| 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) |
0.001s |
passed |
| testMappingFromBadString[2](chr1,100) |
0s |
passed |
| testMappingFromBadString[3](chr1,100,+) |
0s |
passed |
| testMappingFromBadString[4](chr1,100,+,10M) |
0s |
passed |
| testMappingFromBadString[5](chr1,-1,-,10M,60) |
0.001s |
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$FastqRead@34dc85a, [Ljava.lang.String;@67403656, [I@5a6482a9, [Z@7f9ab969, [Lhtsjdk.samtools.Cigar;@12f8b1d8, [I@746cd757, [I@ae372b9, [I@2098d37d) |
0.010s |
passed |
| testMappingFromFastqRead[1](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@2b4786dd, [Ljava.lang.String;@f202d6d, [I@60e21209, [Z@630d1b2f, [Lhtsjdk.samtools.Cigar;@746b18fd, [I@7a2e0858, [I@aac3f4e, [I@1f38957) |
0s |
passed |
| testMappingFromFastqRead[2](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@2715644a, [Ljava.lang.String;@4c2869a9, [I@518cf84a, [Z@62e7dffa, [Lhtsjdk.samtools.Cigar;@6edcd0d8, [I@6136998b, [I@57ce634f, [I@b8a7e43) |
0s |
passed |
| testMappingFromFastqRead[3](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@56f71edb, [Ljava.lang.String;@7207cb51, [I@2a27cb34, [Z@6892cc6f, [Lhtsjdk.samtools.Cigar;@6fd1660, [I@4a6c18ad, [I@5e8604bf, [I@20095ab4) |
0s |
passed |
| testMappingFromGATKRead[0](test chr1:100-199, [Ljava.lang.String;@232cce0, [I@32b9bd12, [Z@352e787a, [Lhtsjdk.samtools.Cigar;@159a48a6, [I@15bc339, [I@7e75bf2d, [I@385ef531) |
0.002s |
passed |
| testMappingFromGATKRead[1](test chr2:101-150, [Ljava.lang.String;@9a2ec9b, [I@58112bc4, [Z@2301b75, [Lhtsjdk.samtools.Cigar;@3104f7bd, [I@2f5c1332, [I@7ec25216, [I@7cab1508) |
0s |
passed |
| testMappingFromGATKRead[2](test 10:51-95, [Ljava.lang.String;@258ee7de, [I@4930539b, [Z@6d171ce0, [Lhtsjdk.samtools.Cigar;@22bd2039, [I@705f83a7, [I@3bb8aabc, [I@6e1d4137) |
0s |
passed |
| testMappingFromGATKRead[3](test X:1231-1275, [Ljava.lang.String;@5327a06e, [I@2679311f, [Z@287f7811, [Lhtsjdk.samtools.Cigar;@451f87af, [I@2b556bb2, [I@44cb460e, [I@17271176) |
0s |
passed |
| testMappingFromString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@3051e0b2, [I@1f52eb6f, [Z@57d0fc89, [Lhtsjdk.samtools.Cigar;@58294867, [I@67c277a0, [I@6fc3e1a4, [I@3fa76c61) |
0s |
passed |
| testMappingFromString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@59546cfe, [I@29ea78b1, [Z@2d2acd89, [Lhtsjdk.samtools.Cigar;@7baf6acf, [I@1e6dad8, [I@7b3315a5, [I@8ed9cf) |
0s |
passed |
| testMappingFromString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@377008df, [I@540dbda9, [Z@22bb5646, [Lhtsjdk.samtools.Cigar;@1be59f28, [I@2ce45a7b, [I@153d4abb, [I@6d4c273c) |
0s |
passed |
| testMappingFromString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@545e57d7, [I@2bc9a775, [Z@27b000f7, [Lhtsjdk.samtools.Cigar;@42f9c19a, [I@64bfd6fd, [I@2ab2710, [I@253b380a) |
0s |
passed |
| testMappingToStringRead[0](test chr1:100-199, [Ljava.lang.String;@12603fa5, [I@7e6f9868, [Z@26276868, [Lhtsjdk.samtools.Cigar;@56c763, [I@13d85ddb, [I@11f63b10, [I@c8f756e) |
0s |
passed |
| testMappingToStringRead[1](test chr2:101-150, [Ljava.lang.String;@6bb37247, [I@4b3dea9a, [Z@3c6ed296, [Lhtsjdk.samtools.Cigar;@2014fd86, [I@50c59289, [I@7488db31, [I@3eb85d54) |
0s |
passed |
| testMappingToStringRead[2](test 10:51-95, [Ljava.lang.String;@456af3a3, [I@7789f96c, [Z@b274834, [Lhtsjdk.samtools.Cigar;@91cdfb7, [I@1bf9d2dc, [I@23031a56, [I@125490ea) |
0s |
passed |
| testMappingToStringRead[3](test X:1231-1275, [Ljava.lang.String;@28e04625, [I@130a38c5, [Z@256f298e, [Lhtsjdk.samtools.Cigar;@8bbd0c7, [I@22406e9b, [I@60ceb606, [I@3c31c0c8) |
0s |
passed |
| testMappingToString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@2a90a8fe, [I@2fb3113a, [Z@225ad262, [Lhtsjdk.samtools.Cigar;@1ddcb450, [I@32a4284d, [I@5a9d5e2, [I@7114def7) |
0.001s |
passed |
| testMappingToString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@1ae73d9e, [I@51aafde5, [Z@69e7241, [Lhtsjdk.samtools.Cigar;@1bc4b731, [I@38ec721a, [I@3eafe537, [I@4bd694d9) |
0s |
passed |
| testMappingToString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@2eb20fa7, [I@6f75d11b, [Z@10faf070, [Lhtsjdk.samtools.Cigar;@4b493d75, [I@7538cc8c, [I@34042639, [I@733a29b9) |
0s |
passed |
| testMappingToString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@42f5ee2d, [I@57d53da4, [Z@7500a106, [Lhtsjdk.samtools.Cigar;@54ba4478, [I@39d34c44, [I@47157ec7, [I@37edefb2) |
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 |