Class picard.util.BedToIntervalListTest

24

tests

0

failures

0

ignored

0.063s

duration

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