| Test |
Duration |
Result |
| testMappingFromBadString[0](null) |
0s |
passed |
| testMappingFromBadString[10](X,100,-,10M,60,.,-1.0) |
0.001s |
passed |
| testMappingFromBadString[11](Y,100,-,10H10M,60,30,30;Y,200,10M10H,60,20,.) |
0s |
passed |
| testMappingFromBadString[1](chr1) |
0.001s |
passed |
| testMappingFromBadString[2](chr1,100) |
0.001s |
passed |
| testMappingFromBadString[3](chr1,100,+) |
0s |
passed |
| testMappingFromBadString[4](chr1,100,+,10M) |
0.001s |
passed |
| testMappingFromBadString[5](chr1,-1,-,10M,60) |
0.003s |
passed |
| testMappingFromBadString[6](chr1,100,blah,10M,60) |
0.001s |
passed |
| testMappingFromBadString[7](chr1,100,,10M,60) |
0.001s |
passed |
| testMappingFromBadString[8](X,100,-,blah,60) |
0.001s |
passed |
| testMappingFromBadString[9](X,100,-,10M,-1) |
0s |
passed |
| testMappingFromFastqRead[0](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@40ab8a8, [Ljava.lang.String;@6ff37443, [I@65cc8228, [Z@53093491, [Lhtsjdk.samtools.Cigar;@21719a0, [I@76b224cd, [I@77ee25f1, [I@6dd93a21) |
0.013s |
passed |
| testMappingFromFastqRead[1](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@14151bc5, [Ljava.lang.String;@3013909b, [I@2a49fe, [Z@66596a88, [Lhtsjdk.samtools.Cigar;@5aae8eb5, [I@76954a33, [I@24a298a6, [I@982bb90) |
0s |
passed |
| testMappingFromFastqRead[2](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@7bef452c, [Ljava.lang.String;@4bb8855f, [I@57fae983, [Z@4a29f290, [Lhtsjdk.samtools.Cigar;@4bee18dc, [I@44f3fe83, [I@44c5a16f, [I@417d6615) |
0.001s |
passed |
| testMappingFromFastqRead[3](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@21325036, [Ljava.lang.String;@489543a6, [I@6272c96f, [Z@6de30571, [Lhtsjdk.samtools.Cigar;@5ee34b1b, [I@3c89bb12, [I@48c4245d, [I@3df978b9) |
0.002s |
passed |
| testMappingFromGATKRead[0](test chr1:100-199, [Ljava.lang.String;@392a04e7, [I@7f02251, [Z@dffa30b, [Lhtsjdk.samtools.Cigar;@4d8126f, [I@6d3c232f, [I@6b587673, [I@1bcf67e8) |
0.004s |
passed |
| testMappingFromGATKRead[1](test chr2:101-150, [Ljava.lang.String;@3a4ba480, [I@27b71f50, [Z@383790cf, [Lhtsjdk.samtools.Cigar;@74971ed9, [I@131fcb6f, [I@ccd1bc3, [I@878537d) |
0s |
passed |
| testMappingFromGATKRead[2](test 10:51-95, [Ljava.lang.String;@29fc1a2b, [I@4d0b0fd4, [Z@7a24eb3, [Lhtsjdk.samtools.Cigar;@6c37bd27, [I@25d3cfc8, [I@30331109, [I@2571066a) |
0.002s |
passed |
| testMappingFromGATKRead[3](test X:1231-1275, [Ljava.lang.String;@4a9486c0, [I@4c27d39d, [Z@40ee0a22, [Lhtsjdk.samtools.Cigar;@7bde1f3a, [I@15923407, [I@67dba613, [I@57540fd0) |
0.001s |
passed |
| testMappingFromString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@629f066f, [I@1542af63, [Z@ecfbe91, [Lhtsjdk.samtools.Cigar;@20ed3303, [I@3adbe50f, [I@3a627c80, [I@49aa766b) |
0s |
passed |
| testMappingFromString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@65004ff6, [I@4cafa9aa, [Z@562c877a, [Lhtsjdk.samtools.Cigar;@67001148, [I@989da1, [I@31cb96e1, [I@3eed0f5) |
0.001s |
passed |
| testMappingFromString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@2032e725, [I@4d23015c, [Z@383f1975, [Lhtsjdk.samtools.Cigar;@441cc260, [I@73a00e09, [I@26dcd8c0, [I@66e889df) |
0s |
passed |
| testMappingFromString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@3766c667, [I@773c0293, [Z@55b8dbda, [Lhtsjdk.samtools.Cigar;@3b569985, [I@3a022576, [I@2dbd803f, [I@3e48e859) |
0.001s |
passed |
| testMappingToStringRead[0](test chr1:100-199, [Ljava.lang.String;@6221295f, [I@1f8a56f, [Z@3ab5ccd5, [Lhtsjdk.samtools.Cigar;@234d2916, [I@48cd97f1, [I@cda805a, [I@189d3670) |
0.001s |
passed |
| testMappingToStringRead[1](test chr2:101-150, [Ljava.lang.String;@7604ce58, [I@2e044892, [Z@5f5bc594, [Lhtsjdk.samtools.Cigar;@18011a4a, [I@4827711c, [I@44ebf052, [I@459dea3e) |
0s |
passed |
| testMappingToStringRead[2](test 10:51-95, [Ljava.lang.String;@26825fbb, [I@3df05259, [Z@179683c3, [Lhtsjdk.samtools.Cigar;@31b280af, [I@5f96ea5, [I@3a2486d9, [I@198f92c5) |
0s |
passed |
| testMappingToStringRead[3](test X:1231-1275, [Ljava.lang.String;@72df13c3, [I@6cd3410f, [Z@9afefea, [Lhtsjdk.samtools.Cigar;@5b95c0ba, [I@515e9100, [I@2773791d, [I@51d502a6) |
0.001s |
passed |
| testMappingToString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@4ea0719e, [I@42ec40dc, [Z@4f3cd332, [Lhtsjdk.samtools.Cigar;@7352de9c, [I@3eb36de9, [I@1e792043, [I@37f5c5fd) |
0s |
passed |
| testMappingToString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@774fa82b, [I@20e3f5b9, [Z@39a00675, [Lhtsjdk.samtools.Cigar;@59aba9b3, [I@532f5c5d, [I@6c5e35bc, [I@557415ec) |
0s |
passed |
| testMappingToString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@78f2bb1b, [I@651c826c, [Z@10323056, [Lhtsjdk.samtools.Cigar;@77052a58, [I@1a427dc0, [I@1b4c8306, [I@1a7da0b9) |
0.001s |
passed |
| testMappingToString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@4dd1d767, [I@327a3968, [Z@45f53ff6, [Lhtsjdk.samtools.Cigar;@21970f32, [I@623e8e88, [I@1ec5ade, [I@6d0acf9a) |
0s |
passed |
| testNonPrimaryAlignmentReadWithSA |
0s |
passed |
| testNonPrimaryAlignmentReadWithoutSA |
0.001s |
passed |
| testNonPrimaryAlignmentWithSAWhereFirstElementHasHardClips |
0.002s |
passed |
| testPrimaryAlignmentWithHardClips |
0.001s |
passed |
| testSimpleRoundTrip |
0.002s |
passed |
| testUnmappedFromFastqRead |
0s |
passed |
| testUnmappedFromGATKRead |
0s |
passed |
| testUnmappedFromString |
0s |
passed |