Class org.broadinstitute.hellbender.utils.smithwaterman.SWNativeAlignerWrapperUnitTest
Tests
| Test |
Duration |
Result |
| testDegenerateAlignmentWithIndelsAtBothEnds |
0.001s |
passed |
| testForIdenticalAlignmentsWithDifferingFlankLengths |
0.002s |
passed |
| testIndelsAtStartAndEnd |
0.001s |
passed |
| testOddNoAlignment[0](AAAGACTACTG, AACGGACACTG, org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters@21e46004, 1, 2M2I3M1D4M) |
0s |
passed |
| testOddNoAlignment[1](AAAGACTACTG, AACGGACACTG, org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters@505df6b4, 0, 11M) |
0s |
passed |
| testReadAlignedToRefComplexAlignment[0](AAAGGACTGACTG, ACTGACTGACTG, 1, 12M) |
0s |
passed |
| testSubstringMatchLong[0](359, 7M, SOFTCLIP) |
0.001s |
passed |
| testSubstringMatchLong[1](0, 1M358D6M29D, INDEL) |
0s |
passed |
| testSubstringMatchLong[2](0, 1M1D6M, LEADING_INDEL) |
0s |
passed |
| testSubstringMatchLong[3](359, 7M, IGNORE) |
0.001s |
passed |
| testSubstringMatch[0](3, 5M, SOFTCLIP) |
0s |
passed |
| testSubstringMatch[1](0, 3D5M, INDEL) |
0s |
passed |
| testSubstringMatch[2](0, 3D5M, LEADING_INDEL) |
0s |
passed |
| testSubstringMatch[3](3, 5M, IGNORE) |
0s |
passed |
Standard output
...............................SSSSSSSSSSSSSSSSSSSS
ACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA
TGTGTGTGTGTGTGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGA
.....SSS
CCCCCGGG
AAACCCCC
..II...D....
AACGGAC-ACTG
AAA--GACTACTG
..*.***....
AACGGACACTG
AAAGACTACTG
.**.........
ACTGACTGACTG
AAAGGACTGACTG
.....
CCCCC
AAACCCCC
DDD.....
---CCCCC
AAACCCCC
DDD.....
---CCCCC
AAACCCCC
.....
CCCCC
AAACCCCC
ATAGAAAATAGTTTTTGGAAATATGGGTGAAGAGACATCTCCTCTTATGGAAAAAGGGATTCTAGAATTTAACAATAAATATTCCCAACTTTCCCCAAGG
CTTTAAAATCTACCTTGAAGGAGCAGCTGATGTATTTCTAGAACAGACTTAGGTGTCTTGGTGTGGCCTGTAAAGAGATACTGTCTTTCTCTTTTGAGTG
TAAGAGAGAAAGGACAGTCTACTCAATAAAGAGTGCTGGGAAAACTGAATATCCACACACAGAATAATAAAACTAGATCCTATCTCTCACCATATACAAA
.......
AAAAAAA
GATCAACTCAAAACAAATTAAAGACCTAAATGTAAGACAAGAAATTATAAAACTACTAGAAAAAAACACAAGGGAAATGCTTCAGGACATTGGC
.DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
A---------------------------------------------------------------------------------------------------
ATAGAAAATAGTTTTTGGAAATATGGGTGAAGAGACATCTCCTCTTATGGAAAAAGGGATTCTAGAATTTAACAATAAATATTCCCAACTTTCCCCAAGG
DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
----------------------------------------------------------------------------------------------------
CTTTAAAATCTACCTTGAAGGAGCAGCTGATGTATTTCTAGAACAGACTTAGGTGTCTTGGTGTGGCCTGTAAAGAGATACTGTCTTTCTCTTTTGAGTG
DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
----------------------------------------------------------------------------------------------------
TAAGAGAGAAAGGACAGTCTACTCAATAAAGAGTGCTGGGAAAACTGAATATCCACACACAGAATAATAAAACTAGATCCTATCTCTCACCATATACAAA
DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD......DDDDDDDDDDDDDDDDDDDDDDDDDDDDD
-----------------------------------------------------------AAAAAA-----------------------------
GATCAACTCAAAACAAATTAAAGACCTAAATGTAAGACAAGAAATTATAAAACTACTAGAAAAAAACACAAGGGAAATGCTTCAGGACATTGGC
.D.*....
A-AAAAAA
ATAGAAAATAGTTTTTGGAAATATGGGTGAAGAGACATCTCCTCTTATGGAAAAAGGGATTCTAGAATTTAACAATAAATATTCCCAACTTTCCCCAAGG
CTTTAAAATCTACCTTGAAGGAGCAGCTGATGTATTTCTAGAACAGACTTAGGTGTCTTGGTGTGGCCTGTAAAGAGATACTGTCTTTCTCTTTTGAGTG
TAAGAGAGAAAGGACAGTCTACTCAATAAAGAGTGCTGGGAAAACTGAATATCCACACACAGAATAATAAAACTAGATCCTATCTCTCACCATATACAAA
GATCAACTCAAAACAAATTAAAGACCTAAATGTAAGACAAGAAATTATAAAACTACTAGAAAAAAACACAAGGGAAATGCTTCAGGACATTGGC
ATAGAAAATAGTTTTTGGAAATATGGGTGAAGAGACATCTCCTCTTATGGAAAAAGGGATTCTAGAATTTAACAATAAATATTCCCAACTTTCCCCAAGG
CTTTAAAATCTACCTTGAAGGAGCAGCTGATGTATTTCTAGAACAGACTTAGGTGTCTTGGTGTGGCCTGTAAAGAGATACTGTCTTTCTCTTTTGAGTG
TAAGAGAGAAAGGACAGTCTACTCAATAAAGAGTGCTGGGAAAACTGAATATCCACACACAGAATAATAAAACTAGATCCTATCTCTCACCATATACAAA
.......
AAAAAAA
GATCAACTCAAAACAAATTAAAGACCTAAATGTAAGACAAGAAATTATAAAACTACTAGAAAAAAACACAAGGGAAATGCTTCAGGACATTGGC
Standard error
20:37:39.612 WARN gatk - testDegenerateAlignmentWithIndelsAtBothEnds