public void OutputStrandBias()
{
var unifiedJson =
JsonUtilities.GetJson(
"chrX 2699246 rs148553620 C A 250.95 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.250;AN=8;BaseQRankSum=1.719;DB;DP=106;Dels=0.00;FS=20.202;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=43.50;MQ0=52;MQRankSum=2.955;QD=4.73;ReadPosRankSum=1.024;SB=-1.368e+02;VQSLOD=-0.3503;culprit=MQ;PLF GT:AD:DP:GQ:PL:AA 0:10,6:16:9:0,9,118:P1,. 0|1:12,11:23:27:115,0,27:M1,M2 0|0:37,0:37:18:0,18,236:M1,P1 1|0:13,17:30:59:177,0,59:M2,P1", _renamer);
const string expectedStrandBias = "-136.8";
Assert.Equal(expectedStrandBias, unifiedJson.StrandBias);
var observedEntry = unifiedJson.ToString();
var expectedEntry = $"\"strandBias\":{expectedStrandBias}";
Assert.Contains(expectedEntry, observedEntry);
}
public void RefNoCallStrelkaFields()
{
var json =
JsonUtilities.GetJson(
"1 205664649 . C . . LowQscore SOMATIC;QSS=3;TQSS=1;NT=ref;QSS_NT=3;TQSS_NT=1;SGT=CC->CC;DP=116;MQ=57.63;MQ0=9;ALTPOS=89;ALTMAP=55;ReadPosRankSum=-1.14;SNVSB=6.63;PNOISE=0.00;PNOISE2=0.00;VQSR=0.15 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 11:4:0:0:0,0:7,8:0,0:0,0 92:28:0:0:5,17:58,62:1,1:0,0", _renamer);
Assert.NotNull(json);
const string expectedRecalibratedQuality = "0.15";
Assert.Equal(expectedRecalibratedQuality, json.RecalibratedQuality);
const string expectedJointSomaticNormalQuality = "3";
Assert.Equal(expectedJointSomaticNormalQuality, json.JointSomaticNormalQuality);
var expectedJointSomaticNormalQualityEntry = $"\"jointSomaticNormalQuality\":{expectedJointSomaticNormalQuality}";
var expectedRecalibratedQualityEntry = $"\"recalibratedQuality\":{expectedRecalibratedQuality}";
Assert.Contains(expectedRecalibratedQualityEntry, json.ToString());
Assert.Contains(expectedJointSomaticNormalQualityEntry, json.ToString());
}
public void OutputStrelkaSnvRelevantFields()
{
var json =
JsonUtilities.GetJson(
"2 167760371 rs267598980 G A . PASS SOMATIC;QSS=34;TQSS=1;NT=ref;QSS_NT=34;TQSS_NT=1;SGT=GG->AG;DP=45;MQ=60.00;MQ0=0;ALTPOS=43;ALTMAP=19;ReadPosRankSum=-1.64;SNVSB=0.00;PNOISE=0.00;PNOISE2=0.00;VQSR=5.54;cosmic=COSM36673;clinvar=other;CSQT=A|XIRP2|ENST00000409195|missense_variant DP:FDP:SDP:SUBDP:AU:CU:GU:TU 19:0:0:0:0,0:0,0:19,19:0,0 26:0:0:0:6,6:0,0:20,20:0,0", _renamer);
Assert.NotNull(json);
const string expectedRecalibratedQuality = "5.54";
Assert.Equal(expectedRecalibratedQuality, json.RecalibratedQuality);
const string expectedJointSomaticNormalQuality = "34";
Assert.Equal(expectedJointSomaticNormalQuality, json.JointSomaticNormalQuality);
var expectedJointSomaticNormalQualityEntry = $"\"jointSomaticNormalQuality\":{expectedJointSomaticNormalQuality}";
var expectedRecalibratedQualityEntry = $"\"recalibratedQuality\":{expectedRecalibratedQuality}";
Assert.Contains(expectedRecalibratedQualityEntry, json.ToString());
Assert.Contains(expectedJointSomaticNormalQualityEntry, json.ToString());
}