Class org.broadinstitute.hellbender.tools.reference.CompareReferencesIntegrationTest

all > org.broadinstitute.hellbender.tools.reference > CompareReferencesIntegrationTest

tests

failures

ignored

2.267s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testCompareReferencesMD5CalculationModes[0](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2snp.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testCompareReferencesMissingValue.table, USE_DICT)	0.069s	passed
testCompareReferencesMD5CalculationModes[1](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_missingmd5.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2snp.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testCompareReferencesRecalculateIfMissing.table, RECALCULATE_IF_MISSING)	0.072s	passed
testCompareReferencesMD5CalculationModes[2](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_missingmd5.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2snp.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testCompareReferencesAlwaysRecalculateMD5.table, ALWAYS_RECALCULATE)	0.080s	passed
testCompareReferencesMissingValue	0.068s	passed
testCompareReferencesMultipleReferences	0.069s	passed
testCompareReferencesRenamedSequence	0.069s	passed
testCompareReferencesToStdOutput	0.068s	passed
testCompareReferencesUseDictMD5MissingValue	0.068s	passed
testFindSNPsMoreThanTwoReferences[0](FULL_ALIGNMENT)	0.069s	passed
testFindSNPsMoreThanTwoReferences[1](FIND_SNPS_ONLY)	0.068s	passed
testFindSNPsNoOutputDir[0](FULL_ALIGNMENT)	0.068s	passed
testFindSNPsNoOutputDir[1](FIND_SNPS_ONLY)	0.068s	passed
testFindSNPsNonexistentOutputDir[0](FULL_ALIGNMENT)	0.068s	passed
testFindSNPsNonexistentOutputDir[1](FIND_SNPS_ONLY)	0.068s	passed
testFindSNPs[0](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2multiplesnps.fasta, hg19mini.fasta_hg19mini_chr2multiplesnps.fasta_snps.tsv, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_chr2multiplesnps.fasta_snps.tsv)	0.072s	passed
testFindSNPs[1](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2iupacsnps.fasta, hg19mini.fasta_hg19mini_chr2iupacsnps.fasta_snps.tsv, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_chr2iupacsnps.fasta_snps.tsv)	0.075s	passed
testFindSNPs[2](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr1indel.fasta, hg19mini.fasta_hg19mini_chr1indel.fasta_snps.tsv, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_chr1indel.fasta_snps.tsv)	0.070s	passed
testFullAlignmentMode[0](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2multiplesnps.fasta, hg19mini.fasta_hg19mini_chr2multiplesnps.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_chr2multiplesnps.fasta.vcf)	0.147s	passed
testFullAlignmentMode[1](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr1indel.fasta, hg19mini.fasta_hg19mini_chr1indel.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testDeletion.hg19mini.fasta_hg19mini_chr1indel.fasta.vcf)	0.141s	passed
testFullAlignmentMode[2](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr1indel.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, hg19mini_chr1indel.fasta_hg19mini.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testInsertion.hg19mini_chr1indel.fasta_hg19mini.fasta.vcf)	0.140s	passed
testFullAlignmentMode[3](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_snpsmultiplecontigs.fasta, hg19mini.fasta_hg19mini_snpsmultiplecontigs.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_snpsmultiplecontigs.fasta.vcf)	0.289s	passed
testFullAlignmentMode[4](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_snpandindel.fasta, hg19mini.fasta_hg19mini_snpandindel.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.SNPandINDEL.hg19mini.fasta_hg19mini_snpandindel.fasta.vcf)	0.218s	passed
testFullAlignmentMode[5](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_manySNPsINDELs.fasta, hg19mini.fasta_hg19mini_manySNPsINDELs.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_manySNPsINDELs.fasta.vcf)	0.143s	passed

Standard output

*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE

*********************************************************
REFERENCE PAIR: hg19mini_missingmd5.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE

*********************************************************
REFERENCE PAIR: hg19mini_missingmd5.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE

*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE

*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_1renamed.fasta
Status:
	DIFFER_IN_SEQUENCE_NAMES

REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE

REFERENCE PAIR: hg19mini_1renamed.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE_NAMES
	DIFFER_IN_SEQUENCE

*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_1renamed.fasta
Status:
	DIFFER_IN_SEQUENCE_NAMES

MD5	Length	hg19mini.fasta	hg19mini_chr2snp.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	1
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	---
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
600ccbfe836f04b26c0eea36dd0485ee	16000	---	2
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_chr2multiplesnps.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	1
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	---
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
a1cdf5289fd7c56ec9be9e2d47695a76	16000	---	2
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2multiplesnps.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_chr2iupacsnps.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	---
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	---
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
eee82532c1dea7dc57397d4205648f13	16000	---	1
a1cdf5289fd7c56ec9be9e2d47695a76	16000	---	2
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2iupacsnps.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_chr1indel.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	---
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	2
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
dfbdb1a2666f8be18b140f07fd80df3a	15920	---	1
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr1indel.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_chr2multiplesnps.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	1
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	---
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
a1cdf5289fd7c56ec9be9e2d47695a76	16000	---	2
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2multiplesnps.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_chr1indel.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	---
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	2
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
dfbdb1a2666f8be18b140f07fd80df3a	15920	---	1
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr1indel.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini_chr1indel.fasta	hg19mini.fasta
dfbdb1a2666f8be18b140f07fd80df3a	15920	1	---
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	2
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
8c0c38e352d8f3309eabe4845456f274	16000	---	1
*********************************************************
REFERENCE PAIR: hg19mini_chr1indel.fasta, hg19mini.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_snpsmultiplecontigs.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	---
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	---
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	---
a16d5419e3aa3b4756b0d4d19f2e6e8f	16000	---	1
cf05678991b4b337be1e39d3c9db6154	16000	---	2
02a72810239374ce9cb60fc664b43eef	16000	---	4
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_snpsmultiplecontigs.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_snpandindel.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	---
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	---
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
483d5c08a04f1ba7beb1d49b25898ced	16000	---	1
a7a6b3d28b24b2457ffd6e4f4762b8a5	15920	---	2
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_snpandindel.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_manySNPsINDELs.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	1
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	2
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	---
5f5f6e0928c1216cc68a6ca80ce3c38b	16080	---	4
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_manySNPsINDELs.fasta
Status:
	DIFFER_IN_SEQUENCE

Standard error

[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:37 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:38 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:38 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:38 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:38 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:38 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:38 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:38 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:39 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480
[June 12, 2025 at 8:43:39 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3386900480