add test case for #24

mbhall88 · Jan 9, 2023 · 0428457 · 0428457
1 parent 02c3c16
commit 0428457
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diff --git a/src/predict.rs b/src/predict.rs
@@ -1999,6 +1999,56 @@ mod tests {
         assert_eq!(actual, expected)
     }
 
+    #[test]
+    fn test_vcf_to_json_partial_gene_deletion_start_lost() {
+        use std::io::Read;
+        use std::iter::Iterator;
+
+        let tmp = TempDir::new().unwrap();
+        let tmpoutdir = tmp.path();
+        let filt = Filterer {
+            min_frs: 0.51,
+            min_covg: 3,
+            min_strand_bias: 0.01,
+            max_indel: Some(20),
+            min_gt_conf: 5.0,
+            ..Default::default()
+        };
+        let pred = Predict {
+            pandora_exec: Some(PathBuf::from("src/ext/pandora")),
+            index: PathBuf::from("tests/cases/predict"),
+            outdir: PathBuf::from(tmpoutdir),
+            sample: Some("test".to_string()),
+            ignore_synonymous: true,
+            filterer: filt,
+            ..Default::default()
+        };
+        let vcf_path = Path::new("tests/cases/predict/SRR6824468.vcf");
+        let result = pred.vcf_to_json(vcf_path);
+        assert!(result.is_ok());
+
+        let json_path = result.unwrap();
+        let file = File::open(json_path).unwrap();
+        let mut reader = BufReader::new(file);
+        let mut buffer = String::new();
+        reader.read_to_string(&mut buffer).unwrap();
+        let actual = buffer
+            .chars()
+            .filter(|c| !c.is_whitespace())
+            .collect::<String>();
+
+        buffer.clear();
+        let file = File::open("tests/cases/predict/SRR6824468.json").unwrap();
+        let mut reader = BufReader::new(file);
+        reader.read_to_string(&mut buffer).unwrap();
+        let expected = buffer
+            .chars()
+            .filter(|c| !c.is_whitespace())
+            .collect::<String>();
+
+        assert_eq!(actual, expected)
+    }
+
     #[test]
     fn test_deduplicate_predictions() {
         let mutations = vec![

diff --git a/tests/cases/predict/SRR6824468.json b/tests/cases/predict/SRR6824468.json
@@ -0,0 +1,110 @@
+{
+  "genes": {
+    "absent": [
+      "ahpC",
+      "ddn",
+      "eis",
+      "embA",
+      "embB",
+      "ethA",
+      "gid",
+      "gyrA",
+      "gyrB",
+      "inhA",
+      "katG",
+      "pncA",
+      "rplC",
+      "rpoB",
+      "rpsL",
+      "rrs",
+      "tlyA"
+    ],
+    "present": [
+      "fabG1"
+    ]
+  },
+  "sample": "test",
+  "susceptibility": {
+    "Amikacin": {
+      "evidence": [],
+      "predict": "S"
+    },
+    "Capreomycin": {
+      "evidence": [],
+      "predict": "S"
+    },
+    "Ciprofloxacin": {
+      "evidence": [],
+      "predict": "S"
+    },
+    "Delamanid": {
+      "evidence": [],
+      "predict": "S"
+    },
+    "Ethambutol": {
