├── .circleci ├── Dockerfile ├── README.md ├── config.yml └── pdf_comment.js ├── .gitattributes ├── .github ├── actions │ └── texlive │ │ ├── action.yaml │ │ └── run.sh └── workflows │ ├── README.md │ ├── pr-comment.yaml │ ├── pr-pdfs-close.yaml │ └── pr-pdfs.yaml ├── .gitignore ├── BCFv1_qref.pdf ├── BCFv1_qref.tex ├── BCFv2_qref.pdf ├── BCFv2_qref.tex ├── BEDv1.pdf ├── BEDv1.tex ├── CRAMcodecs.pdf ├── CRAMcodecs.tex ├── CRAMv2.1.pdf ├── CRAMv2.1.tex ├── CRAMv3.pdf ├── CRAMv3.tex ├── CSIv1.pdf ├── CSIv1.tex ├── MAINTAINERS.md ├── Makefile ├── README.md ├── SAMtags.pdf ├── SAMtags.tex ├── SAMv1.pdf ├── SAMv1.tex ├── VCFv4.1.pdf ├── VCFv4.1.tex ├── VCFv4.2.pdf ├── VCFv4.2.tex ├── VCFv4.3.pdf ├── VCFv4.3.tex ├── VCFv4.4.pdf ├── VCFv4.4.tex ├── VCFv4.5.pdf ├── VCFv4.5.tex ├── _config.yml ├── _includes ├── footer.html ├── head.html ├── icon-github.html └── icon-github.svg ├── _layouts └── default.html ├── crypt4gh.pdf ├── crypt4gh.tex ├── examples └── vcf │ ├── index.md │ ├── simple.vcf │ └── sv44.vcf ├── htsget.md ├── img ├── CRAMFileFormat2-1-fig001.png ├── CRAMFileFormat2-1-fig002.png ├── CRAMFileFormat2-1-fig003.png ├── CRAMFileFormat2-1-fig004.png ├── CRAMFileFormat2-1-fig005.png ├── CRAMFileFormat2-1-fig006.png ├── CRAMFileFormat2-1-fig007.png ├── all_orientations-400x296.png ├── derivation-400x267.png ├── erosion-400x211.png ├── inserted_contig-400x247.png ├── inserted_sequence-400x189.png ├── inversion-400x95.png ├── microhomology-400x248.png ├── multiple_mates-400x280.png ├── phasing-400x259.png ├── range_code.png ├── reciprocal_rearrangement-400x192.png ├── tandem_repeat_notation.png └── telomere-400x251.png ├── index.md ├── pub ├── ga4gh_and_TRUNC512_identifiers.ipynb ├── ga4gh_and_TRUNC512_identifiers.pl ├── htsget-openapi.yaml ├── htsget-ticket.png ├── main.css └── refget-openapi.yaml ├── refget.md ├── scripts ├── genversion.sh └── rerun.sh ├── tabix.pdf ├── tabix.tex └── test ├── SAMtags ├── LICENSE ├── MM-chebi.sam ├── MM-chebi.txt ├── MM-double.sam ├── MM-double.txt ├── MM-explicit.sam ├── MM-explicit.txt ├── MM-multi.sam ├── MM-multi.txt ├── MM-orient.sam ├── MM-orient.txt ├── README.md └── parse_mm.pl ├── bam ├── LICENSE └── passed │ ├── level-1.bam │ └── level-9.bam ├── cram ├── 3.0 │ ├── LICENSE │ ├── README.md │ ├── failed │ │ ├── 0000_empty_noeof.cram │ │ └── 0000_empty_noeof.sam │ └── passed │ │ ├── 0001_empty_eof.cram │ │ ├── 0001_empty_eof.sam │ │ ├── 0100_header1.cram │ │ ├── 0100_header1.sam │ │ ├── 0101_header2.cram │ │ ├── 0101_header2.sam │ │ ├── 0200_cmpr_hdr.cram │ │ ├── 0200_cmpr_hdr.sam │ │ ├── 0300_unmapped.cram │ │ ├── 0300_unmapped.sam │ │ ├── 0301_unmapped.cram │ │ ├── 0301_unmapped.sam │ │ ├── 0302_unmapped.cram │ │ ├── 0302_unmapped.sam │ │ ├── 0303_unmapped.cram │ │ ├── 0303_unmapped.sam │ │ ├── 0400_mapped.cram │ │ ├── 0400_mapped.sam │ │ ├── 0401_mapped.cram │ │ ├── 0401_mapped.sam │ │ ├── 0402_mapped.cram │ │ ├── 0402_mapped.sam │ │ ├── 0403_mapped.cram │ │ ├── 0403_mapped.sam │ │ ├── 0500_mapped.cram │ │ ├── 0500_mapped.sam │ │ ├── 0501_mapped.cram │ │ ├── 0501_mapped.sam │ │ ├── 0502_mapped.cram │ │ ├── 0502_mapped.sam │ │ ├── 0503_mapped.cram │ │ ├── 0503_mapped.sam │ │ ├── 0504_mapped.cram │ │ ├── 0504_mapped.sam │ │ ├── 0505_mapped.cram │ │ ├── 0505_mapped.sam │ │ ├── 0506_mapped.cram │ │ ├── 0506_mapped.sam │ │ ├── 0507_mapped.cram │ │ ├── 0507_mapped.sam │ │ ├── 0600_mapped.cram │ │ ├── 0600_mapped.sam │ │ ├── 0601_mapped.cram │ │ ├── 0601_mapped.sam │ │ ├── 0700_tag.cram │ │ ├── 0700_tag.sam │ │ ├── 0701_tag.cram │ │ ├── 0701_tag.sam │ │ ├── 0702_tag.cram │ │ ├── 0702_tag.sam │ │ ├── 0703_tag.cram │ │ ├── 0703_tag.sam │ │ ├── 0704_tag.cram │ │ ├── 0704_tag.sam │ │ ├── 0705_tag.cram │ │ ├── 0705_tag.sam │ │ ├── 0706_tag.cram │ │ ├── 0706_tag.sam │ │ ├── 0707_tag.cram │ │ ├── 0707_tag.sam │ │ ├── 0708_tag.cram │ │ ├── 0708_tag.sam │ │ ├── 0709_tag.cram │ │ ├── 0709_tag.sam │ │ ├── 0710_tag.cram │ │ ├── 0710_tag.sam │ │ ├── 0800_ctr.cram │ │ ├── 0800_ctr.sam │ │ ├── 0801_ctr.cram │ │ ├── 0801_ctr.sam │ │ ├── 0802_ctr.cram │ │ ├── 0802_ctr.sam │ │ ├── 0900_comp_raw.cram │ │ ├── 0900_comp_raw.sam │ │ ├── 0901_comp_gz.cram │ │ ├── 0901_comp_gz.sam │ │ ├── 0902_comp_bz2.cram │ │ ├── 0902_comp_bz2.sam │ │ ├── 0903_comp_lzma.cram │ │ ├── 0903_comp_lzma.sam │ │ ├── 0904_comp_rans0.cram │ │ ├── 0904_comp_rans0.sam │ │ ├── 0905_comp_rans1.cram │ │ ├── 0905_comp_rans1.sam │ │ ├── 1000_name.cram │ │ ├── 1000_name.sam │ │ ├── 1001_name.cram │ │ ├── 1001_name.sam │ │ ├── 1002_qual.cram │ │ ├── 1002_qual.sam │ │ ├── 1003_qual.cram │ │ ├── 1003_qual.sam │ │ ├── 1004_qual.cram │ │ ├── 1004_qual.sam │ │ ├── 1005_qual.cram │ │ ├── 1005_qual.sam │ │ ├── 1006_seq.cram │ │ ├── 1006_seq.sam │ │ ├── 1007_seq.cram │ │ ├── 1007_seq.sam │ │ ├── 1100_HUFFMAN.cram │ │ ├── 1100_HUFFMAN.sam │ │ ├── 1101_BETA.cram │ │ ├── 1101_BETA.sam │ │ ├── 1200_overflow.cram │ │ ├── 1200_overflow.sam │ │ ├── 1300_slice_aux.cram │ │ ├── 1300_slice_aux.sam │ │ ├── 1301_slice_aux.cram │ │ ├── 1301_slice_aux.sam │ │ ├── 1400_index_simple.cram │ │ ├── 1400_index_simple.cram.crai │ │ ├── 1400_index_simple.sam │ │ ├── 1401_index_unmapped.cram │ │ ├── 1401_index_unmapped.cram.crai │ │ ├── 1401_index_unmapped.sam │ │ ├── 1402_index_3ref.cram │ │ ├── 1402_index_3ref.cram.crai │ │ ├── 1402_index_3ref.sam │ │ ├── 1403_index_multiref.cram │ │ ├── 1403_index_multiref.cram.crai │ │ ├── 1403_index_multiref.sam │ │ ├── 1404_index_multislice.cram │ │ ├── 1404_index_multislice.cram.crai │ │ ├── 1404_index_multislice.sam │ │ ├── 1405_index_multisliceref.cram │ │ ├── 1405_index_multisliceref.cram.crai │ │ ├── 1405_index_multisliceref.sam │ │ ├── 1406_index_long.cram │ │ ├── 1406_index_long.cram.crai │ │ ├── 1406_index_long.sam │ │ ├── level-1.cram │ │ ├── level-2.cram │ │ └── level-4.cram ├── 3.1 │ ├── LICENSE │ ├── README.md │ └── passed │ │ ├── level-1.cram │ │ ├── level-2.cram │ │ ├── level-3.cram │ │ └── level-4.cram ├── ce.fa ├── ce.fa.fai └── codecs │ ├── LICENSE │ ├── README.md │ ├── fqzcomp │ ├── q4.0 │ ├── q4.1 │ ├── q4.2 │ ├── q4.3 │ ├── q40+dir.0 │ ├── q40+dir.1 │ ├── q40+dir.2 │ ├── q40+dir.3 │ ├── q8.0 │ ├── q8.1 │ ├── q8.2 │ ├── q8.3 │ ├── qvar.0 │ ├── qvar.1 │ ├── qvar.2 │ └── qvar.3 │ ├── gzip │ ├── 01.names.gz │ ├── 02.names.gz │ ├── 03.names.gz │ ├── 05.names.gz │ ├── 08.names.gz │ ├── 09.names.gz │ ├── 10.names.gz │ ├── 20.names.gz │ ├── nv.names.gz │ ├── nv2.names.gz │ ├── q4.gz │ ├── q40+dir.gz │ ├── q8.gz │ ├── qvar.gz │ ├── rr.names.gz │ └── u32.gz │ ├── range │ ├── q4.0 │ ├── q4.1 │ ├── q4.128 │ ├── q4.129 │ ├── q4.192 │ ├── q4.193 │ ├── q4.64 │ ├── q4.65 │ ├── q4.8 │ ├── q4.9 │ ├── q40+dir.0 │ ├── q40+dir.1 │ ├── q40+dir.64 │ ├── q40+dir.65 │ ├── q40+dir.8 │ ├── q40+dir.9 │ ├── q8.0 │ ├── q8.1 │ ├── q8.128 │ ├── q8.129 │ ├── q8.192 │ ├── q8.193 │ ├── q8.64 │ ├── q8.65 │ ├── qvar.0 │ ├── qvar.1 │ ├── qvar.64 │ ├── qvar.65 │ ├── u32.1 │ ├── u32.4 │ ├── u32.65 │ └── u32.9 │ ├── rans4x8 │ ├── q4.0 │ ├── q4.1 │ ├── q40+dir.0 │ ├── q40+dir.1 │ ├── q8.0 │ ├── q8.1 │ ├── qvar.0 │ └── qvar.1 │ ├── ransNx16 │ ├── q4.0 │ ├── q4.1 │ ├── q4.128 │ ├── q4.129 │ ├── q4.192 │ ├── q4.193 │ ├── q4.4 │ ├── q4.5 │ ├── q4.64 │ ├── q4.65 │ ├── q40+dir.0 │ ├── q40+dir.1 │ ├── q40+dir.4 │ ├── q40+dir.5 │ ├── q40+dir.8 │ ├── q8.0 │ ├── q8.1 │ ├── q8.128 │ ├── q8.129 │ ├── q8.192 │ ├── q8.193 │ ├── q8.4 │ ├── q8.5 │ ├── q8.64 │ ├── q8.65 │ ├── qvar.0 │ ├── qvar.1 │ ├── qvar.4 │ ├── qvar.5 │ ├── u32.1 │ └── u32.9 │ └── tok3 │ ├── 01.names.1 │ ├── 01.names.11 │ ├── 01.names.13 │ ├── 01.names.15 │ ├── 01.names.17 │ ├── 01.names.19 │ ├── 01.names.3 │ ├── 01.names.5 │ ├── 01.names.7 │ ├── 01.names.9 │ ├── 02.names.1 │ ├── 02.names.11 │ ├── 02.names.13 │ ├── 02.names.15 │ ├── 02.names.17 │ ├── 02.names.19 │ ├── 02.names.3 │ ├── 02.names.5 │ ├── 02.names.7 │ ├── 02.names.9 │ ├── 03.names.1 │ ├── 03.names.11 │ ├── 03.names.13 │ ├── 03.names.15 │ ├── 03.names.17 │ ├── 03.names.19 │ ├── 03.names.3 │ ├── 03.names.5 │ ├── 03.names.7 │ ├── 03.names.9 │ ├── 05.names.1 │ ├── 05.names.11 │ ├── 05.names.13 │ ├── 05.names.15 │ ├── 05.names.17 │ ├── 05.names.19 │ ├── 05.names.3 │ ├── 05.names.5 │ ├── 05.names.7 │ ├── 05.names.9 │ ├── 08.names.1 │ ├── 08.names.11 │ ├── 08.names.13 │ ├── 08.names.15 │ ├── 08.names.17 │ ├── 08.names.19 │ ├── 08.names.3 │ ├── 08.names.5 │ ├── 08.names.7 │ ├── 08.names.9 │ ├── 09.names.1 │ ├── 09.names.11 │ ├── 09.names.13 │ ├── 09.names.15 │ ├── 09.names.17 │ ├── 09.names.19 │ ├── 09.names.3 │ ├── 09.names.5 │ ├── 09.names.7 │ ├── 09.names.9 │ ├── 10.names.1 │ ├── 10.names.11 │ ├── 10.names.13 │ ├── 10.names.15 │ ├── 10.names.17 │ ├── 10.names.19 │ ├── 10.names.3 │ ├── 10.names.5 │ ├── 10.names.7 │ ├── 10.names.9 │ ├── 20.names.1 │ ├── 20.names.11 │ ├── 20.names.13 │ ├── 20.names.15 │ ├── 20.names.17 │ ├── 20.names.19 │ ├── 20.names.3 │ ├── 20.names.5 │ ├── 20.names.7 │ ├── 20.names.9 │ ├── nv.names.1 │ ├── nv.names.11 │ ├── nv.names.13 │ ├── nv.names.15 │ ├── nv.names.17 │ ├── nv.names.19 │ ├── nv.names.3 │ ├── nv.names.5 │ ├── nv.names.7 │ ├── nv.names.9 │ ├── nv2.names.1 │ ├── nv2.names.11 │ ├── nv2.names.13 │ ├── nv2.names.15 │ ├── nv2.names.17 │ ├── nv2.names.19 │ ├── nv2.names.3 │ ├── nv2.names.5 │ ├── nv2.names.7 │ ├── nv2.names.9 │ ├── rr.names.1 │ ├── rr.names.11 │ ├── rr.names.13 │ ├── rr.names.15 │ ├── rr.names.17 │ ├── rr.names.19 │ ├── rr.names.3 │ ├── rr.names.5 │ ├── rr.names.7 │ └── rr.names.9 ├── sam ├── LICENSE ├── README.md ├── compare_sam.pl ├── failed │ ├── aux.fail-A.sam │ ├── aux.fail-A2.sam │ ├── aux.fail-B1.sam │ ├── aux.fail-B2.sam │ ├── aux.fail-B3.sam │ ├── aux.fail-B4.sam │ ├── aux.fail-H1.sam │ ├── aux.fail-H2.sam │ ├── aux.fail-Z1.sam │ ├── aux.fail-f1.sam │ ├── aux.fail-f2.sam │ ├── aux.fail-f3.sam │ ├── aux.fail-f4.sam │ ├── aux.fail-format1.sam │ ├── aux.fail-format2.sam │ ├── aux.fail-format3.sam │ ├── aux.fail-format4.sam │ ├── aux.fail-i1.sam │ ├── aux.fail-i2.sam │ ├── aux.fail-i3.sam │ ├── aux.fail-i4.sam │ ├── aux.fail-tag.sam │ ├── aux.fail-tag2.sam │ ├── cigar.fail1.sam │ ├── cigar.fail2.sam │ ├── cigar.fail3.sam │ ├── cigar.fail4.sam │ ├── cigar.fail5.sam │ ├── flag.fail.sam │ ├── flag.fail1.sam │ ├── flag.fail2.sam │ ├── flag.fail3.sam │ ├── flag.fail4.sam │ ├── hdr.HD1.sam │ ├── hdr.HD2.sam │ ├── hdr.HD3.sam │ ├── hdr.HD4.sam │ ├── hdr.HD5.sam │ ├── hdr.HD6.sam │ ├── hdr.HD7.sam │ ├── hdr.PG1.sam │ ├── hdr.PG2.sam │ ├── hdr.PG3.sam │ ├── hdr.RG0.sam │ ├── hdr.RG1.sam │ ├── hdr.RG2.sam │ ├── hdr.RG3.sam │ ├── hdr.RG4.sam │ ├── hdr.RG5.sam │ ├── hdr.SQ1.sam │ ├── hdr.SQ10.sam │ ├── hdr.SQ11.sam │ ├── hdr.SQ12.sam │ ├── hdr.SQ13.sam │ ├── hdr.SQ14.sam │ ├── hdr.SQ2.sam │ ├── hdr.SQ3.sam │ ├── hdr.SQ4.sam │ ├── hdr.SQ5.sam │ ├── hdr.SQ6.sam │ ├── hdr.SQ7.sam │ ├── hdr.SQ8.sam │ ├── hdr.SQ9.sam │ ├── mapq.fail1.sam │ ├── mapq.fail2.sam │ ├── mapq.fail3.sam │ ├── pnext.fail1.sam │ ├── pnext.fail2.sam │ ├── pnext.fail3.sam │ ├── pos.fail1.sam │ ├── pos.fail2.sam │ ├── pos.fail3.sam │ ├── pos.fail4.sam │ ├── qname.fail1.sam │ ├── qname.fail2.sam │ ├── qname.fail3.sam │ ├── qname.fail4.sam │ ├── qual.fail1.sam │ ├── qual.fail2.sam │ ├── qual.fail3.sam │ ├── qual.fail4.sam │ ├── qual.fail5.sam │ ├── rname.fail1.sam │ ├── rname.fail10.sam │ ├── rname.fail2.sam │ ├── rname.fail3.sam │ ├── rname.fail4.sam │ ├── rname.fail5.sam │ ├── rname.fail6.sam │ ├── rname.fail7.sam │ ├── rname.fail8.sam │ ├── rname.fail9.sam │ ├── rnext.fail1.sam │ ├── rnext.fail10.sam │ ├── rnext.fail2.sam │ ├── rnext.fail3.sam │ ├── rnext.fail4.sam │ ├── rnext.fail5.sam │ ├── rnext.fail6.sam │ ├── rnext.fail7.sam │ ├── rnext.fail8.sam │ ├── rnext.fail9.sam │ ├── seq.fail1.sam │ ├── seq.fail2.sam │ ├── seq.fail3.sam │ ├── tlen.fail1.sam │ ├── tlen.fail2.sam │ └── tlen.fail3.sam └── passed │ ├── aux.pass-A.sam │ ├── aux.pass-B.sam │ ├── aux.pass-H.sam │ ├── aux.pass-Z.sam │ ├── aux.pass-f.sam │ ├── aux.pass-i.sam │ ├── aux.pass-tag.sam │ ├── aux.pass.sam │ ├── cigar.pass1.sam │ ├── cigar.pass2.sam │ ├── cigar.pass3.sam │ ├── cigar.pass4.sam │ ├── cigar.pass5.sam │ ├── cigar.pass6.sam │ ├── cigar.warn1.sam │ ├── cigar.warn2.sam │ ├── flag.pass.sam │ ├── flag.warn.sam │ ├── hdr.CO.sam │ ├── hdr.HD1.sam │ ├── hdr.HD10.sam │ ├── hdr.HD11.sam │ ├── hdr.HD2.sam │ ├── hdr.HD3.sam │ ├── hdr.HD4.sam │ ├── hdr.HD5.sam │ ├── hdr.HD6.sam │ ├── hdr.HD7.sam │ ├── hdr.HD8.sam │ ├── hdr.HD9.sam │ ├── hdr.PG1.sam │ ├── hdr.PG2.sam │ ├── hdr.PG3.sam │ ├── hdr.PG4.sam │ ├── hdr.PG5.sam │ ├── hdr.PG6.sam │ ├── hdr.RG1.sam │ ├── hdr.RG10.sam │ ├── hdr.RG11.sam │ ├── hdr.RG12.sam │ ├── hdr.RG13.sam │ ├── hdr.RG2.sam │ ├── hdr.RG3.sam │ ├── hdr.RG4.sam │ ├── hdr.RG5.sam │ ├── hdr.RG6.sam │ ├── hdr.RG7.sam │ ├── hdr.RG8.sam │ ├── hdr.RG9.sam │ ├── hdr.SQ1.sam │ ├── hdr.SQ10.sam │ ├── hdr.SQ2.sam │ ├── hdr.SQ3.sam │ ├── hdr.SQ4.sam │ ├── hdr.SQ5.sam │ ├── hdr.SQ6.sam │ ├── hdr.SQ7.sam │ ├── hdr.SQ8.sam │ ├── hdr.SQ9.sam │ ├── mapq.pass.sam │ ├── pnext.pair-2nd.sam │ ├── pnext.pair-supp.sam │ ├── pnext.pass.sam │ ├── pnext.triplet-2nd.sam │ ├── pnext.triplet-supp.sam │ ├── pnext.triplet.sam │ ├── pnext.warn-pair-2nd.sam │ ├── pnext.warn-pair-supp.sam │ ├── pnext.warn.sam │ ├── pos.pass.sam │ ├── pos.warn1.sam │ ├── pos.warn2.sam │ ├── qname.pass.sam │ ├── qual.pass.sam │ ├── rname.pass.sam │ ├── rnext.pass.sam │ ├── rnext.warn.sam │ ├── seq.pass.sam │ ├── seq.pass2.sam │ ├── seq.warn.sam │ ├── tlen.pass.sam │ └── tlen.warn.sam └── vcf ├── 4.1 ├── failed │ ├── failed_body_alt_000.vcf │ ├── failed_body_alt_001.vcf │ ├── failed_body_alt_002.vcf │ ├── failed_body_alt_003.vcf │ ├── failed_body_alt_005.vcf │ ├── failed_body_chrom_000.vcf │ ├── failed_body_chrom_001.vcf │ ├── failed_body_chrom_002.vcf │ ├── failed_body_chrom_003.vcf │ ├── failed_body_contiguous_000.vcf │ ├── failed_body_contiguous_001.vcf │ ├── failed_body_duplicated_000.vcf │ ├── failed_body_duplicated_001.vcf │ ├── failed_body_duplicated_002.vcf │ ├── failed_body_duplicated_003.vcf │ ├── failed_body_filter_000.vcf │ ├── failed_body_filter_001.vcf │ ├── failed_body_filter_002.vcf │ ├── failed_body_filter_003.vcf │ ├── failed_body_filter_004.vcf │ ├── failed_body_format_000.vcf │ ├── failed_body_format_001.vcf │ ├── failed_body_format_002.vcf │ ├── failed_body_format_003.vcf │ ├── failed_body_format_004.vcf │ ├── failed_body_id_000.vcf │ ├── failed_body_id_001.vcf │ ├── failed_body_id_002.vcf │ ├── failed_body_info_000.vcf │ ├── failed_body_info_001.vcf │ ├── failed_body_info_002.vcf │ ├── failed_body_info_003.vcf │ ├── failed_body_info_004.vcf │ ├── failed_body_info_005.vcf │ ├── failed_body_info_006.vcf │ ├── failed_body_info_007.vcf │ ├── failed_body_info_008.vcf │ ├── failed_body_info_009.vcf │ ├── failed_body_info_010.vcf │ ├── failed_body_info_011.vcf │ ├── failed_body_info_012.vcf │ ├── failed_body_info_013.vcf │ ├── failed_body_info_014.vcf │ ├── failed_body_info_015.vcf │ ├── failed_body_info_016.vcf │ ├── failed_body_info_017.vcf │ ├── failed_body_info_018.vcf │ ├── failed_body_info_019.vcf │ ├── failed_body_info_020.vcf │ ├── failed_body_info_021.vcf │ ├── failed_body_info_022.vcf │ ├── failed_body_info_023.vcf │ ├── failed_body_info_024.vcf │ ├── failed_body_info_025.vcf │ ├── failed_body_info_026.vcf │ ├── failed_body_info_027.vcf │ ├── failed_body_info_028.vcf │ ├── failed_body_info_029.vcf │ ├── failed_body_info_030.vcf │ ├── failed_body_info_031.vcf │ ├── failed_body_info_033.vcf │ ├── failed_body_info_034.vcf │ ├── failed_body_info_035.vcf │ ├── failed_body_info_036.vcf │ ├── failed_body_pos_000.vcf │ ├── failed_body_pos_001.vcf │ ├── failed_body_pos_002.vcf │ ├── failed_body_qual_000.vcf │ ├── failed_body_qual_001.vcf │ ├── failed_body_ref_000.vcf │ ├── failed_body_ref_001.vcf │ ├── failed_body_ref_002.vcf │ ├── failed_body_sample_000.vcf │ ├── failed_body_sample_001.vcf │ ├── failed_body_sample_002.vcf │ ├── failed_body_sample_003.vcf │ ├── failed_body_sample_004.vcf │ ├── failed_body_sample_005.vcf │ ├── failed_body_sample_006.vcf │ ├── failed_body_sample_007.vcf │ ├── failed_body_sample_008.vcf │ ├── failed_body_sample_009.vcf │ ├── failed_body_sample_011.vcf │ ├── failed_body_samples_ploidy_000.vcf │ ├── failed_body_samples_ploidy_001.vcf │ ├── failed_body_samples_ploidy_002.vcf │ ├── failed_body_samples_ploidy_003.vcf │ ├── failed_body_unsorted_000.vcf │ ├── failed_fileformat_000.vcf │ ├── failed_fileformat_001.vcf │ ├── failed_header_000.vcf │ ├── failed_header_001.vcf │ ├── failed_meta_000.vcf │ ├── failed_meta_001.vcf │ ├── failed_meta_002.vcf │ ├── failed_meta_003.vcf │ ├── failed_meta_004.vcf │ ├── failed_meta_005.vcf │ ├── failed_meta_006.vcf │ ├── failed_meta_007.vcf │ ├── failed_meta_008.vcf │ ├── failed_meta_009.vcf │ ├── failed_meta_alt_000.vcf │ ├── failed_meta_alt_001.vcf │ ├── failed_meta_alt_002.vcf │ ├── failed_meta_alt_003.vcf │ ├── failed_meta_alt_004.vcf │ ├── failed_meta_alt_005.vcf │ ├── failed_meta_alt_006.vcf │ ├── failed_meta_alt_007.vcf │ ├── failed_meta_alt_008.vcf │ ├── failed_meta_alt_009.vcf │ ├── failed_meta_assembly_000.vcf │ ├── failed_meta_assembly_001.vcf │ ├── failed_meta_contig_000.vcf │ ├── failed_meta_contig_001.vcf │ ├── failed_meta_contig_002.vcf │ ├── failed_meta_format_000.vcf │ ├── failed_meta_format_001.vcf │ ├── failed_meta_format_002.vcf │ ├── failed_meta_format_003.vcf │ ├── failed_meta_format_004.vcf │ ├── failed_meta_format_005.vcf │ ├── failed_meta_format_006.vcf │ ├── failed_meta_format_007.vcf │ ├── failed_meta_format_008.vcf │ ├── failed_meta_format_009.vcf │ ├── failed_meta_format_010.vcf │ ├── failed_meta_format_011.vcf │ ├── failed_meta_format_012.vcf │ ├── failed_meta_format_013.vcf │ ├── failed_meta_format_014.vcf │ ├── failed_meta_format_015.vcf │ ├── failed_meta_format_016.vcf │ ├── failed_meta_format_017.vcf │ ├── failed_meta_format_018.vcf │ ├── failed_meta_format_019.vcf │ ├── failed_meta_format_020.vcf │ ├── failed_meta_format_021.vcf │ ├── failed_meta_format_022.vcf │ ├── failed_meta_format_023.vcf │ ├── failed_meta_format_024.vcf │ ├── failed_meta_format_025.vcf │ ├── failed_meta_format_026.vcf │ ├── failed_meta_format_027.vcf │ ├── failed_meta_format_028.vcf │ ├── failed_meta_format_029.vcf │ ├── failed_meta_format_030.vcf │ ├── failed_meta_info_000.vcf │ ├── failed_meta_info_001.vcf │ ├── failed_meta_info_002.vcf │ ├── failed_meta_info_003.vcf │ ├── failed_meta_info_004.vcf │ ├── failed_meta_info_005.vcf │ ├── failed_meta_info_006.vcf │ ├── failed_meta_info_007.vcf │ ├── failed_meta_info_008.vcf │ ├── failed_meta_info_009.vcf │ ├── failed_meta_info_010.vcf │ ├── failed_meta_info_011.vcf │ ├── failed_meta_info_012.vcf │ ├── failed_meta_info_013.vcf │ ├── failed_meta_info_014.vcf │ ├── failed_meta_info_015.vcf │ ├── failed_meta_info_016.vcf │ ├── failed_meta_info_017.vcf │ ├── failed_meta_info_018.vcf │ ├── failed_meta_info_019.vcf │ ├── failed_meta_info_020.vcf │ ├── failed_meta_info_021.vcf │ ├── failed_meta_info_022.vcf │ ├── failed_meta_info_023.vcf │ ├── failed_meta_info_024.vcf │ ├── failed_meta_info_025.vcf │ ├── failed_meta_info_026.vcf │ ├── failed_meta_info_027.vcf │ ├── failed_meta_info_028.vcf │ ├── failed_meta_info_029.vcf │ ├── failed_meta_info_030.vcf │ ├── failed_meta_info_031.vcf │ ├── failed_meta_info_032.vcf │ ├── failed_meta_info_033.vcf │ ├── failed_meta_info_034.vcf │ ├── failed_meta_info_035.vcf │ ├── failed_meta_info_036.vcf │ ├── failed_meta_info_037.vcf │ ├── failed_meta_pedigree_000.vcf │ ├── failed_meta_pedigree_001.vcf │ ├── failed_meta_pedigreedb_000.vcf │ ├── failed_meta_pedigreedb_001.vcf │ ├── failed_meta_pedigreedb_002.vcf │ ├── failed_meta_sample_000.vcf │ └── failed_meta_sample_001.vcf └── passed │ ├── complexfile_passed_000.vcf │ ├── passed_body_alt.vcf │ ├── passed_body_chrom.vcf │ ├── passed_body_filter.vcf │ ├── passed_body_format.vcf │ ├── passed_body_id.vcf │ ├── passed_body_info.vcf │ ├── passed_body_pos.vcf │ ├── passed_body_qual.vcf │ ├── passed_body_ref.vcf │ ├── passed_body_samples.vcf │ ├── passed_fileformat_header_000.vcf │ ├── passed_fileformat_header_001.vcf │ ├── passed_fileformat_header_002.vcf │ ├── passed_meta_alt.vcf │ ├── passed_meta_assembly.vcf │ ├── passed_meta_contig.vcf │ ├── passed_meta_format.vcf │ ├── passed_meta_info.vcf │ ├── passed_meta_pedigree.vcf │ ├── passed_meta_pedigreedb.vcf │ ├── passed_meta_sample.vcf │ ├── passed_ploidy_000.vcf │ ├── passed_ploidy_001.vcf │ └── passed_symbolic_duplicates.vcf ├── 4.2 ├── failed │ ├── failed_body_alt_000.vcf │ ├── failed_body_alt_001.vcf │ ├── failed_body_alt_002.vcf │ ├── failed_body_alt_003.vcf │ ├── failed_body_alt_005.vcf │ ├── failed_body_chrom_000.vcf │ ├── failed_body_chrom_001.vcf │ ├── failed_body_chrom_002.vcf │ ├── failed_body_chrom_003.vcf │ ├── failed_body_contiguous_000.vcf │ ├── failed_body_contiguous_001.vcf │ ├── failed_body_duplicated_000.vcf │ ├── failed_body_duplicated_001.vcf │ ├── failed_body_duplicated_002.vcf │ ├── failed_body_duplicated_003.vcf │ ├── failed_body_filter_000.vcf │ ├── failed_body_filter_001.vcf │ ├── failed_body_filter_002.vcf │ ├── failed_body_filter_003.vcf │ ├── failed_body_filter_004.vcf │ ├── failed_body_format_000.vcf │ ├── failed_body_format_001.vcf │ ├── failed_body_format_002.vcf │ ├── failed_body_format_003.vcf │ ├── failed_body_format_004.vcf │ ├── failed_body_id_000.vcf │ ├── failed_body_id_001.vcf │ ├── failed_body_id_002.vcf │ ├── failed_body_info_000.vcf │ ├── failed_body_info_001.vcf │ ├── failed_body_info_002.vcf │ ├── failed_body_info_003.vcf │ ├── failed_body_info_004.vcf │ ├── failed_body_info_005.vcf │ ├── failed_body_info_006.vcf │ ├── failed_body_info_007.vcf │ ├── failed_body_info_008.vcf │ ├── failed_body_info_009.vcf │ ├── failed_body_info_010.vcf │ ├── failed_body_info_011.vcf │ ├── failed_body_info_012.vcf │ ├── failed_body_info_013.vcf │ ├── failed_body_info_014.vcf │ ├── failed_body_info_015.vcf │ ├── failed_body_info_016.vcf │ ├── failed_body_info_017.vcf │ ├── failed_body_info_018.vcf │ ├── failed_body_info_019.vcf │ ├── failed_body_info_020.vcf │ ├── failed_body_info_021.vcf │ ├── failed_body_info_022.vcf │ ├── failed_body_info_023.vcf │ ├── failed_body_info_024.vcf │ ├── failed_body_info_025.vcf │ ├── failed_body_info_026.vcf │ ├── failed_body_info_027.vcf │ ├── failed_body_info_028.vcf │ ├── failed_body_info_029.vcf │ ├── failed_body_info_030.vcf │ ├── failed_body_info_031.vcf │ ├── failed_body_info_033.vcf │ ├── failed_body_info_036.vcf │ ├── failed_body_pos_000.vcf │ ├── failed_body_pos_001.vcf │ ├── failed_body_pos_002.vcf │ ├── failed_body_qual_000.vcf │ ├── failed_body_qual_001.vcf │ ├── failed_body_ref_000.vcf │ ├── failed_body_ref_001.vcf │ ├── failed_body_ref_002.vcf │ ├── failed_body_sample_000.vcf │ ├── failed_body_sample_001.vcf │ ├── failed_body_sample_002.vcf │ ├── failed_body_sample_003.vcf │ ├── failed_body_sample_004.vcf │ ├── failed_body_sample_005.vcf │ ├── failed_body_sample_006.vcf │ ├── failed_body_sample_007.vcf │ ├── failed_body_sample_008.vcf │ ├── failed_body_sample_009.vcf │ ├── failed_body_sample_010.vcf │ ├── failed_body_sample_011.vcf │ ├── failed_body_samples_ploidy_000.vcf │ ├── failed_body_samples_ploidy_001.vcf │ ├── failed_body_samples_ploidy_002.vcf │ ├── failed_body_samples_ploidy_003.vcf │ ├── failed_body_unsorted_000.vcf │ ├── failed_fileformat_000.vcf │ ├── failed_fileformat_001.vcf │ ├── failed_header_000.vcf │ ├── failed_header_001.vcf │ ├── failed_meta_000.vcf │ ├── failed_meta_001.vcf │ ├── failed_meta_002.vcf │ ├── failed_meta_003.vcf │ ├── failed_meta_004.vcf │ ├── failed_meta_005.vcf │ ├── failed_meta_006.vcf │ ├── failed_meta_007.vcf │ ├── failed_meta_008.vcf │ ├── failed_meta_009.vcf │ ├── failed_meta_alt_000.vcf │ ├── failed_meta_alt_001.vcf │ ├── failed_meta_alt_002.vcf │ ├── failed_meta_alt_003.vcf │ ├── failed_meta_alt_004.vcf │ ├── failed_meta_alt_005.vcf │ ├── failed_meta_alt_006.vcf │ ├── failed_meta_alt_007.vcf │ ├── failed_meta_alt_008.vcf │ ├── failed_meta_alt_009.vcf │ ├── failed_meta_assembly_000.vcf │ ├── failed_meta_assembly_001.vcf │ ├── failed_meta_contig_000.vcf │ ├── failed_meta_contig_001.vcf │ ├── failed_meta_contig_002.vcf │ ├── failed_meta_format_000.vcf │ ├── failed_meta_format_001.vcf │ ├── failed_meta_format_002.vcf │ ├── failed_meta_format_003.vcf │ ├── failed_meta_format_004.vcf │ ├── failed_meta_format_005.vcf │ ├── failed_meta_format_006.vcf │ ├── failed_meta_format_007.vcf │ ├── failed_meta_format_008.vcf │ ├── failed_meta_format_009.vcf │ ├── failed_meta_format_010.vcf │ ├── failed_meta_format_011.vcf │ ├── failed_meta_format_012.vcf │ ├── failed_meta_format_013.vcf │ ├── failed_meta_format_014.vcf │ ├── failed_meta_format_015.vcf │ ├── failed_meta_format_016.vcf │ ├── failed_meta_format_017.vcf │ ├── failed_meta_format_018.vcf │ ├── failed_meta_format_019.vcf │ ├── failed_meta_format_020.vcf │ ├── failed_meta_format_021.vcf │ ├── failed_meta_format_022.vcf │ ├── failed_meta_format_023.vcf │ ├── failed_meta_format_024.vcf │ ├── failed_meta_format_025.vcf │ ├── failed_meta_format_026.vcf │ ├── failed_meta_format_027.vcf │ ├── failed_meta_format_028.vcf │ ├── failed_meta_format_029.vcf │ ├── failed_meta_info_000.vcf │ ├── failed_meta_info_001.vcf │ ├── failed_meta_info_002.vcf │ ├── failed_meta_info_003.vcf │ ├── failed_meta_info_004.vcf │ ├── failed_meta_info_005.vcf │ ├── failed_meta_info_006.vcf │ ├── failed_meta_info_007.vcf │ ├── failed_meta_info_008.vcf │ ├── failed_meta_info_009.vcf │ ├── failed_meta_info_010.vcf │ ├── failed_meta_info_011.vcf │ ├── failed_meta_info_012.vcf │ ├── failed_meta_info_013.vcf │ ├── failed_meta_info_014.vcf │ ├── failed_meta_info_015.vcf │ ├── failed_meta_info_016.vcf │ ├── failed_meta_info_017.vcf │ ├── failed_meta_info_018.vcf │ ├── failed_meta_info_019.vcf │ ├── failed_meta_info_020.vcf │ ├── failed_meta_info_021.vcf │ ├── failed_meta_info_022.vcf │ ├── failed_meta_info_023.vcf │ ├── failed_meta_info_024.vcf │ ├── failed_meta_info_025.vcf │ ├── failed_meta_info_026.vcf │ ├── failed_meta_info_027.vcf │ ├── failed_meta_info_028.vcf │ ├── failed_meta_info_029.vcf │ ├── failed_meta_info_030.vcf │ ├── failed_meta_info_031.vcf │ ├── failed_meta_info_032.vcf │ ├── failed_meta_info_033.vcf │ ├── failed_meta_info_034.vcf │ ├── failed_meta_info_035.vcf │ ├── failed_meta_info_036.vcf │ ├── failed_meta_pedigree_000.vcf │ ├── failed_meta_pedigree_001.vcf │ ├── failed_meta_pedigreedb_000.vcf │ ├── failed_meta_pedigreedb_001.vcf │ ├── failed_meta_pedigreedb_002.vcf │ ├── failed_meta_sample_000.vcf │ └── failed_meta_sample_001.vcf └── passed │ ├── complexfile_passed_000.vcf │ ├── passed_body_alt.vcf │ ├── passed_body_chrom.vcf │ ├── passed_body_filter.vcf │ ├── passed_body_format.vcf │ ├── passed_body_id.vcf │ ├── passed_body_info.vcf │ ├── passed_body_pos.vcf │ ├── passed_body_qual.vcf │ ├── passed_body_ref.vcf │ ├── passed_body_samples.vcf │ ├── passed_fileformat_header_000.vcf │ ├── passed_fileformat_header_001.vcf │ ├── passed_fileformat_header_002.vcf │ ├── passed_meta_alt.vcf │ ├── passed_meta_assembly.vcf │ ├── passed_meta_contig.vcf │ ├── passed_meta_format.vcf │ ├── passed_meta_info.vcf │ ├── passed_meta_pedigree.vcf │ ├── passed_meta_pedigreedb.vcf │ ├── passed_meta_sample.vcf │ ├── passed_ploidy_000.vcf │ ├── passed_ploidy_001.vcf │ └── passed_symbolic_duplicates.vcf ├── 4.3 ├── failed │ ├── failed_body_alt_000.vcf │ ├── failed_body_alt_001.vcf │ ├── failed_body_alt_002.vcf │ ├── failed_body_alt_003.vcf │ ├── failed_body_alt_005.vcf │ ├── failed_body_chrom_000.vcf │ ├── failed_body_chrom_001.vcf │ ├── failed_body_chrom_002.vcf │ ├── failed_body_chrom_003.vcf │ ├── failed_body_chrom_004.vcf │ ├── failed_body_contiguous_000.vcf │ ├── failed_body_contiguous_001.vcf │ ├── failed_body_duplicated_000.vcf │ ├── failed_body_duplicated_001.vcf │ ├── failed_body_duplicated_002.vcf │ ├── failed_body_duplicated_003.vcf │ ├── failed_body_filter_000.vcf │ ├── failed_body_filter_001.vcf │ ├── failed_body_filter_002.vcf │ ├── failed_body_filter_003.vcf │ ├── failed_body_filter_004.vcf │ ├── failed_body_filter_005.vcf │ ├── failed_body_format_000.vcf │ ├── failed_body_format_001.vcf │ ├── failed_body_format_002.vcf │ ├── failed_body_format_003.vcf │ ├── failed_body_format_004.vcf │ ├── failed_body_format_005.vcf │ ├── failed_body_format_006.vcf │ ├── failed_body_format_007.vcf │ ├── failed_body_id_000.vcf │ ├── failed_body_id_001.vcf │ ├── failed_body_id_002.vcf │ ├── failed_body_id_003.vcf │ ├── failed_body_info_000.vcf │ ├── failed_body_info_001.vcf │ ├── failed_body_info_002.vcf │ ├── failed_body_info_003.vcf │ ├── failed_body_info_004.vcf │ ├── failed_body_info_005.vcf │ ├── failed_body_info_006.vcf │ ├── failed_body_info_007.vcf │ ├── failed_body_info_008.vcf │ ├── failed_body_info_009.vcf │ ├── failed_body_info_010.vcf │ ├── failed_body_info_011.vcf │ ├── failed_body_info_012.vcf │ ├── failed_body_info_013.vcf │ ├── failed_body_info_014.vcf │ ├── failed_body_info_015.vcf │ ├── failed_body_info_016.vcf │ ├── failed_body_info_017.vcf │ ├── failed_body_info_018.vcf │ ├── failed_body_info_019.vcf │ ├── failed_body_info_020.vcf │ ├── failed_body_info_021.vcf │ ├── failed_body_info_022.vcf │ ├── failed_body_info_023.vcf │ ├── failed_body_info_024.vcf │ ├── failed_body_info_025.vcf │ ├── failed_body_info_026.vcf │ ├── failed_body_info_027.vcf │ ├── failed_body_info_028.vcf │ ├── failed_body_info_029.vcf │ ├── failed_body_info_030.vcf │ ├── failed_body_info_031.vcf │ ├── failed_body_info_033.vcf │ ├── failed_body_info_036.vcf │ ├── failed_body_info_integer_overflow.vcf │ ├── failed_body_info_integer_reserved.vcf │ ├── failed_body_info_integer_underflow.vcf │ ├── failed_body_no_newline_000.vcf │ ├── failed_body_no_newline_001.vcf │ ├── failed_body_no_newline_002.vcf │ ├── failed_body_no_newline_003.vcf │ ├── failed_body_no_newline_004.vcf │ ├── failed_body_pos_000.vcf │ ├── failed_body_pos_001.vcf │ ├── failed_body_pos_002.vcf │ ├── failed_body_qual_000.vcf │ ├── failed_body_qual_001.vcf │ ├── failed_body_ref_000.vcf │ ├── failed_body_ref_001.vcf │ ├── failed_body_ref_002.vcf │ ├── failed_body_sample_000.vcf │ ├── failed_body_sample_001.vcf │ ├── failed_body_sample_002.vcf │ ├── failed_body_sample_003.vcf │ ├── failed_body_sample_004.vcf │ ├── failed_body_sample_005.vcf │ ├── failed_body_sample_006.vcf │ ├── failed_body_sample_007.vcf │ ├── failed_body_sample_008.vcf │ ├── failed_body_sample_009.vcf │ ├── failed_body_sample_010.vcf │ ├── failed_body_sample_011.vcf │ ├── failed_body_samples_ploidy_000.vcf │ ├── failed_body_samples_ploidy_001.vcf │ ├── failed_body_samples_ploidy_002.vcf │ ├── failed_body_samples_ploidy_003.vcf │ ├── failed_body_unsorted_000.vcf │ ├── failed_empty.vcf │ ├── failed_empty_sample.vcf │ ├── failed_fileformat_000.vcf │ ├── failed_fileformat_001.vcf │ ├── failed_header_000.vcf │ ├── failed_header_001.vcf │ ├── failed_meta_000.vcf │ ├── failed_meta_001.vcf │ ├── failed_meta_002.vcf │ ├── failed_meta_003.vcf │ ├── failed_meta_004.vcf │ ├── failed_meta_005.vcf │ ├── failed_meta_006.vcf │ ├── failed_meta_007.vcf │ ├── failed_meta_008.vcf │ ├── failed_meta_009.vcf │ ├── failed_meta_alt_001.vcf │ ├── failed_meta_alt_002.vcf │ ├── failed_meta_alt_003.vcf │ ├── failed_meta_alt_004.vcf │ ├── failed_meta_alt_005.vcf │ ├── failed_meta_alt_006.vcf │ ├── failed_meta_alt_007.vcf │ ├── failed_meta_alt_008.vcf │ ├── failed_meta_alt_009.vcf │ ├── failed_meta_assembly_000.vcf │ ├── failed_meta_assembly_001.vcf │ ├── failed_meta_contig_000.vcf │ ├── failed_meta_contig_001.vcf │ ├── failed_meta_contig_002.vcf │ ├── failed_meta_contig_003.vcf │ ├── failed_meta_format_000.vcf │ ├── failed_meta_format_001.vcf │ ├── failed_meta_format_002.vcf │ ├── failed_meta_format_003.vcf │ ├── failed_meta_format_004.vcf │ ├── failed_meta_format_005.vcf │ ├── failed_meta_format_006.vcf │ ├── failed_meta_format_007.vcf │ ├── failed_meta_format_008.vcf │ ├── failed_meta_format_009.vcf │ ├── failed_meta_format_010.vcf │ ├── failed_meta_format_011.vcf │ ├── failed_meta_format_012.vcf │ ├── failed_meta_format_013.vcf │ ├── failed_meta_format_014.vcf │ ├── failed_meta_format_015.vcf │ ├── failed_meta_format_016.vcf │ ├── failed_meta_format_017.vcf │ ├── failed_meta_format_018.vcf │ ├── failed_meta_format_019.vcf │ ├── failed_meta_format_020.vcf │ ├── failed_meta_format_021.vcf │ ├── failed_meta_format_022.vcf │ ├── failed_meta_format_023.vcf │ ├── failed_meta_format_024.vcf │ ├── failed_meta_format_025.vcf │ ├── failed_meta_format_026.vcf │ ├── failed_meta_format_027.vcf │ ├── failed_meta_format_028.vcf │ ├── failed_meta_format_029.vcf │ ├── failed_meta_format_030.vcf │ ├── failed_meta_format_031.vcf │ ├── failed_meta_format_032.vcf │ ├── failed_meta_format_033.vcf │ ├── failed_meta_info_000.vcf │ ├── failed_meta_info_001.vcf │ ├── failed_meta_info_002.vcf │ ├── failed_meta_info_003.vcf │ ├── failed_meta_info_004.vcf │ ├── failed_meta_info_005.vcf │ ├── failed_meta_info_006.vcf │ ├── failed_meta_info_007.vcf │ ├── failed_meta_info_008.vcf │ ├── failed_meta_info_009.vcf │ ├── failed_meta_info_010.vcf │ ├── failed_meta_info_011.vcf │ ├── failed_meta_info_012.vcf │ ├── failed_meta_info_013.vcf │ ├── failed_meta_info_014.vcf │ ├── failed_meta_info_015.vcf │ ├── failed_meta_info_016.vcf │ ├── failed_meta_info_017.vcf │ ├── failed_meta_info_018.vcf │ ├── failed_meta_info_019.vcf │ ├── failed_meta_info_020.vcf │ ├── failed_meta_info_021.vcf │ ├── failed_meta_info_022.vcf │ ├── failed_meta_info_023.vcf │ ├── failed_meta_info_024.vcf │ ├── failed_meta_info_025.vcf │ ├── failed_meta_info_026.vcf │ ├── failed_meta_info_027.vcf │ ├── failed_meta_info_028.vcf │ ├── failed_meta_info_029.vcf │ ├── failed_meta_info_030.vcf │ ├── failed_meta_info_031.vcf │ ├── failed_meta_info_032.vcf │ ├── failed_meta_info_033.vcf │ ├── failed_meta_info_034.vcf │ ├── failed_meta_info_035.vcf │ ├── failed_meta_info_036.vcf │ ├── failed_meta_info_037.vcf │ ├── failed_meta_info_038.vcf │ ├── failed_meta_info_039.vcf │ ├── failed_meta_info_040.vcf │ ├── failed_meta_info_041.vcf │ ├── failed_meta_info_042.vcf │ ├── failed_meta_meta_000.vcf │ ├── failed_meta_meta_001.vcf │ ├── failed_meta_meta_002.vcf │ ├── failed_meta_meta_003.vcf │ ├── failed_meta_pedigree_000.vcf │ ├── failed_meta_pedigree_001.vcf │ ├── failed_meta_pedigree_002.vcf │ ├── failed_meta_pedigree_003.vcf │ ├── failed_meta_pedigreedb_000.vcf │ ├── failed_meta_pedigreedb_001.vcf │ ├── failed_meta_pedigreedb_002.vcf │ ├── failed_meta_sample_000.vcf │ ├── failed_meta_sample_001.vcf │ ├── failed_meta_sample_002.vcf │ └── failed_meta_sample_003.vcf └── passed │ ├── complexfile_passed_000.vcf │ ├── passed_body_alt.vcf │ ├── passed_body_chrom.vcf │ ├── passed_body_filter.vcf │ ├── passed_body_id.vcf │ ├── passed_body_info.vcf │ ├── passed_body_pos.vcf │ ├── passed_body_qual.vcf │ ├── passed_body_ref.vcf │ ├── passed_body_samples.vcf │ ├── passed_fileformat_header_000.vcf │ ├── passed_fileformat_header_001.vcf │ ├── passed_fileformat_header_002.vcf │ ├── passed_meta_alt.vcf │ ├── passed_meta_assembly.vcf │ ├── 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-------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type B 3 | b1 4 * 0 0 * * 0 0 CAT QQQ BA:B:F,1 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-B2.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type B 3 | b1 4 * 0 0 * * 0 0 CAT QQQ BC:B:C,-1 bC:B:C,256 bc:B:c,-129 Bc:B:c,128 4 | b2 4 * 0 0 * * 0 0 CAT QQQ bS:B:S,-1 BS:B:S,65536 bS:B:s,-32769 Bs:B:s,32768 5 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-B3.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type B 3 | b1 4 * 0 0 * * 0 0 CAT QQQ BI:B:I,4294967296 bi:B:i,-2147483649 Bi:B:i,2147483648 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-B4.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type B 3 | b1 4 * 0 0 * * 0 0 CAT QQQ BA:B: 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-H1.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type H 3 | h1 4 * 0 0 * * 0 0 CAT QQQ H0:H:9 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-H2.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type H; lowercase 3 | h1 4 * 0 0 * * 0 0 CAT QQQ H0:H:abcd 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-Z1.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type A 3 | z1 4 * 0 0 * * 0 0 CAT QQQ Z0:Z: 4 | z1 4 * 0 0 * * 0 0 CAT QQQ Z0:Z: 5 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-f1.