| Test |
Duration |
Result |
| testMappingFromBadString[0](null) |
0.001s |
passed |
| testMappingFromBadString[10](X,100,-,10M,60,.,-1.0) |
0s |
passed |
| testMappingFromBadString[11](Y,100,-,10H10M,60,30,30;Y,200,10M10H,60,20,.) |
0.002s |
passed |
| testMappingFromBadString[1](chr1) |
0.002s |
passed |
| testMappingFromBadString[2](chr1,100) |
0.001s |
passed |
| testMappingFromBadString[3](chr1,100,+) |
0s |
passed |
| testMappingFromBadString[4](chr1,100,+,10M) |
0s |
passed |
| testMappingFromBadString[5](chr1,-1,-,10M,60) |
0.006s |
passed |
| testMappingFromBadString[6](chr1,100,blah,10M,60) |
0s |
passed |
| testMappingFromBadString[7](chr1,100,,10M,60) |
0s |
passed |
| testMappingFromBadString[8](X,100,-,blah,60) |
0s |
passed |
| testMappingFromBadString[9](X,100,-,10M,-1) |
0.001s |
passed |
| testMappingFromFastqRead[0](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@1b7a4930, [Ljava.lang.String;@591a4d25, [I@4bfe83d, [Z@5906ebfb, [Lhtsjdk.samtools.Cigar;@10fc1a22, [I@1b841e7d, [I@6081f330, [I@eb695e8) |
0.003s |
passed |
| testMappingFromFastqRead[1](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@5e1a7d3, [Ljava.lang.String;@1eda309d, [I@248d2cec, [Z@5d77be8e, [Lhtsjdk.samtools.Cigar;@55a055cc, [I@1ab1d93d, [I@57167ccb, [I@37753b69) |
0.001s |
passed |
| testMappingFromFastqRead[2](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@74c04377, [Ljava.lang.String;@10d49900, [I@e645600, [Z@e7b3e54, [Lhtsjdk.samtools.Cigar;@78d61f17, [I@4cfe9594, [I@60861e5d, [I@37d81587) |
0s |
passed |
| testMappingFromFastqRead[3](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@47d4e28a, [Ljava.lang.String;@177068db, [I@60f3239f, [Z@6b103db7, [Lhtsjdk.samtools.Cigar;@b3042ed, [I@1f12d5e0, [I@6604f246, [I@c1386b4) |
0s |
passed |
| testMappingFromGATKRead[0](test chr1:100-199, [Ljava.lang.String;@552ffa44, [I@6e66b498, [Z@54d35ed5, [Lhtsjdk.samtools.Cigar;@6f7c9755, [I@45abbd24, [I@1e32037d, [I@5059d398) |
0.001s |
passed |
| testMappingFromGATKRead[1](test chr2:101-150, [Ljava.lang.String;@29db008c, [I@1d008e61, [Z@191b44ca, [Lhtsjdk.samtools.Cigar;@5de243bb, [I@2c4cf7eb, [I@35260785, [I@76d828ff) |
0s |
passed |
| testMappingFromGATKRead[2](test 10:51-95, [Ljava.lang.String;@72d0196d, [I@77cf329d, [Z@4067634b, [Lhtsjdk.samtools.Cigar;@3b64f131, [I@490d9c41, [I@47d81427, [I@3c5e4aac) |
0s |
passed |
| testMappingFromGATKRead[3](test X:1231-1275, [Ljava.lang.String;@4cded2cd, [I@12e40e98, [Z@3a9c92b5, [Lhtsjdk.samtools.Cigar;@67c2b55d, [I@5db04bd2, [I@6f921e32, [I@31c5304f) |
0s |
passed |
| testMappingFromString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@1cee3e05, [I@63f2d024, [Z@7b2dd35d, [Lhtsjdk.samtools.Cigar;@405223e4, [I@2d2133fd, [I@58a7a58d, [I@4d8522ff) |
0.001s |
passed |
| testMappingFromString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@3883031d, [I@5d6d424d, [Z@391b01c5, [Lhtsjdk.samtools.Cigar;@6e78177b, [I@4ec37a42, [I@798b36fd, [I@18ff1520) |
0s |
passed |
| testMappingFromString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@63d66761, [I@434a8938, [Z@237cd264, [Lhtsjdk.samtools.Cigar;@51cd2d2, [I@5521407f, [I@42b500aa, [I@71f056a) |
0.001s |
passed |
| testMappingFromString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@3b8b5b40, [I@5151accb, [Z@2e1ad7de, [Lhtsjdk.samtools.Cigar;@7c56c911, [I@1de6dc80, [I@418d1c03, [I@395197cb) |
0s |
passed |
| testMappingToStringRead[0](test chr1:100-199, [Ljava.lang.String;@3be23894, [I@665e9a87, [Z@424ddcb0, [Lhtsjdk.samtools.Cigar;@4ac2d69c, [I@60ce71c8, [I@725645f4, [I@5ed2af52) |
0s |
passed |
| testMappingToStringRead[1](test chr2:101-150, [Ljava.lang.String;@11ab8594, [I@51920bb0, [Z@1a7186ef, [Lhtsjdk.samtools.Cigar;@5f6da867, [I@1227013b, [I@53a95744, [I@45f9f520) |
0s |
passed |
| testMappingToStringRead[2](test 10:51-95, [Ljava.lang.String;@5d61ba76, [I@44ebd5e9, [Z@4eb168a1, [Lhtsjdk.samtools.Cigar;@13121c0c, [I@43f0a612, [I@592e7718, [I@1c9ff8fc) |
0s |
passed |
| testMappingToStringRead[3](test X:1231-1275, [Ljava.lang.String;@59e890c6, [I@73d4aa54, [Z@10efe4ca, [Lhtsjdk.samtools.Cigar;@7c45bd55, [I@61b67cbb, [I@37e6ecd3, [I@58409751) |
0s |
passed |
| testMappingToString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@3fd006e8, [I@1ca73158, [Z@4d7f0350, [Lhtsjdk.samtools.Cigar;@54dfdad7, [I@6b0771e2, [I@4e8fa02b, [I@7bdf5f29) |
0s |
passed |
| testMappingToString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@1a4c84b, [I@3299beac, [Z@33be99c1, [Lhtsjdk.samtools.Cigar;@32dbf42, [I@24ecc9fc, [I@5bff7f13, [I@1cc8953c) |
0s |
passed |
| testMappingToString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@30906ad3, [I@10378c35, [Z@480e8a7a, [Lhtsjdk.samtools.Cigar;@35f03e9d, [I@6850c02, [I@2aff6ec3, [I@161e7cbc) |
0s |
passed |
| testMappingToString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@ce5417f, [I@5d3dbf56, [Z@3823d3d1, [Lhtsjdk.samtools.Cigar;@6f3b07ed, [I@49f35dcc, [I@79849cab, [I@5f9f6511) |
0s |
passed |
| testNonPrimaryAlignmentReadWithSA |
0s |
passed |
| testNonPrimaryAlignmentReadWithoutSA |
0s |
passed |
| testNonPrimaryAlignmentWithSAWhereFirstElementHasHardClips |
0.001s |
passed |
| testPrimaryAlignmentWithHardClips |
0s |
passed |
| testSimpleRoundTrip |
0s |
passed |
| testUnmappedFromFastqRead |
0s |
passed |
| testUnmappedFromGATKRead |
0s |
passed |
| testUnmappedFromString |
0s |
passed |