Class picard.util.BedToIntervalListTest
|
100%
successful |
Tests
Test | Duration | Result |
---|---|---|
testBedToIntervalListBadSequenceDictionary[0](seq_dict_test.dictionary.bad) | 0s | passed |
testBedToIntervalListBadSequenceDictionary[1](seq_dict_test.dictionary.bad.vcf) | 0.001s | passed |
testBedToIntervalListOutOfBounds[0](end_after_chr.bed) | 0.001s | passed |
testBedToIntervalListOutOfBounds[1](end_before_chr.bed) | 0.001s | passed |
testBedToIntervalListOutOfBounds[2](missing_chr.bed) | 0.001s | passed |
testBedToIntervalListOutOfBounds[3](start_after_chr.bed) | 0.001s | passed |
testBedToIntervalListOutOfBounds[4](start_before_chr.bed) | 0.001s | passed |
testBedToIntervalListOutOfBounds[5](off_by_one_interval.bed) | 0.001s | passed |
testBedToIntervalListSequenceDictionary[0](seq_dict_test.dictionary.interval_list) | 0.003s | passed |
testBedToIntervalListSequenceDictionary[1](seq_dict_test.dictionary.fasta) | 0.008s | passed |
testBedToIntervalListSequenceDictionary[2](seq_dict_test.dictionary.dict) | 0.002s | passed |
testBedToIntervalListSequenceDictionary[3](seq_dict_test.dictionary.sam) | 0.003s | passed |
testBedToIntervalListSequenceDictionary[4](seq_dict_test.dictionary.vcf) | 0.002s | passed |
testBedToIntervalList[0](simple.bed) | 0.017s | passed |
testBedToIntervalList[1](overlapping.bed) | 0.003s | passed |
testBedToIntervalList[2](extended.bed) | 0.003s | passed |
testBedToIntervalList[3](one_base_interval.bed) | 0.002s | passed |
testBedToIntervalList[4](zero_base_interval.bed) | 0.002s | passed |
testBedToIntervalList[5](first_base_in_contig.bed) | 0.002s | passed |
testBedToIntervalList[6](zero_length_interval_at_first_position_in_contig.bed) | 0.002s | passed |
testBedToIntervalList[7](last_base_in_contig.bed) | 0.002s | passed |
testBedToIntervalList[8](multi_contig.bed) | 0.003s | passed |
testLengthZeroIntervalsSkipped[0](zero_length_test.bed) | 0.002s | passed |
testRejectStdin | 0s | passed |
Standard error
INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 2 intervals spanning a total of 2900 bases INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 1 intervals spanning a total of 3900 bases INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 2 intervals spanning a total of 2900 bases INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 1 intervals spanning a total of 1 bases WARNING 2025-04-24 13:18:00 BedToIntervalList Input file had 1 entries with length zero. Run with the KEEP_LENGTH_ZERO_INTERVALS flag set to false to remove these. INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 1 intervals spanning a total of 0 bases INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 1 intervals spanning a total of 100 bases WARNING 2025-04-24 13:18:00 BedToIntervalList Input file had 1 entries with length zero. Run with the KEEP_LENGTH_ZERO_INTERVALS flag set to false to remove these. INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 1 intervals spanning a total of 0 bases INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 1 intervals spanning a total of 1000000 bases INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 4 intervals spanning a total of 5800 bases INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases INFO 2025-04-24 13:18:00 BedToIntervalList Skipping writing length zero interval at chr1:1001-1000. INFO 2025-04-24 13:18:00 BedToIntervalList Skipping writing length zero interval at chr3:1001-1000. INFO 2025-04-24 13:18:00 BedToIntervalList Skipped writing a total of 2 entries with length zero in the input file. INFO 2025-04-24 13:18:00 BedToIntervalList Wrote 2 intervals spanning a total of 2000 bases