| 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,.) |
0.002s |
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) |
0.005s |
passed |
| testMappingFromBadString[6](chr1,100,blah,10M,60) |
0s |
passed |
| testMappingFromBadString[7](chr1,100,,10M,60) |
0.001s |
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$FastqRead@188b6035, [Ljava.lang.String;@4a34e9f, [I@6f6621e3, [Z@3fc05ea2, [Lhtsjdk.samtools.Cigar;@7c891ba7, [I@6240651f, [I@3cf7298d, [I@1ff55ff) |
0.003s |
passed |
| testMappingFromFastqRead[1](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@3bd3d05e, [Ljava.lang.String;@6aba5d30, [I@61d34b4, [Z@588307f7, [Lhtsjdk.samtools.Cigar;@7df76d99, [I@459cfcca, [I@2acbc859, [I@6ab7ce48) |
0.001s |
passed |
| testMappingFromFastqRead[2](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@e322ec9, [Ljava.lang.String;@7acfb656, [I@2e5ee2c9, [Z@55a609dd, [Lhtsjdk.samtools.Cigar;@4afd21c6, [I@4d0753c9, [I@1416a80a, [I@719bb3b4) |
0s |
passed |
| testMappingFromFastqRead[3](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@25a5c7db, [Ljava.lang.String;@4d27d9d, [I@28f878a0, [Z@20411320, [Lhtsjdk.samtools.Cigar;@2b5183ec, [I@3c782d8e, [I@572e6fd9, [I@7f5eae0f) |
0.001s |
passed |
| testMappingFromGATKRead[0](test chr1:100-199, [Ljava.lang.String;@73437222, [I@ca93621, [Z@6a48a7f3, [Lhtsjdk.samtools.Cigar;@3f985a86, [I@57a2ed35, [I@12ffd1de, [I@3d278b4d) |
0.002s |
passed |
| testMappingFromGATKRead[1](test chr2:101-150, [Ljava.lang.String;@14d8444b, [I@71466383, [Z@46d63dbb, [Lhtsjdk.samtools.Cigar;@4088741b, [I@16a49a5d, [I@54bca971, [I@23706db8) |
0.001s |
passed |
| testMappingFromGATKRead[2](test 10:51-95, [Ljava.lang.String;@129fed45, [I@23592946, [Z@3e48d38, [Lhtsjdk.samtools.Cigar;@7c2b58c0, [I@11b377c5, [I@7bca6fac, [I@5c60b0a0) |
0.001s |
passed |
| testMappingFromGATKRead[3](test X:1231-1275, [Ljava.lang.String;@10fbbdb, [I@23f3dbf0, [Z@31d6f3fe, [Lhtsjdk.samtools.Cigar;@760cf594, [I@aa149ed, [I@37303f12, [I@31ff6309) |
0s |
passed |
| testMappingFromString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@165e389b, [I@5c73f672, [Z@8ee0c23, [Lhtsjdk.samtools.Cigar;@2ab5afc7, [I@4dc8c0ea, [I@e4b6f47, [I@763cf5b9) |
0.001s |
passed |
| testMappingFromString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@7a34f66a, [I@2f508f3c, [Z@3ed03652, [Lhtsjdk.samtools.Cigar;@4aedaf61, [I@173797f0, [I@3c35c345, [I@3681037) |
0s |
passed |
| testMappingFromString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@ffaaaf0, [I@1dc76fa1, [Z@5eed2d86, [Lhtsjdk.samtools.Cigar;@33d53216, [I@69a2b3b6, [I@4f3e7344, [I@7808f638) |
0s |
passed |
| testMappingFromString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@1e141e42, [I@228cea97, [Z@1d0a61c8, [Lhtsjdk.samtools.Cigar;@46731692, [I@782bf610, [I@3db663d0, [I@73fc518f) |
0.001s |
passed |
| testMappingToStringRead[0](test chr1:100-199, [Ljava.lang.String;@17ae2a19, [I@6b9c30af, [Z@3e0b405c, [Lhtsjdk.samtools.Cigar;@39f326d6, [I@5feb2d13, [I@55f87709, [I@3195d44a) |
0s |
passed |
| testMappingToStringRead[1](test chr2:101-150, [Ljava.lang.String;@17f5b5b0, [I@123c878, [Z@1e8b6b92, [Lhtsjdk.samtools.Cigar;@b67503a, [I@31852cd3, [I@2e7a4293, [I@6be87b35) |
0s |
passed |
| testMappingToStringRead[2](test 10:51-95, [Ljava.lang.String;@42445cc2, [I@3e56e0c3, [Z@16cf05ef, [Lhtsjdk.samtools.Cigar;@34d53f54, [I@5417d740, [I@5dce75f9, [I@33c0f3d2) |
0.001s |
passed |
| testMappingToStringRead[3](test X:1231-1275, [Ljava.lang.String;@44352a38, [I@6afafefa, [Z@5e90de14, [Lhtsjdk.samtools.Cigar;@62f5d1ea, [I@f7c4366, [I@324c615d, [I@6a74797e) |
0s |
passed |
| testMappingToString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@1a1e3023, [I@31d2de28, [Z@5f87417a, [Lhtsjdk.samtools.Cigar;@d55b14b, [I@662107ea, [I@4125a698, [I@24cca357) |
0s |
passed |
| testMappingToString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@6a43c847, [I@6bea2f1, [Z@47a96f6a, [Lhtsjdk.samtools.Cigar;@5f892e12, [I@2b7cd454, [I@582642e0, [I@5478a4b1) |
0s |
passed |
| testMappingToString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@f044be0, [I@655f29a2, [Z@74134494, [Lhtsjdk.samtools.Cigar;@93568ed, [I@24c36960, [I@38cd4663, [I@5694920a) |
0.001s |
passed |
| testMappingToString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@4b7305a4, [I@19dfacf7, [Z@6b296904, [Lhtsjdk.samtools.Cigar;@38efa316, [I@6b62cf8a, [I@f3e6e05, [I@2fff57af) |
0.001s |
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 |
0s |
passed |