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type f 3 | I 4 * 0 0 * * 0 0 CAT QQQ F0:f:1E-46 F1:f:-1E-46 F2:f:3.502823466E+38 F3:f:-3.502823466E+38 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-f2.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type f 3 | I 4 * 0 0 * * 0 0 CAT QQQ F0:f:10. F1:f:9. 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-f3.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type f 3 | I 4 * 0 0 * * 0 0 CAT QQQ F0:f:nan F1:f:inf 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-f4.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type f 3 | I 4 * 0 0 * * 0 0 CAT QQQ F0:f:e F1:f:E 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-format1.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Format 3 | b1 4 * 0 0 * * 0 0 CAT QQQ Z:Z:short 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-format2.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Format 3 | b1 4 * 0 0 * * 0 0 CAT QQQ ZZZ:Z:long 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-format3.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Format 3 | b1 4 * 0 0 * * 0 0 CAT QQQ ZZ:z:case II:I:100 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-format4.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Format 3 | b1 4 * 0 0 * * 0 0 CAT QQQ ZZ:Z:repeat ZZ:Z:repeat2 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-i1.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type i 3 | I 4 * 0 0 * * 0 0 CAT QQQ I0:i:-2147483649 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-i2.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type i 3 | I 4 * 0 0 * * 0 0 CAT QQQ I0:i:4294967296 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-i3.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type i 3 | I 4 * 0 0 * * 0 0 CAT QQQ I0:i: 4 | I 4 * 0 0 * * 0 0 CAT QQQ I0:i: AA:Z:zz 5 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-i4.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type i 3 | I 4 * 0 0 * * 0 0 CAT QQQ I0:i:10.999 4 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-tag.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO TAG checking 3 | tag1 4 * 0 0 * * 0 0 CAT QQQ 0A:Z:0 9a:Z:9 4 | tag2 4 * 0 0 * * 0 0 CAT QQQ A/:Z:/ A_:Z:_ A@:Z:@ A{:Z:{ 5 | -------------------------------------------------------------------------------- /test/sam/failed/aux.fail-tag2.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO TAG checking 3 | tag3 4 * 0 0 * * 0 0 CAT QQQ A:Z:1 AAA:Z:3 4 | -------------------------------------------------------------------------------- /test/sam/failed/cigar.fail4.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO CIGAR: malformed 3 | X 16 CHROMOSOME_I 51 3 50M2 * 0 0 NNAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCNN IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 4 | -------------------------------------------------------------------------------- /test/sam/failed/cigar.fail5.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO CIGAR: malformed 3 | X 16 CHROMOSOME_I 51 3 * 0 0 NNAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCNN IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 4 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.HD1.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.HD2.sam: -------------------------------------------------------------------------------- 1 | @HD SO:query VN:1.6 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.HD3.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.6 GO:none 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.HD4.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.6 SS:unknown:MI 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.HD5.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.6 SS:unsorted:bar code 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.HD6.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:ref LN:1 2 | @HD VN:1.6 3 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.HD7.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.6 2 | @HD VN:1.6 3 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.PG1.sam: -------------------------------------------------------------------------------- 1 | @PG ID:bwa 2 | @PG ID:bwa 3 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.PG2.sam: -------------------------------------------------------------------------------- 1 | @PG VN:1 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.PG3.sam: -------------------------------------------------------------------------------- 1 | @PG ID:bwa PP:missing 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.RG0.sam: -------------------------------------------------------------------------------- 1 | @RG DS:no ID 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.RG1.sam: -------------------------------------------------------------------------------- 1 | @RG ID:RG:r 2 | @RG ID:RG:r 3 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.RG2.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 DT:2020-23-06 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.RG3.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 DT:Tuesday 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.RG4.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 PI:1000-1500 2 | @RG ID:2 PI:small 3 | @RG ID:3 PI:123.456 4 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.RG5.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 PL:454 2 | @RG ID:2 PL:UNKNOWN 3 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ1.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:ref LN:0 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ10.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:A LN:1 M5:7FC56270E7A70FA81A5935B72EACBE29 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ11.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:A LN:1 M5:7fc56270e7a70fa81a5935b72eacbe 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ12.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:A LN:1 M5:7fc56270e7a70fa81a5935b72eacbe2930 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ13.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:ref LN:99 TP:unknown 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ14.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:foo LN:100 DS:duplicate-tag LN:200 2 | @CO Tags may not appear more than once in a single header line 3 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ2.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:* LN:1 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ3.sam: -------------------------------------------------------------------------------- 1 | @SQ SN: LN:1 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ4.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:ref1a LN:101 AH:= 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ5.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:ref2 LN:99 2 | @SQ SN:ref2 LN:99 3 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ6.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:ref1 LN:99 AN:= 2 | @SQ SN:ref2 LN:99 AN:* 3 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ7.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:ref1 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ8.sam: -------------------------------------------------------------------------------- 1 | @SQ LN:99 2 | -------------------------------------------------------------------------------- /test/sam/failed/hdr.SQ9.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:ref0 LN:99 AN:ref2 2 | @SQ SN:ref1 LN:99 AN:1 3 | @SQ SN:ref2 LN:99 AN:2,1 4 | -------------------------------------------------------------------------------- /test/sam/failed/pnext.fail1.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @SQ SN:CHROMOSOME_II LN:5000 3 | @CO Validation of PNEXT 4 | neg 99 CHROMOSOME_I 51 1 50M = -1 200 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 5 | -------------------------------------------------------------------------------- /test/sam/failed/pnext.fail2.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @SQ SN:CHROMOSOME_II LN:5000 3 | @CO Validation of PNEXT 4 | float 99 CHROMOSOME_I 51 1 50M = 1.9 200 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 5 | -------------------------------------------------------------------------------- /test/sam/failed/pnext.fail3.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @SQ SN:CHROMOSOME_II LN:5000 3 | @CO Validation of PNEXT 4 | x 99 CHROMOSOME_I 51 1 50M = * 200 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 5 | -------------------------------------------------------------------------------- /test/sam/failed/pos.fail3.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:long LN:2147483647 2 | @CO Validation of POS. 3 | m1 0 long -1 1 1M * 0 0 C J 4 | m2 0 long -2147483648 1 1M * 0 0 C J 5 | -------------------------------------------------------------------------------- /test/sam/failed/pos.fail4.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:long LN:2147483647 2 | @CO Validation of POS. 3 | m1 0 long * 1 1M * 0 0 C J 4 | -------------------------------------------------------------------------------- /test/sam/failed/qual.fail1.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO Validation of SEQ 3 | char1 0 CHROMOSOME_I 51 40 50M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIII 4 | -------------------------------------------------------------------------------- /test/sam/failed/qual.fail2.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO Validation of SEQ 3 | char1 0 CHROMOSOME_I 51 40 50M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 4 | -------------------------------------------------------------------------------- /test/sam/failed/qual.fail3.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO Validation of SEQ 3 | char1 0 CHROMOSOME_I 51 40 50M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIX 4 | -------------------------------------------------------------------------------- /test/sam/failed/qual.fail4.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO Validation of SEQ 3 | char1 4 * 0 0 * * 0 0 * IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 4 | -------------------------------------------------------------------------------- /test/sam/failed/qual.fail5.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO Validation of SEQ 3 | char1 0 CHROMOSOME_I 51 40 50M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT XX:Z:noqual 4 | -------------------------------------------------------------------------------- /test/sam/failed/seq.fail1.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO Validation of SEQ 3 | chars1 4 * 0 0 * * 0 0 A C III 4 | -------------------------------------------------------------------------------- /test/sam/failed/seq.fail2.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO Validation of SEQ 3 | chars2 4 * 0 0 * * 0 0 *A II 4 | chars3 4 * 0 0 * * 0 0 ~\ II 5 | chars4 4 * 0 0 * * 0 0 0. II 6 | -------------------------------------------------------------------------------- /test/sam/failed/seq.fail3.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO Validation of SEQ 3 | chars1 4 * 0 0 * * 0 0 III 4 | -------------------------------------------------------------------------------- /test/sam/failed/tlen.fail1.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO Validation of TLEN 3 | float 99 CHROMOSOME_I 51 1 50M = 201 199.1 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 4 | -------------------------------------------------------------------------------- /test/sam/failed/tlen.fail2.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO Validation of TLEN 3 | float 99 CHROMOSOME_I 51 1 50M = 201 * CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 4 | -------------------------------------------------------------------------------- /test/sam/failed/tlen.fail3.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO Validation of TLEN 3 | float 99 CHROMOSOME_I 51 1 50M = 201 * CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 4 | -------------------------------------------------------------------------------- /test/sam/passed/aux.pass-H.