Class picard.vcf.FixVcfHeaderTest

all > picard.vcf > FixVcfHeaderTest
7

tests
0

failures
0

ignored
0.337s

duration
100%

successful

Tests

Test Duration Result
testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true) 0.077s passed
testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false) 0.057s passed
testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false) 0.057s passed
testFixVcfHeader[3](-1, null, true) 0.052s passed
testFixVcfHeader[4](1, null, true) 0.043s passed
testFixVcfHeader[5](2147483647, null, true) 0.046s passed
testReplaceHeaderWithDifferentSamplesError 0.005s passed

Standard error

[Tue Aug 16 04:11:45 CDT 2016] picard.vcf.FixVcfHeader    INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/FixVcfHeaderTest3096000430213199138.tmp/output.vcf CHECK_FIRST_N_RECORDS=-1 HEADER=testdata/picard/vcf/FixVcfHeaderTest/header.vcf ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:45 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:45	FixVcfHeader	INFO line found in HEADER will be added to OUTPUT: PLNCIIonWG
INFO	2016-08-16 04:11:45	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: AD
INFO	2016-08-16 04:11:45	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: FT
INFO	2016-08-16 04:11:45	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: GQ
INFO	2016-08-16 04:11:45	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: GT
INFO	2016-08-16 04:11:45	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: PL
INFO	2016-08-16 04:11:45	FixVcfHeader	Writing the output VCF.
[Tue Aug 16 04:11:45 CDT 2016] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1826619392
[Tue Aug 16 04:11:45 CDT 2016] picard.vcf.FixVcfHeader    INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/FixVcfHeaderTest3096000430213199138.tmp/output.vcf CHECK_FIRST_N_RECORDS=-1 HEADER=testdata/picard/vcf/FixVcfHeaderTest/header.vcf ENFORCE_SAME_SAMPLES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:45 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:45	FixVcfHeader	INFO line found in HEADER will be added to OUTPUT: PLNCIIonWG
INFO	2016-08-16 04:11:46	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: AD
INFO	2016-08-16 04:11:46	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: FT
INFO	2016-08-16 04:11:46	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: GQ
INFO	2016-08-16 04:11:46	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: GT
INFO	2016-08-16 04:11:46	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: PL
INFO	2016-08-16 04:11:46	FixVcfHeader	Writing the output VCF.
[Tue Aug 16 04:11:46 CDT 2016] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1826619392
[Tue Aug 16 04:11:46 CDT 2016] picard.vcf.FixVcfHeader    INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/FixVcfHeaderTest3096000430213199138.tmp/output.vcf CHECK_FIRST_N_RECORDS=-1 HEADER=testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf ENFORCE_SAME_SAMPLES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:46 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:46	FixVcfHeader	INFO line found in HEADER will be added to OUTPUT: PLNCIIonWG
INFO	2016-08-16 04:11:46	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: AD
INFO	2016-08-16 04:11:46	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: FT
INFO	2016-08-16 04:11:46	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: GQ
INFO	2016-08-16 04:11:46	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: GT
INFO	2016-08-16 04:11:46	FixVcfHeader	FORMAT line found in HEADER will be added to OUTPUT: PL
INFO	2016-08-16 04:11:46	FixVcfHeader	Writing the output VCF.
[Tue Aug 16 04:11:46 CDT 2016] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1826619392
[Tue Aug 16 04:11:46 CDT 2016] picard.vcf.FixVcfHeader    INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/FixVcfHeaderTest3096000430213199138.tmp/output.vcf CHECK_FIRST_N_RECORDS=-1 ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:46 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:46	FixVcfHeader	Reading in records to re-build the header.
INFO	2016-08-16 04:11:46	FixVcfHeader	Will add an INFO line with id: PLNCIIonWG
INFO	2016-08-16 04:11:46	FixVcfHeader	VCF header re-built.
INFO	2016-08-16 04:11:46	FixVcfHeader	Writing the output VCF.
[Tue Aug 16 04:11:46 CDT 2016] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1826619392
[Tue Aug 16 04:11:46 CDT 2016] picard.vcf.FixVcfHeader    INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/FixVcfHeaderTest3096000430213199138.tmp/output.vcf CHECK_FIRST_N_RECORDS=1 ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:46 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:46	FixVcfHeader	Reading in records to re-build the header.
INFO	2016-08-16 04:11:46	FixVcfHeader	Will add an INFO line with id: PLNCIIonWG
INFO	2016-08-16 04:11:46	FixVcfHeader	VCF header re-built.
INFO	2016-08-16 04:11:46	FixVcfHeader	Writing the output VCF.
[Tue Aug 16 04:11:46 CDT 2016] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1826619392
[Tue Aug 16 04:11:46 CDT 2016] picard.vcf.FixVcfHeader    INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/FixVcfHeaderTest3096000430213199138.tmp/output.vcf CHECK_FIRST_N_RECORDS=2147483647 ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:46 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:46	FixVcfHeader	Reading in records to re-build the header.
INFO	2016-08-16 04:11:46	FixVcfHeader	Will add an INFO line with id: PLNCIIonWG
INFO	2016-08-16 04:11:46	FixVcfHeader	VCF header re-built.
INFO	2016-08-16 04:11:46	FixVcfHeader	Writing the output VCF.
[Tue Aug 16 04:11:46 CDT 2016] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1826619392
[Tue Aug 16 04:11:46 CDT 2016] picard.vcf.FixVcfHeader    INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/FixVcfHeaderTest3096000430213199138.tmp/output.vcf CHECK_FIRST_N_RECORDS=-1 HEADER=testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:46 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
[Tue Aug 16 04:11:46 CDT 2016] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1826619392
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp