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addressing issue #120 fix deletion post primer #124

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merged 15 commits into from
Jul 11, 2022
Merged

addressing issue #120 fix deletion post primer #124

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2141fa6
trim until first base that consumes the reference
cmaceves Mar 29, 2022
b0b8dc5
add in more specific condition for soft clips
cmaceves Apr 4, 2022
21bce80
adding in gene:id
cmaceves Apr 6, 2022
5784cfe
udpating test data to have gene name
cmaceves Apr 6, 2022
b814743
control for case where gene info not present
cmaceves Apr 6, 2022
4a2d275
update test to reflect additional of gene info
cmaceves Apr 6, 2022
5d85909
double check test data up to date
cmaceves Apr 6, 2022
7f5762d
updating attribute key to be gene
cmaceves Apr 6, 2022
02a3d9e
update test again
cmaceves Apr 6, 2022
ba09b79
removing test which is failing without proper cause
cmaceves Apr 6, 2022
2b455d7
adding back test, fixing issue with trailing tab
cmaceves Apr 11, 2022
d7ac90c
Merge branch 'issue_120' of github.com:andersen-lab/ivar into issue_120
cmaceves Apr 11, 2022
a1ab083
changing both tests and primer trim to allow leading deletions
cmaceves Apr 19, 2022
e0df8af
updating unpaired test and removing excess print lines
cmaceves Apr 19, 2022
c9522c3
fixing incorrectly commented out lines
cmaceves Apr 19, 2022
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12 changes: 6 additions & 6 deletions data/test.gff
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Original file line number Diff line number Diff line change
@@ -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
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;
7 changes: 6 additions & 1 deletion src/call_variants.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand All @@ -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;
Expand Down Expand Up @@ -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";
Expand All @@ -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";
Expand All @@ -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();
Expand Down
18 changes: 15 additions & 3 deletions src/ref_seq.cpp
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Expand Up @@ -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;
Expand Down
34 changes: 33 additions & 1 deletion src/trim_primer_quality.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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];
Expand All @@ -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);
Expand All @@ -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,
Expand Down
23 changes: 12 additions & 11 deletions tests/test_primer_trim.cpp
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;
}
}
Expand All @@ -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;
}
}
Expand Down
24 changes: 12 additions & 12 deletions tests/test_unpaired_trim.cpp
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Expand Up @@ -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};
Expand Down
14 changes: 8 additions & 6 deletions tests/test_variants.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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;
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