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO Type H 3 | h1 4 * 0 0 * * 0 0 CAT QQQ H1:H:DEADBEEF H2:H:0123456789ABCDEF 4 | h1 4 * 0 0 * * 0 0 CAT QQQ H0:H: ZZ:Z:empty H1:H: 5 | -------------------------------------------------------------------------------- /test/sam/passed/aux.pass-tag.sam: -------------------------------------------------------------------------------- 1 | @CO Validation of AUX 2 | @CO TAG checking 3 | tag1 4 * 0 0 * * 0 0 CAT QQQ AA:Z:AA aa:Z:aa Aa:Z:Aa aA:Z:aA 4 | tag2 4 * 0 0 * * 0 0 CAT QQQ ZZ:Z:ZZ zz:Z:zz Zz:Z:Zz zZ:Z:zZ 5 | tag3 4 * 0 0 * * 0 0 CAT QQQ Z9:Z:Z9 z9:Z:z9 6 | -------------------------------------------------------------------------------- /test/sam/passed/cigar.warn2.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:CHROMOSOME_I LN:1009800 2 | @CO CIGAR: empty seq 3 | empty1 16 CHROMOSOME_I 51 1 * * 0 0 * * 4 | empty2 16 CHROMOSOME_I 51 1 0M * 0 0 * * 5 | empty3 16 CHROMOSOME_I 51 1 100D * 0 0 * * 6 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.CO.sam: -------------------------------------------------------------------------------- 1 | @CO → 2 | @CO comment tag:value not needed 3 | @CO 4 | @CO → 5 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.HD1.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.6 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.HD10.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.6 SS:coordinate:flag 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.HD11.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.6 SS:queryname:coordinate 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.HD2.sam: -------------------------------------------------------------------------------- 1 | @HD SO:unknown VN:1.6 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.HD3.sam: -------------------------------------------------------------------------------- 1 | @HD SO:unsorted VN:1.6 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.HD4.sam: -------------------------------------------------------------------------------- 1 | @HD SO:queryname VN:1.6 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.HD5.sam: -------------------------------------------------------------------------------- 1 | @HD SO:coordinate VN:1.6 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.HD6.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.6 GO:none 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.HD7.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.6 GO:query 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.HD8.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.6 GO:reference 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.HD9.sam: -------------------------------------------------------------------------------- 1 | @HD VN:1.6 SS:unsorted:MI:coordinate 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.PG1.sam: -------------------------------------------------------------------------------- 1 | @PG ID:bwa-1 2 | @PG ID:bwa-2 3 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.PG2.sam: -------------------------------------------------------------------------------- 1 | @PG ID:bwa-1 PN:bwa 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.PG3.sam: -------------------------------------------------------------------------------- 1 | @PG ID:bwa-1 CL:echo "🐟" 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.PG4.sam: -------------------------------------------------------------------------------- 1 | @PG ID:fork-2 PP:x 2 | @PG ID:x 3 | @PG ID:fork-1a PP:x 4 | @PG ID:fork-1b PP:fork-1b 5 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.PG5.sam: -------------------------------------------------------------------------------- 1 | @PG ID:x DS:☢ description ☢ 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.PG6.sam: -------------------------------------------------------------------------------- 1 | @PG ID:bwa VN:3.14159265 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.RG1.sam: -------------------------------------------------------------------------------- 1 | @RG ID:x 2 | @RG ID:y 3 | @RG ID:read group for library z 4 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.RG10.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 PL:CAPILLARY 2 | @RG ID:2 PL:DNBSEQ 3 | @RG ID:3 PL:HELICOS 4 | @RG ID:4 PL:ILLUMINA 5 | @RG ID:5 PL:IONTORRENT 6 | @RG ID:6 PL:LS454 7 | @RG ID:7 PL:ONT 8 | @RG ID:8 PL:PACBIO 9 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.RG11.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 PL:CAPILLARY PM:ABI 373A 2 | @RG ID:2 PL:ONT PM:Panthion 3 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.RG12.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 PU:xyz-ACGT.1 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.RG13.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 SM:Clupea harengus rubeum 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.RG2.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 BC:ACGT 2 | @RG ID:2 BC:ACGT-A-C-G-T 3 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.RG3.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 CN:Sanger Institute 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.RG4.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 DT:2020-06-23 2 | @RG ID:2 DT:2020-06-23T12:13:47+01:00 3 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.RG5.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 FO:ACGTRYWKMSBDHVN 2 | @RG ID:2 FO:* 3 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.RG6.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 KS:ACGT 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.RG7.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 LB:Library name 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.RG8.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 PG:bwa 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.RG9.sam: -------------------------------------------------------------------------------- 1 | @RG ID:1 PI:1000 2 | @RG ID:2 PI:123 3 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.SQ1.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:ref LN:1 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.SQ10.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:1 LN:100 UR:https://example.com/1 2 | @SQ SN:2 LN:100 UR:/my/ref.fa 3 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.SQ2.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:ref1a LN:101 AH:ref1:100-200 2 | @SQ SN:ref1 LN:1000 3 | @SQ SN:ref1b LN:101 AH:ref1 4 | @SQ SN:ref1c LN:101 AH:* 5 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.SQ3.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:chr1 LN:99 AN:1 2 | @SQ SN:chr2 LN:99 AN:2,Chr2,CHR2 3 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.SQ4.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:chr1 LN:99 AS:my assembly 2 | @SQ SN:chr2 LN:99 AS:my assembly 3 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.SQ5.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:1 LN:99 DS:description 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.SQ6.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:tea LN:99 DS:☕ 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.SQ7.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:A LN:1 M5:7fc56270e7a70fa81a5935b72eacbe29 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.SQ8.sam: -------------------------------------------------------------------------------- 1 | @SQ SP:C. Elegans LN:1 SN:A 2 | -------------------------------------------------------------------------------- /test/sam/passed/hdr.SQ9.sam: -------------------------------------------------------------------------------- 1 | @SQ SN:long LN:2147483647 TP:linear 2 | @SQ SN:short LN:1 TP:circular 3 | -------------------------------------------------------------------------------- /test/sam/passed/seq.pass2.sam: -------------------------------------------------------------------------------- 1 | fwd 4 * 0 0 * * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 2 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_body_sample_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Sample allele is out of range 3 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 4 | 1 55388 rs182711216 C T,G 100 PASS THETA=0.0102;AA=C GT:GS:GL 0/3:0.000:-0.18,-0.48,-2.49 5 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_fileformat_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat= 2 | ##CauseOfFailure=Empty fileformat 3 | #CHROM POS ID REF ALT QUAL FILTER INFO 4 | 1 123 . TC T . . . 5 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_fileformat_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCF v4.1 2 | ##CauseOfFailure=Whitespace in fileformat 3 | #CHROM POS ID REF ALT QUAL FILTER INFO 4 | 1 123 . TC T . . . 5 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_header_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | #CHROM POSITION ID REF ALT QUAL FILTER INFO FORMAT HG00096 3 | 1 123 . TC T . . . GT 0|0 4 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_header_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 3 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##Some random plain text 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Description contains a linebreak 3 | ##ALT= 5 | #CHROM POS ID REF ALT QUAL FILTER INFO 6 | 1 123 . TC T . . . 7 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Non-closed meta entry 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_009.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair (empty value) 3 | ##reference= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_alt_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Incorrect ALT ID value 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_alt_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Incorrect ALT Number value 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_alt_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Incorrect ALT Type value 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_alt_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=ALT Description must be surrounded by double quotes 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_alt_004.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Incorrect order of ALT fields 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_alt_006.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=The ALT ID contains a whitespace 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_alt_007.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=The ALT ID contains a comma 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_alt_008.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=The ALT ID contains an opening angle bracket 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_alt_009.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=The ALT ID contains a closing angle bracket 3 | ##ALT=B,Description="Deletion with invalid suffix"> 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_assembly_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##assembly= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_assembly_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Non-valid URL 3 | ##assembly=ftp://8080:8080/not-valid/host/to/file.fastq 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_contig_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=contig ID missing 3 | ##contig= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_contig_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=contig ID contains a whitespace 3 | ##contig= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_contig_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=contig ID contains a comma 3 | ##contig= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Incorrect FORMAT Number value 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Incorrect FORMAT Type value 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Incorrect order of FORMAT fields 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_004.