Add support for tox (http://tox.testrun.org/)

Output of tox:

```
[last: 0] marca@SCML-MarcA:~/dev/git-repos/PyVCF$ tox
GLOB sdist-make: /Users/marca/dev/git-repos/PyVCF/setup.py
py26 sdist-reinst: /Users/marca/dev/git-repos/PyVCF/.tox/dist/PyVCF-0.5.0-pre.zip
py26 runtests: commands[0]
running test
running build_py
running egg_info
writing requirements to PyVCF.egg-info/requires.txt
writing PyVCF.egg-info/PKG-INFO
writing top-level names to PyVCF.egg-info/top_level.txt
writing dependency_links to PyVCF.egg-info/dependency_links.txt
writing entry points to PyVCF.egg-info/entry_points.txt
reading manifest file 'PyVCF.egg-info/SOURCES.txt'
writing manifest file 'PyVCF.egg-info/SOURCES.txt'
running egg_info
writing requirements to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/requires.txt
writing /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/PKG-INFO
writing top-level names to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/top_level.txt
writing dependency_links to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/dependency_links.txt
writing entry points to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/entry_points.txt
reading manifest file '/Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/SOURCES.txt'
writing manifest file '/Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/SOURCES.txt'
running build_ext
Doctest: vcf ... ok
testCalls (vcf.test.test_vcf.TestGatkOutput) ... ok
testFormats (vcf.test.test_vcf.TestGatkOutput) ... ok
testInfos (vcf.test.test_vcf.TestGatkOutput) ... ok
testSamples (vcf.test.test_vcf.TestGatkOutput) ... ok
testCalls (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testFormats (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testInfos (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testParse (vcf.test.test_vcf.TestFreebayesOutput) ... ['BLANK', 'NA12878', 'NA12891', 'NA12892', 'NA19238', 'NA19239', 'NA19240']
ok
testSamples (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testParse (vcf.test.test_vcf.TestSamtoolsOutput) ... ok
testWrite (vcf.test.test_vcf.TestWriter) ... ok
testFetchRange (vcf.test.test_vcf.TestTabix) ... ok
testFetchSite (vcf.test.test_vcf.TestTabix) ... ok
testOpenFilehandle (vcf.test.test_vcf.TestOpenMethods) ... ok
testOpenFilehandleGzipped (vcf.test.test_vcf.TestOpenMethods) ... ok
testOpenFilename (vcf.test.test_vcf.TestOpenMethods) ... ok
testOpenFilenameGzipped (vcf.test.test_vcf.TestOpenMethods) ... ok
testApplyFilter (vcf.test.test_vcf.TestFilter) ... ok
testApplyMultipleFilters (vcf.test.test_vcf.TestFilter) ... ok
testParse (vcf.test.test_vcf.Test1kg) ... ok
docstring for test_issue_49 ... ok
test_aaf (vcf.test.test_vcf.TestRecord) ... ok
test_call_rate (vcf.test.test_vcf.TestRecord) ... ok
test_is_deletion (vcf.test.test_vcf.TestRecord) ... ok
test_is_indel (vcf.test.test_vcf.TestRecord) ... ok
test_is_snp (vcf.test.test_vcf.TestRecord) ... Record(CHROM=20, POS=14370, REF=G, ALT=[A])
Call(sample=NA00001, GT=0|0, HQ=[51, 51], DP=1, GQ=48)
Call(sample=NA00002, GT=1|0, HQ=[51, 51], DP=8, GQ=48)
Call(sample=NA00003, GT=1/1, HQ=[None, None], DP=5, GQ=43)
Record(CHROM=20, POS=17330, REF=T, ALT=[A])
Call(sample=NA00001, GT=0|0, HQ=[58, 50], DP=3, GQ=49)
Call(sample=NA00002, GT=0|1, HQ=[65, 3], DP=5, GQ=3)
Call(sample=NA00003, GT=0/0, HQ=None, DP=3, GQ=41)
Record(CHROM=20, POS=1110696, REF=A, ALT=[G, T])
Call(sample=NA00001, GT=1|2, HQ=[23, 27], DP=6, GQ=21)
Call(sample=NA00002, GT=2|1, HQ=[18, 2], DP=0, GQ=2)
Call(sample=NA00003, GT=2/2, HQ=None, DP=4, GQ=35)
Record(CHROM=20, POS=1230237, REF=T, ALT=[None])
Call(sample=NA00001, GT=0|0, HQ=[56, 60], DP=7, GQ=54)
Call(sample=NA00002, GT=0|0, HQ=[51, 51], DP=4, GQ=48)
Call(sample=NA00003, GT=0/0, HQ=None, DP=2, GQ=61)
Record(CHROM=20, POS=1234567, REF=GTCT, ALT=[G, GTACT])
Call(sample=NA00001, GT=None, DP=4, GQ=35)
Call(sample=NA00002, GT=0/2, DP=2, GQ=17)
Call(sample=NA00003, GT=1/1, DP=3, GQ=40)
ok
test_is_sv (vcf.test.test_vcf.TestRecord) ... ok
test_is_sv_precise (vcf.test.test_vcf.TestRecord) ... ok
test_is_transition (vcf.test.test_vcf.TestRecord) ... ok
test_num_calls (vcf.test.test_vcf.TestRecord) ... ok
test_pi (vcf.test.test_vcf.TestRecord) ... ok
test_qual (vcf.test.test_vcf.TestRecord) ... ok
test_sv_end (vcf.test.test_vcf.TestRecord) ... ok
