_codon[0], alt_codon[1], alt_codon[2]);
+    fout << codon2aa(alt_codon[0], alt_codon[1], alt_codon[2]) << "\t";
+    
+    //adding amino acid position
+    int64_t start = it->get_start();
+    int64_t aa_pos = ((pos - start) / 3)+1;
+    fout << aa_pos;
     fout << std::endl;
 
     delete[] ref_codon;
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};
diff --git a/tests/test_variants.cpp b/tests/test_variants.cpp
index 4d21f01c..d7d42dc4 100755
--- a/tests/test_variants.cpp
+++ b/tests/test_variants.cpp
@@ -12,11 +12,13 @@ int call_var_check_outfile(std::string prefix, uint8_t min_qual, uint8_t min_dep
   std::string l;
   getline(outFile, l);		// Ignore first line
   int comp = 0, ctr = 0;
+  
   while(ctr < len){
     getline(outFile, l);
     std::cout << l << std::endl;
     std::cout << out[ctr] << " -> CORRECT" << std::endl;
     comp += l.compare(out[ctr]);
+    std::cout << l.compare(out[ctr]) << "\n"; 
     ctr++;
   }
   return comp;
@@ -25,20 +27,20 @@ int call_var_check_outfile(std::string prefix, uint8_t min_qual, uint8_t min_dep
 int main() {
   int num_success = 0;
   // Quality threshold 20. Frequency threshold: 0.03. Total_DP = 3. Indel passes filters with total_depth 4. Has two lines.
-  std::string t_20_02_1[4] = {"test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-test3\tAAG\tK\tATG\tM", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit2\tAGA\tR\tTGA\t*", "test\t210\tA\t+GT\t1\t1\t41\t1\t0\t20\t0.25\t4\t0.4\tFALSE\tNA\tNA\tNA\tNA\tNA"};
+  std::string t_20_02_1[4] = {"test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneKatyPerry:id-test3\tAAG\tK\tATG\tM\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneTaylorSwift:id-testedit2\tAGA\tR\tTGA\t*\t70", "test\t210\tA\t+GT\t1\t1\t41\t1\t0\t20\t0.25\t4\t0.4\tFALSE\tNA\tNA\tNA\tNA\tNA\tNA"};
   // Quality threshold 3-. Frequency threshold: 0.03. Total_DP = 3. Freq = 0.666667 No Indel
-  std::string t_20_03[3] = {"test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-test3\tAAG\tK\tATG\tM", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit2\tAGA\tR\tTGA\t*"};
+  std::string t_20_03[3] = {"test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneKatyPerry:id-test3\tAAG\tK\tATG\tM\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneTaylorSwift:id-testedit2\tAGA\tR\tTGA\t*\t70"};
   // Quality threshold 25. Frequency threshold: 0.03. Total_DP = 2. Freq = 0.5 No Indel.
-  std::string t_25_03[3] = {"test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tid-test3\tAAG\tK\tATG\tM", "test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD", "test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tid-testedit2\tAGA\tR\tTGA\t*"};
+  std::string t_25_03[3] = {"test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tgeneKatyPerry:id-test3\tAAG\tK\tATG\tM\t70", "test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD\t70", "test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tgeneTaylorSwift:id-testedit2\tAGA\tR\tTGA\t*\t70"};
   // Minimum depth threshold. Should be empty
   std::string t_25_03_20[] = {};
   num_success = call_var_check_outfile("../data/test.indel", 20, 0, 0.02, t_20_02_1, 4);
   std::cout << num_success << std::endl;
-  num_success += call_var_check_outfile("../data/test.indel", 20, 0, 0.03, t_20_03, 3);
+  num_success += call_var_check_outfile("../data/test.indel2", 20, 0, 0.03, t_20_03, 3);
   std::cout << num_success << std::endl;
-  num_success += call_var_check_outfile("../data/test.indel", 25, 0, 0.03, t_25_03, 3);
+  num_success += call_var_check_outfile("../data/test.indel3", 25, 0, 0.03, t_25_03, 3);
   std::cout << num_success << std::endl;
-  num_success += call_var_check_outfile("../data/test.indel", 25, 20, 0.03, t_25_03_20, 0);
+  num_success += call_var_check_outfile("../data/test.indel4", 25, 20, 0.03, t_25_03_20, 0);
   std::cout << num_success << std::endl;
   if(num_success == 0)
     return 0;