| Test |
Duration |
Result |
| testMappingFromBadString[0](null) |
0.001s |
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) |
0.001s |
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) |
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$FastqRead@127f9161, [Ljava.lang.String;@2bf94401, [I@2532b351, [Z@4349754, [Lhtsjdk.samtools.Cigar;@6a2eea2a, [I@b967222, [I@3b0ee03a, [I@1ba05e38) |
0.027s |
passed |
| testMappingFromFastqRead[1](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@518cf84a, [Ljava.lang.String;@62e7dffa, [I@6edcd0d8, [Z@6136998b, [Lhtsjdk.samtools.Cigar;@57ce634f, [I@b8a7e43, [I@35835fa, [I@56f71edb) |
0.001s |
passed |
| testMappingFromFastqRead[2](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@2a27cb34, [Ljava.lang.String;@6892cc6f, [I@6fd1660, [Z@4a6c18ad, [Lhtsjdk.samtools.Cigar;@5e8604bf, [I@20095ab4, [I@4e2916c3, [I@64aad6db) |
0.001s |
passed |
| testMappingFromFastqRead[3](org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils$FastqRead@60d1b21f, [Ljava.lang.String;@66c83fc8, [I@546621c4, [Z@621f89b8, [Lhtsjdk.samtools.Cigar;@f339eae, [I@2822c6ff, [I@4dafba3e, [I@53e3a87a) |
0s |
passed |
| testMappingFromGATKRead[0](test chr1:100-199, [Ljava.lang.String;@73044cdf, [I@3cbcd8f3, [Z@719843e5, [Lhtsjdk.samtools.Cigar;@9a2ec9b, [I@58112bc4, [I@2301b75, [I@3104f7bd) |
0.003s |
passed |
| testMappingFromGATKRead[1](test chr2:101-150, [Ljava.lang.String;@4930539b, [I@6d171ce0, [Z@22bd2039, [Lhtsjdk.samtools.Cigar;@705f83a7, [I@3bb8aabc, [I@6e1d4137, [I@256a1825) |
0.001s |
passed |
| testMappingFromGATKRead[2](test 10:51-95, [Ljava.lang.String;@57b75756, [I@5327a06e, [Z@2679311f, [Lhtsjdk.samtools.Cigar;@287f7811, [I@451f87af, [I@2b556bb2, [I@44cb460e) |
0.001s |
passed |
| testMappingFromGATKRead[3](test X:1231-1275, [Ljava.lang.String;@3051e0b2, [I@1f52eb6f, [Z@57d0fc89, [Lhtsjdk.samtools.Cigar;@58294867, [I@67c277a0, [I@6fc3e1a4, [I@3fa76c61) |
0.001s |
passed |
| testMappingFromString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@29ea78b1, [I@2d2acd89, [Z@7baf6acf, [Lhtsjdk.samtools.Cigar;@1e6dad8, [I@7b3315a5, [I@8ed9cf, [I@f72203) |
0.001s |
passed |
| testMappingFromString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@540dbda9, [I@22bb5646, [Z@1be59f28, [Lhtsjdk.samtools.Cigar;@2ce45a7b, [I@153d4abb, [I@6d4c273c, [I@5a67e962) |
0s |
passed |
| testMappingFromString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@2bc9a775, [I@27b000f7, [Z@42f9c19a, [Lhtsjdk.samtools.Cigar;@64bfd6fd, [I@2ab2710, [I@253b380a, [I@29c2c826) |
0s |
passed |
| testMappingFromString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@6818d900, [I@149f5761, [Z@2ba33e2c, [Lhtsjdk.samtools.Cigar;@1f193686, [I@31e72cbc, [I@5fad41be, [I@6dcd5639) |
0s |
passed |
| testMappingToStringRead[0](test chr1:100-199, [Ljava.lang.String;@1bad6995, [I@8c790e7, [Z@47dd7b9a, [Lhtsjdk.samtools.Cigar;@b7a9093, [I@7beba1a8, [I@4f1f569a, [I@6332f548) |
0s |
passed |
| testMappingToStringRead[1](test chr2:101-150, [Ljava.lang.String;@1ad30f6e, [I@2fcd3128, [Z@5ba1192c, [Lhtsjdk.samtools.Cigar;@7feb4b4a, [I@7d4193a6, [I@3b43a957, [I@68f8bf6a) |
0s |
passed |
| testMappingToStringRead[2](test 10:51-95, [Ljava.lang.String;@3cc16e8c, [I@1aee6152, [Z@37c09e8a, [Lhtsjdk.samtools.Cigar;@1a408d7e, [I@2d4235b4, [I@444f35bf, [I@77c8c772) |
0s |
passed |
| testMappingToStringRead[3](test X:1231-1275, [Ljava.lang.String;@55aee896, [I@6871cd51, [Z@5933647a, [Lhtsjdk.samtools.Cigar;@5cb7311b, [I@7e7f9843, [I@1882d998, [I@5ad07e46) |
0.001s |
passed |
| testMappingToString[0](chr1,100,+,100M,60,2,35, [Ljava.lang.String;@3d425217, [I@6c5be07c, [Z@3f5673d0, [Lhtsjdk.samtools.Cigar;@58c7073f, [I@77ba34da, [I@44517251, [I@489541f8) |
0.001s |
passed |
| testMappingToString[1](chr2,101,-,50M,60,.,10, [Ljava.lang.String;@e31b415, [I@413d8c78, [Z@23458f26, [Lhtsjdk.samtools.Cigar;@5175d07d, [I@5267575a, [I@7f145f22, [I@7027c359) |
0s |
passed |
| testMappingToString[2](10,51,+,10S45M,30;20,1213,-,10M45H,.,10,30, [Ljava.lang.String;@671b4820, [I@3aabf6ae, [Z@7458d7a9, [Lhtsjdk.samtools.Cigar;@b91bce9, [I@36f6aff3, [I@530d3105, [I@615a5152) |
0s |
passed |
| testMappingToString[3](X,1231,-,10S45M31S,20,.;Y,3112,+,10M76H,255;MT,1,-,55H31M,60,0,112, [Ljava.lang.String;@64a07d55, [I@5e9feddd, [Z@6dfce79d, [Lhtsjdk.samtools.Cigar;@5c1c44b9, [I@3b31c0ba, [I@1ae12304, [I@10abffca) |
0.001s |
passed |
| testNonPrimaryAlignmentReadWithSA |
0s |
passed |
| testNonPrimaryAlignmentReadWithoutSA |
0s |
passed |
| testNonPrimaryAlignmentWithSAWhereFirstElementHasHardClips |
0.001s |
passed |
| testPrimaryAlignmentWithHardClips |
0.001s |
passed |
| testSimpleRoundTrip |
0.001s |
passed |
| testUnmappedFromFastqRead |
0s |
passed |
| testUnmappedFromGATKRead |
0s |
passed |
| testUnmappedFromString |
0s |
passed |