test_var_subtype (vcf.test.test_vcf.TestRecord) ... ok
test_var_type (vcf.test.test_vcf.TestRecord) ... ok
test_gt_bases (vcf.test.test_vcf.TestCall) ... ok
test_gt_types (vcf.test.test_vcf.TestCall) ... {'GT': '0|0', 'HQ': [51, 51], 'DP': 1, 'GQ': 48}
{'GT': '1|0', 'HQ': [51, 51], 'DP': 8, 'GQ': 48}
{'GT': '1/1', 'HQ': [None, None], 'DP': 5, 'GQ': 43}
{'GT': '0|0', 'HQ': [58, 50], 'DP': 3, 'GQ': 49}
{'GT': '0|1', 'HQ': [65, 3], 'DP': 5, 'GQ': 3}
{'GT': '0/0', 'HQ': None, 'DP': 3, 'GQ': 41}
{'GT': '1|2', 'HQ': [23, 27], 'DP': 6, 'GQ': 21}
{'GT': '2|1', 'HQ': [18, 2], 'DP': 0, 'GQ': 2}
{'GT': '2/2', 'HQ': None, 'DP': 4, 'GQ': 35}
{'GT': '0|0', 'HQ': [56, 60], 'DP': 7, 'GQ': 54}
{'GT': '0|0', 'HQ': [51, 51], 'DP': 4, 'GQ': 48}
{'GT': '0/0', 'HQ': None, 'DP': 2, 'GQ': 61}
{'GT': None, 'DP': 4, 'GQ': 35}
{'GT': '0/2', 'DP': 2, 'GQ': 17}
{'GT': '1/1', 'DP': 3, 'GQ': 40}
ok
test_phased (vcf.test.test_vcf.TestCall) ... ok
test_issue_16 (vcf.test.test_vcf.TestRegression) ... ok
test_null_mono (vcf.test.test_vcf.TestRegression) ... /Users/marca/dev/git-repos/PyVCF/build/lib/vcf/test/null_genotype_mono.vcf
##fileformat=VCFv4.1
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[np_control.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[tests/read_chr.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/data/reference/ucsc/hg19/ucsc.hg19.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=info log_to_file=null help=false genotype_likelihoods_model=SNP p_nonref_model=EXACT heterozygosity=0.001 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig={'length': '249250621', 'assembly': 'hg19', 'ID': 'chr1'}
##contig={'length': '135534747', 'assembly': 'hg19', 'ID': 'chr10'}
##contig={'length': '135006516', 'assembly': 'hg19', 'ID': 'chr11'}
##contig={'length': '40103', 'assembly': 'hg19', 'ID': 'chr11_gl000202_random'}
##contig={'length': '133851895', 'assembly': 'hg19', 'ID': 'chr12'}
##contig={'length': '115169878', 'assembly': 'hg19', 'ID': 'chr13'}
##contig={'length': '107349540', 'assembly': 'hg19', 'ID': 'chr14'}
##contig={'length': '102531392', 'assembly': 'hg19', 'ID': 'chr15'}
##contig={'length': '90354753', 'assembly': 'hg19', 'ID': 'chr16'}
##contig={'length': '81195210', 'assembly': 'hg19', 'ID': 'chr17'}
##contig={'length': '1680828', 'assembly': 'hg19', 'ID': 'chr17_ctg5_hap1'}
##contig={'length': '37498', 'assembly': 'hg19', 'ID': 'chr17_gl000203_random'}
##contig={'length': '81310', 'assembly': 'hg19', 'ID': 'chr17_gl000204_random'}
##contig={'length': '174588', 'assembly': 'hg19', 'ID': 'chr17_gl000205_random'}
##contig={'length': '41001', 'assembly': 'hg19', 'ID': 'chr17_gl000206_random'}
##contig={'length': '78077248', 'assembly': 'hg19', 'ID': 'chr18'}
##contig={'length': '4262', 'assembly': 'hg19', 'ID': 'chr18_gl000207_random'}
##contig={'length': '59128983', 'assembly': 'hg19', 'ID': 'chr19'}
##contig={'length': '92689', 'assembly': 'hg19', 'ID': 'chr19_gl000208_random'}
##contig={'length': '159169', 'assembly': 'hg19', 'ID': 'chr19_gl000209_random'}
##contig={'length': '106433', 'assembly': 'hg19', 'ID': 'chr1_gl000191_random'}
##contig={'length': '547496', 'assembly': 'hg19', 'ID': 'chr1_gl000192_random'}
##contig={'length': '243199373', 'assembly': 'hg19', 'ID': 'chr2'}
##contig={'length': '63025520', 'assembly': 'hg19', 'ID': 'chr20'}
##contig={'length': '48129895', 'assembly': 'hg19', 'ID': 'chr21'}
##contig={'length': '27682', 'assembly': 'hg19', 'ID': 'chr21_gl000210_random'}
##contig={'length': '51304566', 'assembly': 'hg19', 'ID': 'chr22'}
##contig={'length': '198022430', 'assembly': 'hg19', 'ID': 'chr3'}
##contig={'length': '191154276', 'assembly': 'hg19', 'ID': 'chr4'}
##contig={'length': '590426', 'assembly': 'hg19', 'ID': 'chr4_ctg9_hap1'}
##contig={'length': '189789', 'assembly': 'hg19', 'ID': 'chr4_gl000193_random'}
##contig={'length': '191469', 'assembly': 'hg19', 'ID': 'chr4_gl000194_random'}
##contig={'length': '180915260', 'assembly': 'hg19', 'ID': 'chr5'}
##contig={'length': '171115067', 'assembly': 'hg19', 'ID': 'chr6'}
##contig={'length': '4622290', 'assembly': 'hg19', 'ID': 'chr6_apd_hap1'}
##contig={'length': '4795371', 'assembly': 'hg19', 'ID': 'chr6_cox_hap2'}
##contig={'length': '4610396', 'assembly': 'hg19', 'ID': 'chr6_dbb_hap3'}
