| 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) |
0s |
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) |
0.002s |
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$FastqRead@67403656, [Ljava.lang.String;@5a6482a9, [I@7f9ab969, [Z@12f8b1d8, [Lhtsjdk.samtools.Cigar;@746cd757, [I@ae372b9, [I@2098d37d, [I@77b9d0c7) |
0.010s |
passed |
| testMappingFromFastqRead[1](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@f202d6d, [Ljava.lang.String;@60e21209, [I@630d1b2f, [Z@746b18fd, [Lhtsjdk.samtools.Cigar;@7a2e0858, [I@aac3f4e, [I@1f38957, [I@2df3c564) |
0s |
passed |
| testMappingFromFastqRead[2](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@4c2869a9, [Ljava.lang.String;@518cf84a, [I@62e7dffa, [Z@6edcd0d8, [Lhtsjdk.samtools.Cigar;@6136998b, [I@57ce634f, [I@b8a7e43, [I@35835fa) |
0s |
passed |
| testMappingFromFastqRead[3](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@7207cb51, [Ljava.lang.String;@2a27cb34, [I@6892cc6f, [Z@6fd1660, [Lhtsjdk.samtools.Cigar;@4a6c18ad, [I@5e8604bf, [I@20095ab4, [I@4e2916c3) |
0s |
passed |
| testMappingFromGATKRead[0](test chr1:100-199, [Ljava.lang.String;@32b9bd12, [I@352e787a, [Z@159a48a6, [Lhtsjdk.samtools.Cigar;@15bc339, [I@7e75bf2d, [I@385ef531, [I@7fc645e4) |
0.003s |
passed |
| testMappingFromGATKRead[1](test chr2:101-150, [Ljava.lang.String;@58112bc4, [I@2301b75, [Z@3104f7bd, [Lhtsjdk.samtools.Cigar;@2f5c1332, [I@7ec25216, [I@7cab1508, [I@6a84bc3f) |
0s |
passed |
| testMappingFromGATKRead[2](test 10:51-95, [Ljava.lang.String;@4930539b, [I@6d171ce0, [Z@22bd2039, [Lhtsjdk.samtools.Cigar;@705f83a7, [I@3bb8aabc, [I@6e1d4137, [I@256a1825) |
0.001s |
passed |
| testMappingFromGATKRead[3](test X:1231-1275, [Ljava.lang.String;@2679311f, [I@287f7811, [Z@451f87af, [Lhtsjdk.samtools.Cigar;@2b556bb2, [I@44cb460e, [I@17271176, [I@2e3cdec2) |
0.001s |
passed |
| testMappingFromString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@1f52eb6f, [I@57d0fc89, [Z@58294867, [Lhtsjdk.samtools.Cigar;@67c277a0, [I@6fc3e1a4, [I@3fa76c61, [I@2d5f7182) |
0s |
passed |
| testMappingFromString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@29ea78b1, [I@2d2acd89, [Z@7baf6acf, [Lhtsjdk.samtools.Cigar;@1e6dad8, [I@7b3315a5, [I@8ed9cf, [I@f72203) |
0s |
passed |
| testMappingFromString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@540dbda9, [I@22bb5646, [Z@1be59f28, [Lhtsjdk.samtools.Cigar;@2ce45a7b, [I@153d4abb, [I@6d4c273c, [I@5a67e962) |
0.001s |
passed |
| testMappingFromString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@2bc9a775, [I@27b000f7, [Z@42f9c19a, [Lhtsjdk.samtools.Cigar;@64bfd6fd, [I@2ab2710, [I@253b380a, [I@29c2c826) |
0s |
passed |
| testMappingToStringRead[0](test chr1:100-199, [Ljava.lang.String;@27241127, [I@5631baf5, [Z@5f546133, [Lhtsjdk.samtools.Cigar;@379ebfa0, [I@30b43d5d, [I@6b89dfac, [I@17287617) |
0.001s |
passed |
| testMappingToStringRead[1](test chr2:101-150, [Ljava.lang.String;@44c639d4, [I@6197fa5f, [Z@35dba0b4, [Lhtsjdk.samtools.Cigar;@2d8d2832, [I@58f0acce, [I@66bf08d, [I@6edd2ef4) |
0s |
passed |
| testMappingToStringRead[2](test 10:51-95, [Ljava.lang.String;@771e08ed, [I@2ea8611b, [Z@298550b4, [Lhtsjdk.samtools.Cigar;@29ed425e, [I@2eb37eee, [I@43fe629a, [I@40fd8aa1) |
0s |
passed |
| testMappingToStringRead[3](test X:1231-1275, [Ljava.lang.String;@36b085da, [I@66adb24, [Z@2aeef1ca, [Lhtsjdk.samtools.Cigar;@27d8008a, [I@15f4dffe, [I@4517959f, [I@182a5c56) |
0s |
passed |
| testMappingToString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@22489e92, [I@1d483c89, [Z@44f01009, [Lhtsjdk.samtools.Cigar;@7609b7c5, [I@10d31b98, [I@4c23d17f, [I@817e0aa) |
0s |
passed |
| testMappingToString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@3b1c0bd2, [I@69668de7, [Z@5e4332d1, [Lhtsjdk.samtools.Cigar;@337ab4a2, [I@68e36b84, [I@3537caca, [I@7225a307) |
0s |
passed |
| testMappingToString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@67503009, [I@6cbad7b3, [Z@33587cb8, [Lhtsjdk.samtools.Cigar;@4184aa78, [I@27320a39, [I@1d8f4623, [I@6d425496) |
0.001s |
passed |
| testMappingToString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@3e2544e9, [I@597ca350, [Z@2665ba0d, [Lhtsjdk.samtools.Cigar;@20337a79, [I@3425709a, [I@87f336d, [I@3c155bd) |
0s |
passed |
| testNonPrimaryAlignmentReadWithSA |
0s |
passed |
| testNonPrimaryAlignmentReadWithoutSA |
0s |
passed |
| testNonPrimaryAlignmentWithSAWhereFirstElementHasHardClips |
0.004s |
passed |
| testPrimaryAlignmentWithHardClips |
0.001s |
passed |
| testSimpleRoundTrip |
0.001s |
passed |
| testUnmappedFromFastqRead |
0s |
passed |
| testUnmappedFromGATKRead |
0.001s |
passed |
| testUnmappedFromString |
0s |
passed |