+      "evidence": [],
+      "predict": "S"
+    },
+    "Ethionamide": {
+      "evidence": [
+        {
+          "gene": "fabG1",
+          "residue": "DNA",
+          "variant": "CTG607CTA",
+          "vcfid": "0745e4ee"
+        }
+      ],
+      "predict": "R"
+    },
+    "Isoniazid": {
+      "evidence": [
+        {
+          "gene": "fabG1",
+          "residue": "DNA",
+          "variant": "CTG607CTA",
+          "vcfid": "0745e4ee"
+        }
+      ],
+      "predict": "R"
+    },
+    "Kanamycin": {
+      "evidence": [],
+      "predict": "S"
+    },
+    "Levofloxacin": {
+      "evidence": [],
+      "predict": "S"
+    },
+    "Linezolid": {
+      "evidence": [],
+      "predict": "S"
+    },
+    "Moxifloxacin": {
+      "evidence": [],
+      "predict": "S"
+    },
+    "Ofloxacin": {
+      "evidence": [],
+      "predict": "S"
+    },
+    "Pyrazinamide": {
+      "evidence": [
+        {
+          "gene": "pncA",
+          "residue": "DNA",
+          "variant": "gene_absent",
+          "vcfid": ""
+        }
+      ],
+      "predict": "R"
+    },
+    "Rifampicin": {
+      "evidence": [],
+      "predict": "S"
+    },
+    "Streptomycin": {
+      "evidence": [],
+      "predict": "S"
+    }
+  }
+}
diff --git a/tests/cases/predict/SRR6824468.vcf b/tests/cases/predict/SRR6824468.vcf
@@ -0,0 +1,60 @@
+##fileformat=VCFv4.3
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate==05/01/23
+##ALT=<ID=SNP,Description="SNP">
+##ALT=<ID=PH_SNPs,Description="Phased SNPs">
+##ALT=<ID=INDEL,Description="Insertion-deletion">
+##ALT=<ID=COMPLEX,Description="Complex variant, collection of SNPs and indels">
+##INFO=<ID=VC,Number=1,Type=String,Description="Type (class) of variant">
+##ALT=<ID=SIMPLE,Description="Graph bubble is simple">
+##ALT=<ID=NESTED,Description="Variation site was a nested feature in the graph">
+##ALT=<ID=TOO_MANY_ALTS,Description="Variation site was a multinested feature with too many alts to include all in the VCF">
+##INFO=<ID=GRAPHTYPE,Number=1,Type=String,Description="Type of graph feature">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MEAN_FWD_COVG,Number=R,Type=Integer,Description="Mean forward coverage">
+##FORMAT=<ID=MEAN_REV_COVG,Number=R,Type=Integer,Description="Mean reverse coverage">
+##FORMAT=<ID=MED_FWD_COVG,Number=R,Type=Integer,Description="Med forward coverage">
+##FORMAT=<ID=MED_REV_COVG,Number=R,Type=Integer,Description="Med reverse coverage">
+##FORMAT=<ID=SUM_FWD_COVG,Number=R,Type=Integer,Description="Sum forward coverage">
+##FORMAT=<ID=SUM_REV_COVG,Number=R,Type=Integer,Description="Sum reverse coverage">
+##FORMAT=<ID=GAPS,Number=R,Type=Float,Description="Number of gap bases">
+##FORMAT=<ID=LIKELIHOOD,Number=R,Type=Float,Description="Likelihood">
+##FORMAT=<ID=GT_CONF,Number=1,Type=Float,Description="Genotype confidence">
+##contig=<ID=ahpC>
+##contig=<ID=ddn>
+##contig=<ID=eis>
+##contig=<ID=embA>