##contig={'length': '4683263', 'assembly': 'hg19', 'ID': 'chr6_mann_hap4'}
##contig={'length': '4833398', 'assembly': 'hg19', 'ID': 'chr6_mcf_hap5'}
##contig={'length': '4611984', 'assembly': 'hg19', 'ID': 'chr6_qbl_hap6'}
##contig={'length': '4928567', 'assembly': 'hg19', 'ID': 'chr6_ssto_hap7'}
##contig={'length': '159138663', 'assembly': 'hg19', 'ID': 'chr7'}
##contig={'length': '182896', 'assembly': 'hg19', 'ID': 'chr7_gl000195_random'}
##contig={'length': '146364022', 'assembly': 'hg19', 'ID': 'chr8'}
##contig={'length': '38914', 'assembly': 'hg19', 'ID': 'chr8_gl000196_random'}
##contig={'length': '37175', 'assembly': 'hg19', 'ID': 'chr8_gl000197_random'}
##contig={'length': '141213431', 'assembly': 'hg19', 'ID': 'chr9'}
##contig={'length': '90085', 'assembly': 'hg19', 'ID': 'chr9_gl000198_random'}
##contig={'length': '169874', 'assembly': 'hg19', 'ID': 'chr9_gl000199_random'}
##contig={'length': '187035', 'assembly': 'hg19', 'ID': 'chr9_gl000200_random'}
##contig={'length': '36148', 'assembly': 'hg19', 'ID': 'chr9_gl000201_random'}
##contig={'length': '16571', 'assembly': 'hg19', 'ID': 'chrM'}
##contig={'length': '166566', 'assembly': 'hg19', 'ID': 'chrUn_gl000211'}
##contig={'length': '186858', 'assembly': 'hg19', 'ID': 'chrUn_gl000212'}
##contig={'length': '164239', 'assembly': 'hg19', 'ID': 'chrUn_gl000213'}
##contig={'length': '137718', 'assembly': 'hg19', 'ID': 'chrUn_gl000214'}
##contig={'length': '172545', 'assembly': 'hg19', 'ID': 'chrUn_gl000215'}
##contig={'length': '172294', 'assembly': 'hg19', 'ID': 'chrUn_gl000216'}
##contig={'length': '172149', 'assembly': 'hg19', 'ID': 'chrUn_gl000217'}
##contig={'length': '161147', 'assembly': 'hg19', 'ID': 'chrUn_gl000218'}
##contig={'length': '179198', 'assembly': 'hg19', 'ID': 'chrUn_gl000219'}
##contig={'length': '161802', 'assembly': 'hg19', 'ID': 'chrUn_gl000220'}
##contig={'length': '155397', 'assembly': 'hg19', 'ID': 'chrUn_gl000221'}
##contig={'length': '186861', 'assembly': 'hg19', 'ID': 'chrUn_gl000222'}
##contig={'length': '180455', 'assembly': 'hg19', 'ID': 'chrUn_gl000223'}
##contig={'length': '179693', 'assembly': 'hg19', 'ID': 'chrUn_gl000224'}
##contig={'length': '211173', 'assembly': 'hg19', 'ID': 'chrUn_gl000225'}
##contig={'length': '15008', 'assembly': 'hg19', 'ID': 'chrUn_gl000226'}
##contig={'length': '128374', 'assembly': 'hg19', 'ID': 'chrUn_gl000227'}
##contig={'length': '129120', 'assembly': 'hg19', 'ID': 'chrUn_gl000228'}
##contig={'length': '19913', 'assembly': 'hg19', 'ID': 'chrUn_gl000229'}
##contig={'length': '43691', 'assembly': 'hg19', 'ID': 'chrUn_gl000230'}
##contig={'length': '27386', 'assembly': 'hg19', 'ID': 'chrUn_gl000231'}
##contig={'length': '40652', 'assembly': 'hg19', 'ID': 'chrUn_gl000232'}
##contig={'length': '45941', 'assembly': 'hg19', 'ID': 'chrUn_gl000233'}
##contig={'length': '40531', 'assembly': 'hg19', 'ID': 'chrUn_gl000234'}
##contig={'length': '34474', 'assembly': 'hg19', 'ID': 'chrUn_gl000235'}
##contig={'length': '41934', 'assembly': 'hg19', 'ID': 'chrUn_gl000236'}
##contig={'length': '45867', 'assembly': 'hg19', 'ID': 'chrUn_gl000237'}
##contig={'length': '39939', 'assembly': 'hg19', 'ID': 'chrUn_gl000238'}
##contig={'length': '33824', 'assembly': 'hg19', 'ID': 'chrUn_gl000239'}
##contig={'length': '41933', 'assembly': 'hg19', 'ID': 'chrUn_gl000240'}
##contig={'length': '42152', 'assembly': 'hg19', 'ID': 'chrUn_gl000241'}
##contig={'length': '43523', 'assembly': 'hg19', 'ID': 'chrUn_gl000242'}
##contig={'length': '43341', 'assembly': 'hg19', 'ID': 'chrUn_gl000243'}
##contig={'length': '39929', 'assembly': 'hg19', 'ID': 'chrUn_gl000244'}
##contig={'length': '36651', 'assembly': 'hg19', 'ID': 'chrUn_gl000245'}
##contig={'length': '38154', 'assembly': 'hg19', 'ID': 'chrUn_gl000246'}
##contig={'length': '36422', 'assembly': 'hg19', 'ID': 'chrUn_gl000247'}
##contig={'length': '39786', 'assembly': 'hg19', 'ID': 'chrUn_gl000248'}
##contig={'length': '38502', 'assembly': 'hg19', 'ID': 'chrUn_gl000249'}
##contig={'length': '155270560', 'assembly': 'hg19', 'ID': 'chrX'}
##contig={'length': '59373566', 'assembly': 'hg19', 'ID': 'chrY'}
##reference=file:///data/reference/ucsc/hg19/ucsc.hg19.fasta
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA19239
chr1	65312657	.	G	.	.	.	.	GT	./.

