| Test |
Duration |
Result |
| testMappingFromBadString[0](null) |
0s |
passed |
| testMappingFromBadString[10](X,100,-,10M,60,.,-1.0) |
0s |
passed |
| testMappingFromBadString[11](Y,100,-,10H10M,60,30,30;Y,200,10M10H,60,20,.) |
0.001s |
passed |
| testMappingFromBadString[1](chr1) |
0.002s |
passed |
| testMappingFromBadString[2](chr1,100) |
0s |
passed |
| testMappingFromBadString[3](chr1,100,+) |
0s |
passed |
| testMappingFromBadString[4](chr1,100,+,10M) |
0.001s |
passed |
| testMappingFromBadString[5](chr1,-1,-,10M,60) |
0.004s |
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) |
0s |
passed |
| testMappingFromFastqRead[0](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@1744a475, [Ljava.lang.String;@444cc791, [I@1c5c616f, [Z@1c6c6f24, [Lhtsjdk.samtools.Cigar;@2eb917d0, [I@c6b2dd9, [I@73437222, [I@ca93621) |
0.003s |
passed |
| testMappingFromFastqRead[1](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@14d8444b, [Ljava.lang.String;@71466383, [I@46d63dbb, [Z@4088741b, [Lhtsjdk.samtools.Cigar;@16a49a5d, [I@54bca971, [I@23706db8, [I@205bed61) |
0s |
passed |
| testMappingFromFastqRead[2](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@23592946, [Ljava.lang.String;@3e48d38, [I@7c2b58c0, [Z@11b377c5, [Lhtsjdk.samtools.Cigar;@7bca6fac, [I@5c60b0a0, [I@7a2b1eb4, [I@702c436b) |
0.001s |
passed |
| testMappingFromFastqRead[3](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@10fbbdb, [Ljava.lang.String;@23f3dbf0, [I@31d6f3fe, [Z@760cf594, [Lhtsjdk.samtools.Cigar;@aa149ed, [I@37303f12, [I@31ff6309, [I@204e90f7) |
0s |
passed |
| testMappingFromGATKRead[0](test chr1:100-199, [Ljava.lang.String;@62d73ead, [I@1e141e42, [Z@228cea97, [Lhtsjdk.samtools.Cigar;@1d0a61c8, [I@46731692, [I@782bf610, [I@3db663d0) |
0.003s |
passed |
| testMappingFromGATKRead[1](test chr2:101-150, [Ljava.lang.String;@2cc03cd1, [I@4e17913b, [Z@149c3204, [Lhtsjdk.samtools.Cigar;@64f16277, [I@497aec8c, [I@3b9632d1, [I@4e6f2bb5) |
0s |
passed |
| testMappingFromGATKRead[2](test 10:51-95, [Ljava.lang.String;@3f628ce9, [I@35e8316e, [Z@26d96e5, [Lhtsjdk.samtools.Cigar;@336880df, [I@1846579f, [I@6cd166b8, [I@2650f79) |
0s |
passed |
| testMappingFromGATKRead[3](test X:1231-1275, [Ljava.lang.String;@129bd55d, [I@7be7e15, [Z@3abfe845, [Lhtsjdk.samtools.Cigar;@7a0f244f, [I@3672276e, [I@4248b963, [I@7f08caf) |
0s |
passed |
| testMappingFromString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@24b4d544, [I@27a2a089, [Z@54657dd2, [Lhtsjdk.samtools.Cigar;@706eab5d, [I@72725ee1, [I@40e60ece, [I@3f9270ed) |
0s |
passed |
| testMappingFromString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@5ac6c4f2, [I@2aa6311a, [Z@61f39bb, [Lhtsjdk.samtools.Cigar;@249e0271, [I@4893b344, [I@53a665ad, [I@2c0b4c83) |
0.001s |
passed |
| testMappingFromString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@2d0ecb24, [I@4d654825, [Z@3bfc6a5e, [Lhtsjdk.samtools.Cigar;@51b35e4e, [I@abff8b7, [I@6d7cada5, [I@350a94ce) |
0s |
passed |
| testMappingFromString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@b0fc838, [I@3964d79, [Z@62db0521, [Lhtsjdk.samtools.Cigar;@1b4ae4e0, [I@6ef1a1b9, [I@5fbdc49b, [I@65753040) |
0s |
passed |
| testMappingToStringRead[0](test chr1:100-199, [Ljava.lang.String;@5ed85a18, [I@3f575bad, [Z@15e89472, [Lhtsjdk.samtools.Cigar;@71965d0c, [I@6d82d1bc, [I@688d7592, [I@399737f5) |
0s |
passed |
| testMappingToStringRead[1](test chr2:101-150, [Ljava.lang.String;@15e422e, [I@27c9672, [Z@2d43157, [Lhtsjdk.samtools.Cigar;@2bc8c738, [I@58f4bf5d, [I@3e5d7d37, [I@1da0ad22) |
0s |
passed |
| testMappingToStringRead[2](test 10:51-95, [Ljava.lang.String;@dcf0fa4, [I@58ae7fef, [Z@40ff1065, [Lhtsjdk.samtools.Cigar;@529461d3, [I@2753f60a, [I@ca9a408, [I@346df1c0) |
0.001s |
passed |
| testMappingToStringRead[3](test X:1231-1275, [Ljava.lang.String;@7d5dc96b, [I@3c15ab2c, [Z@67adae9f, [Lhtsjdk.samtools.Cigar;@16f9bba1, [I@57c3e84, [I@1421a9cc, [I@1e723481) |
0s |
passed |
| testMappingToString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@6a8965a, [I@3144dd1a, [Z@5246f452, [Lhtsjdk.samtools.Cigar;@604f8e79, [I@2217de6c, [I@352c7b39, [I@50adedaa) |
0s |
passed |
| testMappingToString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@50f5cec3, [I@6d68257, [Z@39a9ef9a, [Lhtsjdk.samtools.Cigar;@19e884a2, [I@6795c28a, [I@55633015, [I@23c0d01c) |
0s |
passed |
| testMappingToString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@37988190, [I@7b37fcee, [Z@5e5283a4, [Lhtsjdk.samtools.Cigar;@24922f21, [I@57f5be22, [I@13e1f8be, [I@596416c5) |
0.001s |
passed |
| testMappingToString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@164466e4, [I@a7c489a, [Z@7357a52e, [Lhtsjdk.samtools.Cigar;@49d83712, [I@7c9e0b8b, [I@144ea41a, [I@5a7e1d68) |
0s |
passed |
| testNonPrimaryAlignmentReadWithSA |
0.001s |
passed |
| testNonPrimaryAlignmentReadWithoutSA |
0s |
passed |
| testNonPrimaryAlignmentWithSAWhereFirstElementHasHardClips |
0s |
passed |
| testPrimaryAlignmentWithHardClips |
0.001s |
passed |
| testSimpleRoundTrip |
0.001s |
passed |
| testUnmappedFromFastqRead |
0s |
passed |
| testUnmappedFromGATKRead |
0s |
passed |
| testUnmappedFromString |
0.001s |
passed |