+##contig=<ID=embB>
+##contig=<ID=ethA>
+##contig=<ID=fabG1>
+##contig=<ID=gid>
+##contig=<ID=gyrA>
+##contig=<ID=gyrB>
+##contig=<ID=inhA>
+##contig=<ID=katG>
+##contig=<ID=pncA>
+##contig=<ID=rplC>
+##contig=<ID=rpoB>
+##contig=<ID=rpsL>
+##contig=<ID=rrs>
+##contig=<ID=tlyA>
+##FILTER=<ID=ld,Description="Kmer coverage on called allele less than 3">
+##FILTER=<ID=sb,Description="A strand on the called allele has less than 1.00% of the coverage for that allele">
+##FILTER=<ID=lgc,Description="Genotype confidence score less than 5.0">
+##FILTER=<ID=frs,Description="Fraction of read support on called allele is less than 0.51">
+##INFO=<ID=VARID,Number=.,Type=String,Description="The identifier for the panel variant(s) the record overlaps with">
+##INFO=<ID=PREDICT,Number=.,Type=String,Description="The drug resistance prediction(s) for the corresponding VARID(s), where 'R' = resistant, 'S' = susceptible, 'F' = failed, and 'U' = unknown">
+##INFO=<ID=OGT,Number=1,Type=String,Description="Original genotype after adjusting for minor allele depth proportions of 0.1">
+##INFO=<ID=PDP,Number=R,Type=Float,Description="Proportion of the total position depth found on this allele">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
+pncA	1	6c5cbac2	GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATTCCT	G,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATTCCT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCGGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATATCTT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCCGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATTCCT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACCTCTCCGGCACACCGGACTATTCCT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATATCTT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACGACTTCTCCGGCACACCGGACTATTCCT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACTACTTCTCCGGCACACCGGACTATTCCT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCCGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATTCCT,GTCATGTTCGCGATCGTCGCGGCGTCATGGACCCTATATCTGTGGCTGCCGCGTCGGTAGGCAAACTGCCCGGGCAGTCGCCCGAACGTGTGGTGGACGTATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATTCCT	.	ld;lgc	VC=INDEL;GRAPHTYPE=SIMPLE;VARID=pncA_S66L,pncA_D8Y,pncA_S65F,pncA_V7F,pncA_T-1TC,pncA_G55C,pncA_H51L,pncA_TGC40TAA,pncA_TTG10TAA,pncA_I31N,pncA_D49Y,pncA_TA-1T,pncA_Q10H,pncA_GGT46GGG,pncA_G17D,pncA_GAA109TGA,pncA_K48T,pncA_H57L,pncA_C185CGGACTATTC,pncA_H51D,pncA_Y34D,pncA_A38G,pncA_D12N,pncA_D63A,pncA_Q10E,pncA_CGGGTGACCA161A,pncA_T-1TTC,pncA_P62A,pncA_D63Y,pncA_Q10P,pncA_GA-5A,pncA_GCG112GCT,pncA_TAT190TAG,pncA_G16R,pncA_CTG55CTC,pncA_M1L,pncA_T-1TAC,pncA_Q10R,pncA_CCG184CCA,pncA_ACTATTCCTCGTCG188AG,pncA_Q10L,pncA_T47P,pncA_TGC40TAG,pncA_D49A,pncA_P62S,pncA_P62T,pncA_TTG10TGA,pncA_H57Y,pncA_H42N,pncA_D8V,pncA_AAG142TGA,pncA_V7L,pncA_M1T,pncA_TAT190TAA,pncA_G16V,pncA_D63H,pncA_A36S,pncA_D8H,