ok
test_vcf_4_0 (vcf.test.test_vcf.TestVcfSpecs) ... ok
test_vcf_4_1 (vcf.test.test_vcf.TestVcfSpecs) ... ok
test_vcf_4_1_bnd (vcf.test.test_vcf.TestVcfSpecs) ... Record(CHROM=1, POS=2, REF=A, ALT=[T])
Call(sample=Germline, GT=0|1, HAP=[35, 46], MQ=['0', '40'])
Call(sample=Tumor, GT=0|1, HAP=[35, 46], MQ=['0', '0'])
Record(CHROM=1, POS=2, REF=T, ALT=[<vcf.parser._Breakend object at 0x1012e9f50>])
Call(sample=Germline, GT=0|0, MQ=['0', '0'], BHAP=['35>35', '46>46'])
Call(sample=Tumor, GT=0|1, MQ=['0', '40'], BHAP=['35>35', '46>17'])
Record(CHROM=1, POS=3, REF=A, ALT=[<vcf.parser._Breakend object at 0x1012e9510>])
Call(sample=Germline, GT=0|0, MQ=['0', '0'], BHAP=['35>35', '46>46'])
Call(sample=Tumor, GT=0|1, MQ=['0', '40'], BHAP=['35>35', '46>17'])
Record(CHROM=2, POS=1, REF=G, ALT=[T])
Call(sample=Germline, GT=1|0, HAP=[17, 23], MQ=['0', '40'])
Call(sample=Tumor, GT=1|0, HAP=[17, 23], MQ=['0', '0'])
Record(CHROM=2, POS=2, REF=G, ALT=[<vcf.parser._Breakend object at 0x102334f10>])
Call(sample=Germline, GT=0|0, BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|1, BCN=['2', '1'], MQ=['0', '40'], BHAP=['23>23', '17>46'])
Record(CHROM=2, POS=3, REF=G, ALT=[<vcf.parser._Breakend object at 0x102334f90>])
Call(sample=Germline, GT=0|0, BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|1, BCN=['2', '1'], MQ=['0', '40'], BHAP=['23>23', '17>46'])
Record(CHROM=2, POS=4, REF=G, ALT=[<vcf.parser._Breakend object at 0x102334d10>])
Call(sample=Germline, GT=0|0, AHAP=[17, 23], BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|0|1, AHAP=[17, 23, 23], BCN=['1', '2', '2'], MQ=['0', '0', '40'], BHAP=['17>17', '23>23', '24>23'])
Record(CHROM=2, POS=6, REF=T, ALT=[<vcf.parser._Breakend object at 0x102334d50>])
Call(sample=Germline, GT=0|0, AHAP=[17, 23], BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|1|0, AHAP=[17, 23, 23], BCN=['1', '2', '2'], MQ=['0', '40', '0'], BHAP=['17>17', '23>24', '24>24'])
Record(CHROM=2, POS=6, REF=T, ALT=[A])
Call(sample=Germline, GT=0|1, HAP=[23, 17], AHAP=[23, 17], MQ=['0', '40'])
Call(sample=Tumor, GT=0|1|1, HAP=[17, 23, 24], AHAP=[17, 23, 23], MQ=['0', '0', '0'])
Record(CHROM=2, POS=8, REF=T, ALT=[A])
Call(sample=Germline, GT=0|0, HAP=[23, 17], AHAP=[23, 17], MQ=['0', '0'])
Call(sample=Tumor, GT=0|1|1, HAP=[17, 23, 24], AHAP=[17, 23, 23], MQ=['0', '40', '40'])
ok
test_vcf_4_1_sv (vcf.test.test_vcf.TestVcfSpecs) ... Record(CHROM=1, POS=2827693, REF=CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA, ALT=[C])
Call(sample=NA00001, GT=1/1, GQ=13.9)
Record(CHROM=2, POS=321682, REF=T, ALT=[<DEL>])
Call(sample=NA00001, GT=0/1, GQ=12.0)
Record(CHROM=2, POS=14477084, REF=C, ALT=[<DEL:ME:ALU>])
Call(sample=NA00001, GT=0/1, GQ=12.0)
Record(CHROM=3, POS=9425916, REF=C, ALT=[<INS:ME:L1>])
Call(sample=NA00001, GT=1/1, GQ=15.0)
Record(CHROM=3, POS=12665100, REF=A, ALT=[<DUP>])
Call(sample=NA00001, GT=None, CN=3, GQ=0.0, CNQ=16.2)
Record(CHROM=4, POS=18665128, REF=T, ALT=[<DUP:TANDEM>])
Call(sample=NA00001, GT=None, CN=5, GQ=0.0, CNQ=8.3)
ok

----------------------------------------------------------------------
Ran 45 tests in 8.240s

OK
py27 sdist-reinst: /Users/marca/dev/git-repos/PyVCF/.tox/dist/PyVCF-0.5.0-pre.zip
py27 runtests: commands[0]
running test
running build_py
running egg_info
writing requirements to PyVCF.egg-info/requires.txt
writing PyVCF.egg-info/PKG-INFO
writing top-level names to PyVCF.egg-info/top_level.txt
writing dependency_links to PyVCF.egg-info/dependency_links.txt
writing entry points to PyVCF.egg-info/entry_points.txt
reading manifest file 'PyVCF.egg-info/SOURCES.txt'
writing manifest file 'PyVCF.egg-info/SOURCES.txt'
running egg_info
writing requirements to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/requires.txt
writing /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/PKG-INFO
writing top-level names to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/top_level.txt
writing dependency_links to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/dependency_links.txt
writing entry points to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/entry_points.txt
reading manifest file '/Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/SOURCES.txt'
writing manifest file '/Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/SOURCES.txt'
running build_ext
/Users/marca/dev/git-repos/PyVCF/.tox/py27/lib/python2.7/site-packages/distribute-0.6.27-py2.7.egg/setuptools/command/test.py:115: UserWarning: Module argparse was already imported from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/argparse.pyc, but /Users/marca/dev/git-repos/PyVCF/.tox/py27/lib/python2.7/site-packages is being added to sys.path
