Class org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorUnitTest

all > org.broadinstitute.hellbender.tools.walkers.annotator.flow > FlowAnnotatorUnitTest
9

tests
0

failures
0

ignored
0.006s

duration
100%

successful

Tests

Test Duration Result
testBasic[0](GTATC A ACATCGGA, C, NA, , 0, , GTATC, ACATC, 0.3, non-skip, snp) 0.002s passed
testBasic[1](GTATC A TCATCGGA, C, NA, , 0, , GTATC, TCATC, 0.3, possible-cycle-skip, snp) 0.001s passed
testBasic[2](GTATC A ACATCGGA, T, NA, , 0, , GTATC, ACATC, 0.3, cycle-skip, snp) 0s passed
testBasic[3](TATCT CA TTGACCAA, C, del, 1, 1, A, ATCTC, TTGAC, 0.3, NA, h-indel) 0.001s passed
testBasic[4](TATCTC AT TGACCAA, A, del, 1, 2, T, TCTCA, GACCA, 0.4, NA, h-indel) 0s passed
testBasic[5](TATCT C ATTGACCAA, CA, ins, 1, 2, A, ATCTC, TTGAC, 0.3, NA, h-indel) 0s passed
testBasic[6](ATCT C ATTGACCAA, CA, ins, 1, 2, A, null, TTGAC, 0.3, NA, h-indel) 0.001s passed
testBasic[7](TATCT C ATT, CA, ins, 1, 2, A, ATCTC, null, null, NA, h-indel) 0.001s passed
testBasic[8](TATCT C , CA, ins, 1, null, null, ATCTC, null, null, NA, non-h-indel) 0s passed

Standard error

20:33:36.603 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
20:33:36.603 DEBUG GenomeLocParser -  1 (16000 bp)
20:33:36.603 DEBUG GenomeLocParser -  2 (16000 bp)
20:33:36.603 DEBUG GenomeLocParser -  3 (16000 bp)
20:33:36.603 DEBUG GenomeLocParser -  4 (16000 bp)
20:33:36.608 WARN  FlowAnnotatorBase - Failed to get motif from reference, probably because the variant is very close to the start of the chromosome. LeftMotif annotation will not be calculated. Variant position: chr1:5
20:33:36.608 WARN  FlowAnnotatorBase - Failed to get motif from reference, probably because the variant is very close to the start of the chromosome. LeftMotif annotation will not be calculated. Variant position: chr1:5
20:33:36.609 WARN  FlowAnnotatorBase - gcContent will not be calculated at position chr1:6 because the variant is too close to the edge of the chromosome
20:33:36.609 WARN  FlowAnnotatorBase - Failed to get hmer from reference, too close to the edge. Position: chr1:6
20:33:36.609 WARN  FlowAnnotatorBase - Failed to get hmer from reference, too close to the edge. Position: chr1:6
20:33:36.609 WARN  FlowAnnotatorBase - Failed to get hmer from reference, too close to the edge. Position: chr1:6