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Incorrect FORMAT Number value 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_005.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT DP Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_006.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT DP Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_011.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT GL Type is not Float 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_012.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT GL Number is not G 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_014.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT GP Number is not G 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_015.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT GQ Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_016.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT GQ Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_017.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT GT Type is not String 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_018.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT GT Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_019.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT HQ Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_020.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT HQ Number is not 2 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_021.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT MQ Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_022.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT MQ Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_025.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT PQ Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_026.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT PQ Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_027.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT PS Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_format_028.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=FORMAT PS Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Incorrect INFO Number value 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Incorrect INFO Type value 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Incorrect order of INFO fields 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_004.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Incorrect INFO Number value 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_005.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO AA Type is not String 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . AA=1 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_006.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO AA Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . AA=C 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_013.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO BQ Type is not Float 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . BQ=2 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_014.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO BQ Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . BQ=0.2 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_017.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO DB Type is not Flag 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_018.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO DB Number is not 0 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . DB=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_019.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO DP Type is not Integer 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . DP=X 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_020.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO DP Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . DP=2 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_023.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO H2 Type is not Flag 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_024.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO H2 Number is not 0 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . H2=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_025.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO H3 Type is not Flag 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_026.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO H3 Number is not 0 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . H3=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_027.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO MQ Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . MQ=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_028.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO MQ0 Type is not Integer 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . MQ0=0.2 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_029.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO MQ0 Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . MQ0=2 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_030.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO NS Type is not Integer 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . NS=0.2 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_031.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO NS Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . NS=2 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_036.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO 1000G Type is not Flag 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_info_037.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=INFO 1000G Number is not 0 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . 1000G=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_pedigree_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Genome ID with whitespace 3 | ##PEDIGREE= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_pedigree_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Genome ID with non-accepted punctuation character 3 | ##PEDIGREE= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_pedigreedb_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##pedigreeDB= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_pedigreedb_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##pedigreeDB=<> 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_pedigreedb_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Non-valid URL 3 | ##pedigreeDB=ftp://8080:8080/not-valid/host/to/pedigreeDB 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/failed/failed_meta_sample_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##CauseOfFailure=Genomes field missing 3 | ##SAMPLE= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/passed/passed_fileformat_header_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | #CHROM POS ID REF ALT QUAL FILTER INFO 3 | -------------------------------------------------------------------------------- /test/vcf/4.1/passed/passed_fileformat_header_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 SAMPLE2 SAMPLE3 3 | -------------------------------------------------------------------------------- /test/vcf/4.1/passed/passed_fileformat_header_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 3 | 1 123 . TC T . . . GT 0|0 4 | -------------------------------------------------------------------------------- /test/vcf/4.1/passed/passed_meta_assembly.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##assembly=ftp://www.ebi.ac.uk:8080/valid/host/to/file.fastq 3 | ##assembly=http://123.0.1.2:8080/valid/host/to/file.fastq 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/passed/passed_meta_pedigree.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##PEDIGREE= 3 | #CHROM POS ID REF ALT QUAL FILTER INFO 4 | 1 123 . TC T . . . 5 | -------------------------------------------------------------------------------- /test/vcf/4.1/passed/passed_meta_pedigreedb.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##pedigreeDB=ftp://www.ebi.ac.uk:8080/valid/host/to/file.db 3 | ##pedigreeDB=http://123.0.1.2:8080/valid/host/to/file.db 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.1/passed/passed_meta_sample.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##SAMPLE= 3 | #CHROM POS ID REF ALT QUAL FILTER INFO 4 | 1 123 . TC T . . . 5 | -------------------------------------------------------------------------------- /test/vcf/4.1/passed/passed_ploidy_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 3 | 1 61462 rs56992750 T A 100 PASS . GT 0|0|1 0|1 4 | 1 61480 rs56992751 T A 100 PASS . GT 0 0|1 5 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_fileformat_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat= 2 | ##CauseOfFailure=Empty fileformat 3 | #CHROM POS ID REF ALT QUAL FILTER INFO 4 | 1 123 . TC T . . . 5 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_fileformat_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCF v4.2 2 | ##CauseOfFailure=Whitespace in fileformat 3 | #CHROM POS ID REF ALT QUAL FILTER INFO 4 | 1 123 . TC T . . . 5 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_header_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | #CHROM POSITION ID REF ALT QUAL FILTER INFO FORMAT HG00096 3 | 1 123 . TC T . . . GT 0|0 4 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_header_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 3 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##Some random plain text 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Description contains a linebreak 3 | ##ALT= 5 | #CHROM POS ID REF ALT QUAL FILTER INFO 6 | 1 123 . TC T . . . 7 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_004.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Unstructured meta entry 3 | sdfasI23rt'0'0ºo 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_009.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair (empty value) 3 | ##reference= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_alt_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Incorrect ALT ID value 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_alt_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Incorrect ALT Number value 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_alt_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Incorrect ALT Type value 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_alt_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=ALT Description must be surrounded by double quotes 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_alt_004.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Incorrect order of ALT fields 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_alt_006.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=The ALT ID contains a whitespace 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_alt_007.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=The ALT ID contains a comma 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_alt_008.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=The ALT ID contains an opening angle bracket 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_alt_009.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=The ALT ID contains a closing angle bracket 3 | ##ALT=B,Description="Deletion with invalid suffix"> 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_assembly_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##assembly= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_assembly_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##assembly=ftp://8080:8080/not-valid/host/to/file.fastq 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_contig_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=contig ID missing 3 | ##contig= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_contig_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=contig ID contains a whitespace 3 | ##contig= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_contig_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=contig ID contains a comma 3 | ##contig= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Incorrect FORMAT Number value 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Incorrect FORMAT Type value 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Incorrect order of FORMAT fields 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_004.