  add_activation_listener(lambda dist: dist.activate())
vcf ()
Doctest: vcf ... ok
testCalls (vcf.test.test_vcf.TestGatkOutput) ... ok
testFormats (vcf.test.test_vcf.TestGatkOutput) ... ok
testInfos (vcf.test.test_vcf.TestGatkOutput) ... ok
testSamples (vcf.test.test_vcf.TestGatkOutput) ... ok
testCalls (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testFormats (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testInfos (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testParse (vcf.test.test_vcf.TestFreebayesOutput) ... ['BLANK', 'NA12878', 'NA12891', 'NA12892', 'NA19238', 'NA19239', 'NA19240']
ok
testSamples (vcf.test.test_vcf.TestFreebayesOutput) ... ok
testParse (vcf.test.test_vcf.TestSamtoolsOutput) ... ok
testWrite (vcf.test.test_vcf.TestWriter) ... ok
testFetchRange (vcf.test.test_vcf.TestTabix) ... ok
testFetchSite (vcf.test.test_vcf.TestTabix) ... ok
testOpenFilehandle (vcf.test.test_vcf.TestOpenMethods) ... ok
testOpenFilehandleGzipped (vcf.test.test_vcf.TestOpenMethods) ... ok
testOpenFilename (vcf.test.test_vcf.TestOpenMethods) ... ok
testOpenFilenameGzipped (vcf.test.test_vcf.TestOpenMethods) ... ok
testApplyFilter (vcf.test.test_vcf.TestFilter) ... ok
testApplyMultipleFilters (vcf.test.test_vcf.TestFilter) ... ok
testParse (vcf.test.test_vcf.Test1kg) ... ok
test_issue_49 (vcf.test.test_vcf.Test1kg)
docstring for test_issue_49 ... ok
test_aaf (vcf.test.test_vcf.TestRecord) ... ok
test_call_rate (vcf.test.test_vcf.TestRecord) ... ok
test_is_deletion (vcf.test.test_vcf.TestRecord) ... ok
test_is_indel (vcf.test.test_vcf.TestRecord) ... ok
test_is_snp (vcf.test.test_vcf.TestRecord) ... Record(CHROM=20, POS=14370, REF=G, ALT=[A])
Call(sample=NA00001, GT=0|0, HQ=[51, 51], DP=1, GQ=48)
Call(sample=NA00002, GT=1|0, HQ=[51, 51], DP=8, GQ=48)
Call(sample=NA00003, GT=1/1, HQ=[None, None], DP=5, GQ=43)
Record(CHROM=20, POS=17330, REF=T, ALT=[A])
Call(sample=NA00001, GT=0|0, HQ=[58, 50], DP=3, GQ=49)
Call(sample=NA00002, GT=0|1, HQ=[65, 3], DP=5, GQ=3)
Call(sample=NA00003, GT=0/0, HQ=None, DP=3, GQ=41)
Record(CHROM=20, POS=1110696, REF=A, ALT=[G, T])
Call(sample=NA00001, GT=1|2, HQ=[23, 27], DP=6, GQ=21)
Call(sample=NA00002, GT=2|1, HQ=[18, 2], DP=0, GQ=2)
Call(sample=NA00003, GT=2/2, HQ=None, DP=4, GQ=35)
Record(CHROM=20, POS=1230237, REF=T, ALT=[None])
Call(sample=NA00001, GT=0|0, HQ=[56, 60], DP=7, GQ=54)
Call(sample=NA00002, GT=0|0, HQ=[51, 51], DP=4, GQ=48)
Call(sample=NA00003, GT=0/0, HQ=None, DP=2, GQ=61)
Record(CHROM=20, POS=1234567, REF=GTCT, ALT=[G, GTACT])
Call(sample=NA00001, GT=None, DP=4, GQ=35)
Call(sample=NA00002, GT=0/2, DP=2, GQ=17)
Call(sample=NA00003, GT=1/1, DP=3, GQ=40)
ok
test_is_sv (vcf.test.test_vcf.TestRecord) ... ok
test_is_sv_precise (vcf.test.test_vcf.TestRecord) ... ok
test_is_transition (vcf.test.test_vcf.TestRecord) ... ok
test_num_calls (vcf.test.test_vcf.TestRecord) ... ok
test_pi (vcf.test.test_vcf.TestRecord) ... ok
test_qual (vcf.test.test_vcf.TestRecord) ... ok
test_sv_end (vcf.test.test_vcf.TestRecord) ... ok
test_var_subtype (vcf.test.test_vcf.TestRecord) ... ok
test_var_type (vcf.test.test_vcf.TestRecord) ... ok
test_gt_bases (vcf.test.test_vcf.TestCall) ... ok
test_gt_types (vcf.test.test_vcf.TestCall) ... {'GT': '0|0', 'HQ': [51, 51], 'DP': 1, 'GQ': 48}
{'GT': '1|0', 'HQ': [51, 51], 'DP': 8, 'GQ': 48}
{'GT': '1/1', 'HQ': [None, None], 'DP': 5, 'GQ': 43}
{'GT': '0|0', 'HQ': [58, 50], 'DP': 3, 'GQ': 49}
{'GT': '0|1', 'HQ': [65, 3], 'DP': 5, 'GQ': 3}
{'GT': '0/0', 'HQ': None, 'DP': 3, 'GQ': 41}
{'GT': '1|2', 'HQ': [23, 27], 'DP': 6, 'GQ': 21}
{'GT': '2|1', 'HQ': [18, 2], 'DP': 0, 'GQ': 2}
{'GT': '2/2', 'HQ': None, 'DP': 4, 'GQ': 35}
{'GT': '0|0', 'HQ': [56, 60], 'DP': 7, 'GQ': 54}
{'GT': '0|0', 'HQ': [51, 51], 'DP': 4, 'GQ': 48}
{'GT': '0/0', 'HQ': None, 'DP': 2, 'GQ': 61}
{'GT': None, 'DP': 4, 'GQ': 35}
{'GT': '0/2', 'DP': 2, 'GQ': 17}
{'GT': '1/1', 'DP': 3, 'GQ': 40}
ok
test_phased (vcf.test.test_vcf.TestCall) ... ok
test_issue_16 (vcf.test.test_vcf.TestRegression) ... ok
test_null_mono (vcf.test.test_vcf.TestRegression) ... /Users/marca/dev/git-repos/PyVCF/build/lib/vcf/test/null_genotype_mono.vcf
##fileformat=VCFv4.1
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[np_control.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[tests/read_chr.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/data/reference/ucsc/hg19/ucsc.hg19.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=info log_to_file=null help=false genotype_likelihoods_model=SNP p_nonref_model=EXACT heterozygosity=0.001 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig={'length': '249250621', 'assembly': 'hg19', 'ID': 'chr1'}
##contig={'length': '135534747', 'assembly': 'hg19', 'ID': 'chr10'}
##contig={'length': '135006516', 'assembly': 'hg19', 'ID': 'chr11'}
##contig={'length': '40103', 'assembly': 'hg19', 'ID': 'chr11_gl000202_random'}
##contig={'length': '133851895', 'assembly': 'hg19', 'ID': 'chr12'}
##contig={'length': '115169878', 'assembly': 'hg19', 'ID': 'chr13'}
##contig={'length': '107349540', 'assembly': 'hg19', 'ID': 'chr14'}
##contig={'length': '102531392', 'assembly': 'hg19', 'ID': 'chr15'}
##contig={'length': '90354753', 'assembly': 'hg19', 'ID': 'chr16'}
##contig={'length': '81195210', 'assembly': 'hg19', 'ID': 'chr17'}
##contig={'length': '1680828', 'assembly': 'hg19', 'ID': 'chr17_ctg5_hap1'}
##contig={'length': '37498', 'assembly': 'hg19', 'ID': 'chr17_gl000203_random'}
##contig={'length': '81310', 'assembly': 'hg19', 'ID': 'chr17_gl000204_random'}
##contig={'length': '174588', 'assembly': 'hg19', 'ID': 'chr17_gl000205_random'}
##contig={'length': '41001', 'assembly': 'hg19', 'ID': 'chr17_gl000206_random'}
##contig={'length': '78077248', 'assembly': 'hg19', 'ID': 'chr18'}
##contig={'length': '4262', 'assembly': 'hg19', 'ID': 'chr18_gl000207_random'}
##contig={'length': '59128983', 'assembly': 'hg19', 'ID': 'chr19'}
##contig={'length': '92689', 'assembly': 'hg19', 'ID': 'chr19_gl000208_random'}
##contig={'length': '159169', 'assembly': 'hg19', 'ID': 'chr19_gl000209_random'}
##contig={'length': '106433', 'assembly': 'hg19', 'ID': 'chr1_gl000191_random'}
##contig={'length': '547496', 'assembly': 'hg19', 'ID': 'chr1_gl000192_random'}
##contig={'length': '243199373', 'assembly': 'hg19', 'ID': 'chr2'}
##contig={'length': '63025520', 'assembly': 'hg19', 'ID': 'chr20'}
##contig={'length': '48129895', 'assembly': 'hg19', 'ID': 'chr21'}
##contig={'length': '27682', 'assembly': 'hg19', 'ID': 'chr21_gl000210_random'}
##contig={'length': '51304566', 'assembly': 'hg19', 'ID': 'chr22'}
##contig={'length': '198022430', 'assembly': 'hg19', 'ID': 'chr3'}
##contig={'length': '191154276', 'assembly': 'hg19', 'ID': 'chr4'}
##contig={'length': '590426', 'assembly': 'hg19', 'ID': 'chr4_ctg9_hap1'}
##contig={'length': '189789', 'assembly': 'hg19', 'ID': 'chr4_gl000193_random'}
##contig={'length': '191469', 'assembly': 'hg19', 'ID': 'chr4_gl000194_random'}
##contig={'length': '180915260', 'assembly': 'hg19', 'ID': 'chr5'}
##contig={'length': '171115067', 'assembly': 'hg19', 'ID': 'chr6'}
##contig={'length': '4622290', 'assembly': 'hg19', 'ID': 'chr6_apd_hap1'}
##contig={'length': '4795371', 'assembly': 'hg19', 'ID': 'chr6_cox_hap2'}
##contig={'length': '4610396', 'assembly': 'hg19', 'ID': 'chr6_dbb_hap3'}
##contig={'length': '4683263', 'assembly': 'hg19', 'ID': 'chr6_mann_hap4'}
##contig={'length': '4833398', 'assembly': 'hg19', 'ID': 'chr6_mcf_hap5'}
##contig={'length': '4611984', 'assembly': 'hg19', 'ID': 'chr6_qbl_hap6'}
##contig={'length': '4928567', 'assembly': 'hg19', 'ID': 'chr6_ssto_hap7'}
##contig={'length': '159138663', 'assembly': 'hg19', 'ID': 'chr7'}
##contig={'length': '182896', 'assembly': 'hg19', 'ID': 'chr7_gl000195_random'}
##contig={'length': '146364022', 'assembly': 'hg19', 'ID': 'chr8'}
##contig={'length': '38914', 'assembly': 'hg19', 'ID': 'chr8_gl000196_random'}
##contig={'length': '37175', 'assembly': 'hg19', 'ID': 'chr8_gl000197_random'}
##contig={'length': '141213431', 'assembly': 'hg19', 'ID': 'chr9'}
##contig={'length': '90085', 'assembly': 'hg19', 'ID': 'chr9_gl000198_random'}
##contig={'length': '169874', 'assembly': 'hg19', 'ID': 'chr9_gl000199_random'}
##contig={'length': '187035', 'assembly': 'hg19', 'ID': 'chr9_gl000200_random'}
##contig={'length': '36148', 'assembly': 'hg19', 'ID': 'chr9_gl000201_random'}
##contig={'length': '16571', 'assembly': 'hg19', 'ID': 'chrM'}
##contig={'length': '166566', 'assembly': 'hg19', 'ID': 'chrUn_gl000211'}
##contig={'length': '186858', 'assembly': 'hg19', 'ID': 'chrUn_gl000212'}
##contig={'length': '164239', 'assembly': 'hg19', 'ID': 'chrUn_gl000213'}
##contig={'length': '137718', 'assembly': 'hg19', 'ID': 'chrUn_gl000214'}
##contig={'length': '172545', 'assembly': 'hg19', 'ID': 'chrUn_gl000215'}
##contig={'length': '172294', 'assembly': 'hg19', 'ID': 'chrUn_gl000216'}
##contig={'length': '172149', 'assembly': 'hg19', 'ID': 'chrUn_gl000217'}
##contig={'length': '161147', 'assembly': 'hg19', 'ID': 'chrUn_gl000218'}
##contig={'length': '179198', 'assembly': 'hg19', 'ID': 'chrUn_gl000219'}
##contig={'length': '161802', 'assembly': 'hg19', 'ID': 'chrUn_gl000220'}
##contig={'length': '155397', 'assembly': 'hg19', 'ID': 'chrUn_gl000221'}