pncA_F58S,pncA_V21G,pncA_I5N,pncA_T47S,pncA_H57P,pncA_H51N,pncA_A46P,pncA_GAC166GAT,pncA_GAC-5AC,pncA_TCG196TAG,pncA_GCG7GCA,pncA_CTG55TTA,pncA_D49H,pncA_V21A,pncA_GAG43TGA,pncA_D8G,pncA_G23V,pncA_G24V,pncA_D8E,pncA_GCG7GCC,pncA_S59F,pncA_AAG142TAA,pncA_GCA136GCT,pncA_D12G,pncA_P54L,pncA_L35P,pncA_A-11G,pncA_CTG55TTG,pncA_H51Q,pncA_A3E,pncA_I31S,pncA_CTCG195G,pncA_T-1TCT,pncA_TGGCTCGCTGGCGGTAACCGGTGGCGCC48C,pncA_L4F,pncA_C14Y,pncA_T22I,pncA_I6M,pncA_A30S,pncA_V7A,pncA_T-1TT,pncA_T-1TA,pncA_S32N,pncA_P54Q,pncA_TCG196TGA,pncA_I5S,pncA_TAT-1T,pncA_TGC40TGA,pncA_P54T,pncA_GGGTG162TG,pncA_V9G,pncA_GCA136GCG,pncA_AAG142TAG,pncA_A46V,pncA_N11T,pncA_S18T,pncA_L35R,pncA_CGGCACACCGGACTATTCCTCGTCG177ACCGGACTATTCCTCGTCG,pncA_T-1TGA,pncA_D12A,pncA_V21E,pncA_CTG55CTT,pncA_D12H,pncA_T-1TCG,pncA_CTG55CTA,pncA_T-1TAA,pncA_CAG28TGA,pncA_D12E,pncA_T-1TAG,pncA_H42Q,pncA_A46E,pncA_T47A,pncA_T-1TAT,pncA_H51Y,pncA_V7G,pncA_P62Q,pncA_D8N,pncA_F13Y,pncA_G17C,pncA_D63E,pncA_T-1TCC,pncA_I31T,pncA_I6F,pncA_H57Q,pncA_T37GCCAGCGAGCCACCCTCGCAGAAGTCGT,pncA_D8A,pncA_T-1TGT,pncA_Y64D,pncA_P62R,pncA_H57R,pncA_T-12C,pncA_L19P,pncA_GAA109TAG,pncA_I6L,pncA_CAG28TAA,pncA_P54R,pncA_S59P,pncA_TAT190TGA,pncA_F13L,pncA_D49G,pncA_F58L,pncA_I5F,pncA_TAC121TAG,pncA_A36D,pncA_TAC121TAA,pncA_CCG184CCC,pncA_L19Q,pncA_A28S,pncA_R29C,pncA_L27P,pncA_V44G,pncA_S32I,pncA_L27Q,pncA_D49V,pncA_D63G,pncA_GAG43TAA,pncA_GCG112GCA,pncA_A-11C,pncA_L4S,pncA_I31F,pncA_L4W,pncA_T-1TGG,pncA_GATCATCGT12CATCAT,pncA_K48E,pncA_I52T,pncA_GGT46GGA,pncA_GTGGCTCGCTGGCGGTAACCGGTGGCGC47G,pncA_A-11T,pncA_GCGTTGATCAT7AT,pncA_V44D,pncA_T-1TTT,pncA_GAG43TAG,pncA_C14R,pncA_S18L,pncA_GAA109TAA,pncA_F58I,pncA_T-7C,pncA_TCG52TAG,pncA_TCG52TGA,pncA_A30V,pncA_I6T,pncA_T-1TTA,pncA_TTC148TTT,pncA_TCG196TAA,pncA_GGT46GGC,pncA_I5M,pncA_T-1TGC,pncA_T-1TTG,pncA_TAC100TAT,pncA_H51P,pncA_A26V,pncA_A30P,pncA_TCG52TAA,pncA_D49N,pncA_T-1TG,pncA_GCG7GCT,pncA_D49E,pncA_TTG10TAG,pncA_D12Y,pncA_S66P,pncA_H43P,pncA_CCG184CCT,pncA_H57D,pncA_TAC121TAT,pncA_V7D,pncA_P62L,pncA_F13I,pncA_TAC121TGA,pncA_GCA136GCC,pncA_H51R,pncA_G24D,pncA_E15G,pncA_A38S,pncA_CAG28TAG,pncA_H43Q,pncA_T-1TCA,pncA_Y41H,pncA_L4V,pncA_H57N;PREDICT=F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F,F	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	.:0,0,0,0,0,0,0,0,0,0,0:0,0,0,0,0,0,0,0,0,0,0:0,0,0,0,0,0,0,0,0,0,0:0,0,0,0,0,0,0,0,0,0,0:0,0,0,0,0,0,0,0,0,0,0:0,0,0,0,0,0,0,0,0,0,0:1,1,1,1,1,1,1,1,1,1,1:-496,-496,-496,-496,-496,-496,-496,-496,-496,-496,-496:0
+pncA	302	af9f6ba6	TGGCC	GGGCC,TGGCCACCGCATT	.	PASS	VC=PH_SNPs;GRAPHTYPE=NESTED;PDP=0.643478,0.217391,0.13913;VARID=pncA_W68R,pncA_TGG202TAA,pncA_P69Q,pncA_P69L,pncA_TGG202TGA,pncA_W68C,pncA_W68G,pncA_TGG202TAG,pncA_W68L;PREDICT=.,.,.,.,.,.,.,.,.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:70,24,15:78,26,17:92,0,0:103,0,0:282,98,90:314,107,102:0.25,0.75,0.833333:-466.642,-1135.74,-1271.62:669.095