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT DP Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_005.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT DP Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_010.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT GL Type is not Float 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_011.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT GL Number is not G 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_013.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT GP Number is not G 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_014.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT GQ Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_015.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT GQ Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_016.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT GT Type is not String 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_017.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT GT Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_018.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT HQ Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_019.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT HQ Number is not 2 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_020.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT MQ Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_021.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT MQ Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_024.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT PQ Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_025.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT PQ Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_026.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT PS Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_format_027.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=FORMAT PS Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Incorrect INFO Number value 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Incorrect INFO Type value 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Incorrect order of INFO fields 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_004.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO AA Type is not String 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . AA=1 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_005.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO AA Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . AA=C 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_012.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO BQ Type is not Float 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . BQ=2 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_013.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO BQ Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . BQ=0.2 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_016.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO DB Type is not Flag 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_017.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO DB Number is not 0 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . DB=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_018.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO DP Type is not Integer 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . DP=X 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_019.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO DP Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . DP=2 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_022.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO H2 Type is not Flag 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_023.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO H2 Number is not 0 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . H2=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_024.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO H3 Type is not Flag 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_025.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO H3 Number is not 0 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . H3=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_026.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO MQ Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . MQ=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_027.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO MQ0 Type is not Integer 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . MQ0=0.2 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_028.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO MQ0 Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . MQ0=2 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_029.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO NS Type is not Integer 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . NS=0.2 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_030.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO NS Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . NS=2 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_035.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO 1000G Type is not Flag 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_info_036.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=INFO 1000G Number is not 0 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . 1000G=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_pedigree_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Genome ID with whitespace 3 | ##PEDIGREE= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_pedigree_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Genome ID with non-accepted punctuation character 3 | ##PEDIGREE= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_pedigreedb_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##pedigreeDB= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_pedigreedb_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##pedigreeDB=<> 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_pedigreedb_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Non-valid URL 3 | ##pedigreeDB=ftp://8080:8080/not-valid/host/to/pedigreeDB 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/failed/failed_meta_sample_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##CauseOfFailure=Genomes field missing 3 | ##SAMPLE= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/passed/passed_fileformat_header_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | #CHROM POS ID REF ALT QUAL FILTER INFO 3 | -------------------------------------------------------------------------------- /test/vcf/4.2/passed/passed_fileformat_header_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 SAMPLE2 SAMPLE3 3 | -------------------------------------------------------------------------------- /test/vcf/4.2/passed/passed_fileformat_header_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 3 | 1 123 . TC T . . . GT 0|0 4 | -------------------------------------------------------------------------------- /test/vcf/4.2/passed/passed_meta_assembly.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##assembly=ftp://www.ebi.ac.uk:8080/valid/host/to/file.fastq 3 | ##assembly=http://123.0.1.2:8080/valid/host/to/file.fastq 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/passed/passed_meta_pedigree.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##PEDIGREE= 3 | #CHROM POS ID REF ALT QUAL FILTER INFO 4 | 1 123 . TC T . . . 5 | -------------------------------------------------------------------------------- /test/vcf/4.2/passed/passed_meta_pedigreedb.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##pedigreeDB=ftp://www.ebi.ac.uk:8080/valid/host/to/file.db 3 | ##pedigreeDB=http://123.0.1.2:8080/valid/host/to/file.db 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.2/passed/passed_meta_sample.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.2 2 | ##SAMPLE= 3 | #CHROM POS ID REF ALT QUAL FILTER INFO 4 | 1 123 . TC T . . . 5 | -------------------------------------------------------------------------------- /test/vcf/4.2/passed/passed_ploidy_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 3 | 1 61462 rs56992750 T A 100 PASS . GT 0|0|1 0|1 4 | 1 61480 rs56992751 T A 100 PASS . GT 0 0|1 5 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_body_info_integer_overflow.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##INFO= 3 | ##CauseOfFailure=INFO integer overflow 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . C T 100 PASS INT=2147483648 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_body_no_newline_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=no newline at end of file 3 | #CHROM POS ID REF ALT QUAL FILTER INFO 4 | 1 100 rs180734498 C T 100 PASS AN=2184;AC=249;AF=0.11 -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_body_no_newline_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=no newline at end of file 3 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 4 | 1 100 rs180734498 C T 100 PASS AN=2184;AC=249;AF=0.11 GT 0|0 0|1 -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_body_no_newline_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=no newline at end of file 3 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_body_no_newline_004.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=no newline at end of file 3 | #CHROM POS ID REF ALT QUAL FILTER INFO -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_empty.vcf: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_empty_sample.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/samtools/hts-specs/0d7f8774658f7cee0a4540b0682174e460726432/test/vcf/4.3/failed/failed_empty_sample.vcf -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_fileformat_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat= 2 | ##CauseOfFailure=Empty fileformat 3 | #CHROM POS ID REF ALT QUAL FILTER INFO 4 | 1 123 . TC T . . . 5 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_fileformat_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCF v4.3 2 | ##CauseOfFailure=Whitespace in fileformat 3 | #CHROM POS ID REF ALT QUAL FILTER INFO 4 | 1 123 . TC T . . . 5 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_header_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | #CHROM POSITION ID REF ALT QUAL FILTER INFO FORMAT HG00096 3 | 1 123 . TC T . . . GT 0|0 4 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_header_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 3 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##Some random plain text 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Description contains a linebreak 3 | ##ALT= 5 | #CHROM POS ID REF ALT QUAL FILTER INFO 6 | 1 123 . TC T . . . 7 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_004.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Unstructured meta entry 3 | sdfasI23rt'0'0ºo 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_009.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair (empty value) 3 | ##reference= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_alt_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Incorrect ALT Number value 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_alt_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Incorrect ALT Type value 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_alt_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=ALT Description must be surrounded by double quotes 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_alt_004.