##contig={'length': '186861', 'assembly': 'hg19', 'ID': 'chrUn_gl000222'}
##contig={'length': '180455', 'assembly': 'hg19', 'ID': 'chrUn_gl000223'}
##contig={'length': '179693', 'assembly': 'hg19', 'ID': 'chrUn_gl000224'}
##contig={'length': '211173', 'assembly': 'hg19', 'ID': 'chrUn_gl000225'}
##contig={'length': '15008', 'assembly': 'hg19', 'ID': 'chrUn_gl000226'}
##contig={'length': '128374', 'assembly': 'hg19', 'ID': 'chrUn_gl000227'}
##contig={'length': '129120', 'assembly': 'hg19', 'ID': 'chrUn_gl000228'}
##contig={'length': '19913', 'assembly': 'hg19', 'ID': 'chrUn_gl000229'}
##contig={'length': '43691', 'assembly': 'hg19', 'ID': 'chrUn_gl000230'}
##contig={'length': '27386', 'assembly': 'hg19', 'ID': 'chrUn_gl000231'}
##contig={'length': '40652', 'assembly': 'hg19', 'ID': 'chrUn_gl000232'}
##contig={'length': '45941', 'assembly': 'hg19', 'ID': 'chrUn_gl000233'}
##contig={'length': '40531', 'assembly': 'hg19', 'ID': 'chrUn_gl000234'}
##contig={'length': '34474', 'assembly': 'hg19', 'ID': 'chrUn_gl000235'}
##contig={'length': '41934', 'assembly': 'hg19', 'ID': 'chrUn_gl000236'}
##contig={'length': '45867', 'assembly': 'hg19', 'ID': 'chrUn_gl000237'}
##contig={'length': '39939', 'assembly': 'hg19', 'ID': 'chrUn_gl000238'}
##contig={'length': '33824', 'assembly': 'hg19', 'ID': 'chrUn_gl000239'}
##contig={'length': '41933', 'assembly': 'hg19', 'ID': 'chrUn_gl000240'}
##contig={'length': '42152', 'assembly': 'hg19', 'ID': 'chrUn_gl000241'}
##contig={'length': '43523', 'assembly': 'hg19', 'ID': 'chrUn_gl000242'}
##contig={'length': '43341', 'assembly': 'hg19', 'ID': 'chrUn_gl000243'}
##contig={'length': '39929', 'assembly': 'hg19', 'ID': 'chrUn_gl000244'}
##contig={'length': '36651', 'assembly': 'hg19', 'ID': 'chrUn_gl000245'}
##contig={'length': '38154', 'assembly': 'hg19', 'ID': 'chrUn_gl000246'}
##contig={'length': '36422', 'assembly': 'hg19', 'ID': 'chrUn_gl000247'}
##contig={'length': '39786', 'assembly': 'hg19', 'ID': 'chrUn_gl000248'}
##contig={'length': '38502', 'assembly': 'hg19', 'ID': 'chrUn_gl000249'}
##contig={'length': '155270560', 'assembly': 'hg19', 'ID': 'chrX'}
##contig={'length': '59373566', 'assembly': 'hg19', 'ID': 'chrY'}
##reference=file:///data/reference/ucsc/hg19/ucsc.hg19.fasta
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA19239
chr1	65312657	.	G	.	.	.	.	GT	./.

ok
test_vcf_4_0 (vcf.test.test_vcf.TestVcfSpecs) ... ok
test_vcf_4_1 (vcf.test.test_vcf.TestVcfSpecs) ... ok
test_vcf_4_1_bnd (vcf.test.test_vcf.TestVcfSpecs) ... Record(CHROM=1, POS=2, REF=A, ALT=[T])
Call(sample=Germline, GT=0|1, HAP=[35, 46], MQ=['0', '40'])
Call(sample=Tumor, GT=0|1, HAP=[35, 46], MQ=['0', '0'])
Record(CHROM=1, POS=2, REF=T, ALT=[<vcf.parser._Breakend object at 0x10139b850>])
Call(sample=Germline, GT=0|0, MQ=['0', '0'], BHAP=['35>35', '46>46'])
Call(sample=Tumor, GT=0|1, MQ=['0', '40'], BHAP=['35>35', '46>17'])
Record(CHROM=1, POS=3, REF=A, ALT=[<vcf.parser._Breakend object at 0x10139b8d0>])
Call(sample=Germline, GT=0|0, MQ=['0', '0'], BHAP=['35>35', '46>46'])
Call(sample=Tumor, GT=0|1, MQ=['0', '40'], BHAP=['35>35', '46>17'])
Record(CHROM=2, POS=1, REF=G, ALT=[T])
Call(sample=Germline, GT=1|0, HAP=[17, 23], MQ=['0', '40'])
Call(sample=Tumor, GT=1|0, HAP=[17, 23], MQ=['0', '0'])
Record(CHROM=2, POS=2, REF=G, ALT=[<vcf.parser._Breakend object at 0x10139b710>])
Call(sample=Germline, GT=0|0, BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|1, BCN=['2', '1'], MQ=['0', '40'], BHAP=['23>23', '17>46'])
Record(CHROM=2, POS=3, REF=G, ALT=[<vcf.parser._Breakend object at 0x10139bf10>])
Call(sample=Germline, GT=0|0, BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|1, BCN=['2', '1'], MQ=['0', '40'], BHAP=['23>23', '17>46'])
Record(CHROM=2, POS=4, REF=G, ALT=[<vcf.parser._Breakend object at 0x10139b810>])
Call(sample=Germline, GT=0|0, AHAP=[17, 23], BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|0|1, AHAP=[17, 23, 23], BCN=['1', '2', '2'], MQ=['0', '0', '40'], BHAP=['17>17', '23>23', '24>23'])
Record(CHROM=2, POS=6, REF=T, ALT=[<vcf.parser._Breakend object at 0x101368a90>])
Call(sample=Germline, GT=0|0, AHAP=[17, 23], BCN=['1', '1'], MQ=['0', '0'], BHAP=['17>17', '23>23'])
Call(sample=Tumor, GT=0|1|0, AHAP=[17, 23, 23], BCN=['1', '2', '2'], MQ=['0', '40', '0'], BHAP=['17>17', '23>24', '24>24'])
Record(CHROM=2, POS=6, REF=T, ALT=[A])
Call(sample=Germline, GT=0|1, HAP=[23, 17], AHAP=[23, 17], MQ=['0', '40'])
Call(sample=Tumor, GT=0|1|1, HAP=[17, 23, 24], AHAP=[17, 23, 23], MQ=['0', '0', '0'])
Record(CHROM=2, POS=8, REF=T, ALT=[A])
Call(sample=Germline, GT=0|0, HAP=[23, 17], AHAP=[23, 17], MQ=['0', '0'])
Call(sample=Tumor, GT=0|1|1, HAP=[17, 23, 24], AHAP=[17, 23, 23], MQ=['0', '40', '40'])
