| 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,.) |
0.001s |
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) |
0.005s |
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$FastqRead@5e2a3040, [Ljava.lang.String;@6d025d1d, [I@74294c1a, [Z@9e2ad91, [Lhtsjdk.samtools.Cigar;@64524dd, [I@79d06bbd, [I@47a7a101, [I@5bb51241) |
0.003s |
passed |
| testMappingFromFastqRead[1](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@7fcf294e, [Ljava.lang.String;@4867ab9f, [I@65f2f9b0, [Z@5fe7f967, [Lhtsjdk.samtools.Cigar;@59e43e8c, [I@2caa5d7c, [I@5e671e20, [I@3eabe84a) |
0s |
passed |
| testMappingFromFastqRead[2](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@38fc5554, [Ljava.lang.String;@5e8cda75, [I@3f049056, [Z@64968732, [Lhtsjdk.samtools.Cigar;@3e1a3801, [I@6fd12c5, [I@1de0a46c, [I@4d1f1ff5) |
0.001s |
passed |
| testMappingFromFastqRead[3](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@4c2fb9dd, [Ljava.lang.String;@54f4a7f0, [I@61a1ea2c, [Z@149debbb, [Lhtsjdk.samtools.Cigar;@25cd49a4, [I@5477a1ca, [I@3ae9d1e2, [I@41522537) |
0.001s |
passed |
| testMappingFromGATKRead[0](test chr1:100-199, [Ljava.lang.String;@408e96d9, [I@59901c4d, [Z@168cd36b, [Lhtsjdk.samtools.Cigar;@d8d9199, [I@3901f6af, [I@602ae7b6, [I@10cd6753) |
0.002s |
passed |
| testMappingFromGATKRead[1](test chr2:101-150, [Ljava.lang.String;@2c8662ac, [I@260ff5b7, [Z@3724b43e, [Lhtsjdk.samtools.Cigar;@77eb5790, [I@68e7c8c3, [I@319c3a25, [I@238bfd6c) |
0s |
passed |
| testMappingFromGATKRead[2](test 10:51-95, [Ljava.lang.String;@58860997, [I@81b5db0, [Z@7487b142, [Lhtsjdk.samtools.Cigar;@7139bd31, [I@199bc830, [I@4b3fe06e, [I@27b45ea) |
0.001s |
passed |
| testMappingFromGATKRead[3](test X:1231-1275, [Ljava.lang.String;@150ede8b, [I@161f6623, [Z@3e15bb06, [Lhtsjdk.samtools.Cigar;@6778aea6, [I@4e1ce44, [I@69228e85, [I@7a7cc52c) |
0.001s |
passed |
| testMappingFromString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@2f61d591, [I@332820f4, [Z@7173ae5b, [Lhtsjdk.samtools.Cigar;@72456279, [I@53a9fcfd, [I@21f459fc, [I@4d192aef) |
0s |
passed |
| testMappingFromString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@84487f4, [I@bfc14b9, [Z@fb6097b, [Lhtsjdk.samtools.Cigar;@2dfe5525, [I@1290c49, [I@6a9b9909, [I@55d9b8f0) |
0s |
passed |
| testMappingFromString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@43d38654, [I@75361cf6, [Z@6d303498, [Lhtsjdk.samtools.Cigar;@6ba7383d, [I@3419e23b, [I@710d89e2, [I@1d75e7af) |
0s |
passed |
| testMappingFromString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@34b27915, [I@29eda4f8, [Z@1b9776f5, [Lhtsjdk.samtools.Cigar;@5e048149, [I@79d9214d, [I@3d5790ea, [I@1dd7796b) |
0s |
passed |
| testMappingToStringRead[0](test chr1:100-199, [Ljava.lang.String;@310e6969, [I@54c17694, [Z@5f8958af, [Lhtsjdk.samtools.Cigar;@439e956c, [I@199f957, [I@5eb35a26, [I@4b6a3d7f) |
0s |
passed |
| testMappingToStringRead[1](test chr2:101-150, [Ljava.lang.String;@3275f900, [I@76d3e702, [Z@6cc8ad62, [Lhtsjdk.samtools.Cigar;@573fc0cc, [I@4a9f9ed2, [I@239d9b74, [I@a9781d8) |
0s |
passed |
| testMappingToStringRead[2](test 10:51-95, [Ljava.lang.String;@15d87a4a, [I@5a5115be, [Z@6cfec66d, [Lhtsjdk.samtools.Cigar;@77ad3a2d, [I@21f104b8, [I@73df09dd, [I@69886465) |
0s |
passed |
| testMappingToStringRead[3](test X:1231-1275, [Ljava.lang.String;@5e9749ba, [I@558d3254, [Z@7f8ccfcc, [Lhtsjdk.samtools.Cigar;@5a7a1c19, [I@3e445475, [I@2e7ce7b, [I@1b0c9344) |
0s |
passed |
| testMappingToString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@f7df01f, [I@4ebf6ee1, [Z@46202302, [Lhtsjdk.samtools.Cigar;@2130262a, [I@412dd71b, [I@745061b9, [I@332f6402) |
0s |
passed |
| testMappingToString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@3cb49d5e, [I@4b1e6ed8, [Z@3590ccd, [Lhtsjdk.samtools.Cigar;@609df650, [I@785bc970, [I@400b100d, [I@b7f53a5) |
0s |
passed |
| testMappingToString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@22e9424e, [I@3afab566, [Z@4b693be7, [Lhtsjdk.samtools.Cigar;@3795591d, [I@5f069693, [I@30384990, [I@320cfa73) |
0.001s |
passed |
| testMappingToString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@4415b9fa, [I@36930c21, [Z@6399a7e2, [Lhtsjdk.samtools.Cigar;@2c1e93ff, [I@452d25ef, [I@6bf1cb6f, [I@45f9c744) |
0s |
passed |
| testNonPrimaryAlignmentReadWithSA |
0.001s |
passed |
| testNonPrimaryAlignmentReadWithoutSA |
0s |
passed |
| testNonPrimaryAlignmentWithSAWhereFirstElementHasHardClips |
0.001s |
passed |
| testPrimaryAlignmentWithHardClips |
0s |
passed |
| testSimpleRoundTrip |
0.001s |
passed |
| testUnmappedFromFastqRead |
0s |
passed |
| testUnmappedFromGATKRead |
0s |
passed |
| testUnmappedFromString |
0s |
passed |