Class picard.sam.util.SamComparisonTest

all > picard.sam.util > SamComparisonTest
30

tests
0

failures
0

ignored
0.189s

duration
100%

successful

Tests

Test Duration Result
testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false) 0.001s passed
testSamComparison[10](group_same_coord.sam, diff_coords.sam, false, false, 0, 5, 0, 0, 0, 0, 0, 0, false) 0.002s passed
testSamComparison[11](genomic_sorted.sam, unmapped_first.sam, false, false, 1, 0, 0, 0, 1, 0, 0, 0, false) 0.001s passed
testSamComparison[12](genomic_sorted.sam, unmapped_second.sam, false, false, 1, 0, 0, 0, 1, 0, 0, 1, false) 0.001s passed
testSamComparison[13](unmapped_first.sam, unmapped_second.sam, false, false, 0, 0, 0, 1, 1, 0, 0, 1, false) 0.002s passed
testSamComparison[14](unmapped_first.sam, unmapped_first.sam, false, false, 1, 0, 1, 0, 0, 0, 0, 0, true) 0.001s passed
testSamComparison[15](unsorted.sam, unsorted.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, true) 0.002s passed
testSamComparison[16](unsorted.sam, unsorted2.sam, false, false, 0, 1, 0, 0, 0, 0, 1, 0, false) 0.002s passed
testSamComparison[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, true, false, 14, 0, 0, 0, 0, 0, 0, 0, true) 0.030s passed
testSamComparison[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, true, false, 13, 1, 0, 0, 0, 0, 0, 4, false) 0.013s passed
testSamComparison[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, true, false, 14, 0, 0, 0, 0, 0, 0, 2, false) 0.013s passed
testSamComparison[1](genomic_sorted.sam, chr21.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false) 0.002s passed
testSamComparison[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, true, false, 14, 0, 0, 0, 0, 0, 0, 4, false) 0.022s passed
testSamComparison[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, false, false, 14, 0, 0, 0, 0, 0, 0, 4, false) 0.003s passed
testSamComparison[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, true, false, 14, 0, 0, 0, 0, 0, 0, 0, true) 0.019s passed
testSamComparison[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, true, false, 13, 1, 0, 0, 0, 0, 0, 4, false) 0.024s passed
testSamComparison[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, true, false, 14, 0, 0, 0, 0, 0, 0, 2, false) 0.013s passed
testSamComparison[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, true, false, 14, 0, 0, 0, 0, 0, 0, 4, false) 0.013s passed
testSamComparison[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, false, false, 14, 0, 0, 0, 0, 0, 0, 4, false) 0.001s passed
testSamComparison[27](genomic_sorted.sam, mq0_2.sam, false, true, 1, 1, 0, 0, 0, 0, 0, 0, false) 0.002s passed
testSamComparison[28](mq0_1.sam, mq0_2.sam, false, true, 2, 0, 0, 0, 0, 0, 0, 0, true) 0.008s passed
testSamComparison[29](mq0_1.sam, mq0_2.sam, false, false, 1, 1, 0, 0, 0, 0, 0, 0, false) 0.001s passed
testSamComparison[2](genomic_sorted.sam, bigger_seq_dict.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false) 0.001s passed
testSamComparison[3](bigger_seq_dict.sam, bigger_seq_dict.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, true) 0.002s passed
testSamComparison[4](genomic_sorted.sam, genomic_sorted.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, true) 0.002s passed
testSamComparison[5](genomic_sorted.sam, has_non_primary.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, true) 0.001s passed
testSamComparison[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, false, false, 3, 2, 0, 0, 0, 3, 0, 0, false) 0.002s passed
testSamComparison[7](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, false) 0.002s passed
testSamComparison[8](group_same_coord.sam, group_same_coord_diff_order.sam, false, false, 3, 0, 0, 0, 0, 1, 2, 0, false) 0.002s passed
testSamComparison[9](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, true) 0.001s passed

Standard output

Sort order differs.
File 1: coordinate
File 2: null
Sort Order differs.
File 1: coordinate
File 2: unsorted
Cannot compare alignments if sort orders differ.
Sort order differs.
File 1: null
File 2: coordinate
Sort Order differs.
File 1: unsorted
File 2: coordinate
Cannot compare alignments if sort orders differ.
Name of sequence record 1 differs.
File 1: chr20
File 2: chr21
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
Name of sequence record 1 differs.
File 1: chr21
File 2: chr20
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
Length of sequence dictionaries differs.
File 1: 1
File 2: 2
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
Length of sequence dictionaries differs.
File 1: 2
File 2: 1
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
File format version differs.
File 1: 1.0
File 2: 1.6
File format version differs.
File 1: 1.6
File 2: 1.0