ok
test_vcf_4_1_sv (vcf.test.test_vcf.TestVcfSpecs) ... Record(CHROM=1, POS=2827693, REF=CCGTGGATGCGGGGACCCGCATCCCCTCTCCCTTCACAGCTGAGTGACCCACATCCCCTCTCCCCTCGCA, ALT=[C])
Call(sample=NA00001, GT=1/1, GQ=13.9)
Record(CHROM=2, POS=321682, REF=T, ALT=[<DEL>])
Call(sample=NA00001, GT=0/1, GQ=12.0)
Record(CHROM=2, POS=14477084, REF=C, ALT=[<DEL:ME:ALU>])
Call(sample=NA00001, GT=0/1, GQ=12.0)
Record(CHROM=3, POS=9425916, REF=C, ALT=[<INS:ME:L1>])
Call(sample=NA00001, GT=1/1, GQ=15.0)
Record(CHROM=3, POS=12665100, REF=A, ALT=[<DUP>])
Call(sample=NA00001, GT=None, CN=3, GQ=0.0, CNQ=16.2)
Record(CHROM=4, POS=18665128, REF=T, ALT=[<DUP:TANDEM>])
Call(sample=NA00001, GT=None, CN=5, GQ=0.0, CNQ=8.3)
ok

----------------------------------------------------------------------
Ran 45 tests in 7.879s

OK
py32 sdist-reinst: /Users/marca/dev/git-repos/PyVCF/.tox/dist/PyVCF-0.5.0-pre.zip
py32 runtests: commands[0]
running test
running build_py
running egg_info
writing requirements to PyVCF.egg-info/requires.txt
writing PyVCF.egg-info/PKG-INFO
writing top-level names to PyVCF.egg-info/top_level.txt
writing dependency_links to PyVCF.egg-info/dependency_links.txt
writing entry points to PyVCF.egg-info/entry_points.txt
reading manifest file 'PyVCF.egg-info/SOURCES.txt'
writing manifest file 'PyVCF.egg-info/SOURCES.txt'
running egg_info
writing requirements to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/requires.txt
writing /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/PKG-INFO
writing top-level names to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/top_level.txt
writing dependency_links to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/dependency_links.txt
writing entry points to /Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/entry_points.txt
reading manifest file '/Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/SOURCES.txt'
writing manifest file '/Users/marca/dev/git-repos/PyVCF/build/lib/PyVCF.egg-info/SOURCES.txt'
running build_ext
/Users/marca/dev/git-repos/PyVCF/.tox/py32/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/test.py:115: UserWarning: Module argparse was already imported from /Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/argparse.py, but /Users/marca/dev/git-repos/PyVCF/.tox/py32/lib/python3.2/site-packages is being added to sys.path
  add_activation_listener(lambda dist: dist.activate())
Traceback (most recent call last):
  File "setup.py", line 65, in <module>
    '': ['*.vcf', '*.gz', '*.tbi'],
  File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 917, in run_commands
    self.run_command(cmd)
  File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 936, in run_command
    cmd_obj.run()
  File "/Users/marca/dev/git-repos/PyVCF/.tox/py32/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/test.py", line 137, in run
    self.with_project_on_sys_path(self.run_tests)
  File "/Users/marca/dev/git-repos/PyVCF/.tox/py32/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/test.py", line 117, in with_project_on_sys_path
    func()
  File "/Users/marca/dev/git-repos/PyVCF/.tox/py32/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/test.py", line 146, in run_tests
    testLoader = loader_class()
  File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/unittest/main.py", line 123, in __init__
    self.parseArgs(argv)
  File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/unittest/main.py", line 191, in parseArgs
    self.createTests()
  File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/unittest/main.py", line 198, in createTests
    self.module)
  File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/unittest/loader.py", line 132, in loadTestsFromNames
    suites = [self.loadTestsFromName(name, module) for name in names]
  File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/unittest/loader.py", line 132, in <listcomp>
    suites = [self.loadTestsFromName(name, module) for name in names]
  File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/unittest/loader.py", line 91, in loadTestsFromName
    module = __import__('.'.join(parts_copy))
  File "/Users/marca/dev/git-repos/PyVCF/build/lib/vcf/__init__.py", line 166, in <module>
    from parser import Reader, Writer
ImportError: cannot import name Reader
ERROR: InvocationError: '/Users/marca/dev/git-repos/PyVCF/.tox/py32/bin/python setup.py test'
_________________________________________________________________________ summary __________________________________________________________________________
  py26: commands succeeded
  py27: commands succeeded
ERROR:   py32: commands failed
```