+pncA	326	25d5a078	A	C	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=0.995536,0.00446429;VARID=pncA_T76P,pncA_T76I,pncA_T76S,pncA_AGCGGTACTCCCG220G;PREDICT=.,.,.,.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:107,0:116,1:110,0:118,1:321,0:350,4:0,1:-9.53276,-1517.44:1507.91
+pncA	381	5ca6778b	T	C	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=pncA_TTC280TTT,pncA_F94C,pncA_F94S,pncA_F94L;PREDICT=.,.,.,.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:130,0:145,0:130,0:145,0:260,0:291,0:0,1:-5.14677,-1762.42:1757.28
+pncA	389	28333f21	G	C	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=pncA_G97R,pncA_G97V,pncA_G97S,pncA_G97D,pncA_G97C;PREDICT=.,.,.,.,.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:125,0:143,0:123,0:143,0:376,0:429,0:0,1:-4.50035,-1730.19:1725.69
+pncA	441	8eca3735	C	T	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=pncA_T114P,pncA_ACG340ACC,pncA_ACG340ACA,pncA_ACG340ACT,pncA_T114M,pncA_T114A;PREDICT=.,.,.,.,.,.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:133,0:141,0:133,0:141,0:133,0:141,0:0,1:-5.04343,-1757.82:1752.77
+pncA	489	1358054f	T	TG	.	PASS	VC=INDEL;GRAPHTYPE=SIMPLE;PDP=0.805921,0.194079;VARID=pncA_AGGTCGATGT380T,pncA_CGATGAGGTCGATGTG375G,pncA_ATGTGGTCGG386G,pncA_V130E,pncA_V130G,pncA_TGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTAT359TGCGGCAACGCGGCGTCGATGAGGTCGGTAT,pncA_TGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTAT359TGCGGCAACGCGGCGTGGTCGGTAT;PREDICT=.,.,.,.,.,.,.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:121,29:124,30:121,0:124,0:242,117:248,120:0,0.75:-275.393,-1421.51:1146.12
+pncA	495	6c285c3e	G	GTATTGCCACCGATCAT	.	PASS	VC=INDEL;GRAPHTYPE=SIMPLE;PDP=0.66756,0.33244;VARID=pncA_ATGTGGTCGG386G,pncA_TGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTAT359TGCGGCAACGCGGCGTGGTCGGTAT,pncA_G132R,pncA_G132V,pncA_G132S,pncA_GTATTGCCACCGA395A,pncA_TGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTAT359TGCGGCAACGCGGCGTCGATGAGGTCGGTAT,pncA_G132D,pncA_G132A,pncA_G132C;PREDICT=.,.,.,.,.,.,.,.,.,.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:122,61:127,63:124,59:128,60:366,367:382,382:0,0.5:-574.721,-1312.07:737.346
+pncA	524	0c0971be	A	G	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=0.79402,0.20598;VARID=pncA_ACG424ACT,pncA_ACG424ACA,pncA_T142R,pncA_T142M,pncA_T142K,pncA_ACG424ACC,pncA_T142A;PREDICT=.,.,.,.,.,.,.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:116,29:123,33:115,0:122,0:466,118:493,133:0,0.75:-289.343,-1389.67:1100.33
+pncA	564	b8a4a3bb	T	G	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=pncA_V155M,pncA_V155E,pncA_V155G;PREDICT=.,.,.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:127,0:123,0:130,0:127,0:381,0:370,0:0,1:-3.68805,-1647.29:1643.6
+pncA	760	2f7460f5	GG	AG	.	PASS	VC=PH_SNPs;GRAPHTYPE=SIMPLE;PDP=1,0	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:80,0:86,0:80,0:86,0:80,0:86,0:0,1:-18.8362,-1260.46:1241.62