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Incorrect order of ALT fields 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_alt_006.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=The ALT ID contains a whitespace 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_alt_007.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=The ALT ID contains a comma 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_alt_008.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=The ALT ID contains an opening angle bracket 3 | ##ALT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_alt_009.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=The ALT ID contains a closing angle bracket 3 | ##ALT=B,Description="Deletion with invalid suffix"> 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_assembly_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##assembly= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_assembly_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##assembly=ftp://8080:8080/not-valid/host/to/file.fastq 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_contig_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=contig ID missing 3 | ##contig= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_contig_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=contig ID contains a whitespace 3 | ##contig= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_contig_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=contig ID contains a comma 3 | ##contig= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_contig_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=contig ID contains illegal character 3 | ##contig= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Incorrect FORMAT Number value 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Incorrect FORMAT Type value 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Incorrect order of FORMAT fields 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_004.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT AD Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_005.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT AD Number is not R 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_010.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT DP Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_011.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT DP Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_016.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT GL Type is not Float 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_017.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT GL Number is not G 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_019.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT GP Number is not G 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_020.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT GQ Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_021.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT GQ Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_022.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT GT Type is not String 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_023.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT GT Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_024.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT HQ Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_025.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT HQ Number is not 2 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_026.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT MQ Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_027.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT MQ Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_030.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT PQ Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_031.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT PQ Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_032.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT PS Type is not Integer 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_format_033.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=FORMAT PS Number is not 1 3 | ##FORMAT= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Incorrect INFO Number value 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Incorrect INFO Type value 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Incorrect order of INFO fields 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_004.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO AA Type is not String 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . AA=1 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_005.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO AA Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . AA=C 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_009.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO AD Number is not R 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . AD=1 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_018.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO BQ Type is not Float 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . BQ=2 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_019.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO BQ Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . BQ=0.2 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_022.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO DB Type is not Flag 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_023.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO DB Number is not 0 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . DB=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_024.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO DP Type is not Integer 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . DP=X 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_025.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO DP Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . DP=2 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_028.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO H2 Type is not Flag 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_029.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO H2 Number is not 0 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . H2=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_030.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO H3 Type is not Flag 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_031.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO H3 Number is not 0 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . H3=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_032.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO MQ Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . MQ=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_033.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO MQ0 Type is not Integer 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . MQ0=0.2 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_034.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO MQ0 Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . MQ0=2 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_035.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO NS Type is not Integer 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . NS=0.2 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_036.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO NS Number is not 1 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . NS=2 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_041.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO 1000G Type is not Flag 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_info_042.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=INFO 1000G Number is not 0 3 | ##INFO= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . 1000G=0 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_meta_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Incorrect META Number value 3 | ##META= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_meta_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Incorrect META Type value 3 | ##META= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_meta_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=META Values must be surrounded by square brackets 3 | ##META= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_meta_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Incorrect order of META fields 3 | ##META= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_pedigree_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Value with whitespace 3 | ##PEDIGREE= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_pedigree_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Original value contains an illegal character 3 | ##PEDIGREE= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_pedigree_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=PEDIGREE ID is missing 3 | ##PEDIGREE= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_pedigreedb_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##pedigreeDB= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_pedigreedb_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Meta-data entry is not a key-value pair 3 | ##pedigreeDB=<> 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_pedigreedb_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=Non-valid URL 3 | ##pedigreeDB=ftp://8080:8080/not-valid/host/to/pedigreeDB 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_sample_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=SAMPLE ID missing 3 | ##SAMPLE= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_sample_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=SAMPLE ID contains a whitespace 3 | ##SAMPLE= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_sample_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=SAMPLE ID contains a comma 3 | ##SAMPLE= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/failed/failed_meta_sample_003.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##CauseOfFailure=SAMPLE ID contains illegal character 3 | ##SAMPLE= 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/passed/passed_fileformat_header_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | #CHROM POS ID REF ALT QUAL FILTER INFO 3 | -------------------------------------------------------------------------------- /test/vcf/4.3/passed/passed_fileformat_header_001.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 SAMPLE2 SAMPLE3 3 | -------------------------------------------------------------------------------- /test/vcf/4.3/passed/passed_fileformat_header_002.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 3 | 1 123 . TC T . . . GT 0|0 4 | -------------------------------------------------------------------------------- /test/vcf/4.3/passed/passed_meta_assembly.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##assembly=ftp://www.ebi.ac.uk:8080/valid/host/to/file.fastq 3 | ##assembly=http://123.0.1.2:8080/valid/host/to/file.fastq 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/passed/passed_meta_pedigreedb.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##pedigreeDB=ftp://www.ebi.ac.uk:8080/valid/host/to/file.db 3 | ##pedigreeDB=http://123.0.1.2:8080/valid/host/to/file.db 4 | #CHROM POS ID REF ALT QUAL FILTER INFO 5 | 1 123 . TC T . . . 6 | -------------------------------------------------------------------------------- /test/vcf/4.3/passed/passed_ploidy_000.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 3 | 1 61462 rs56992750 T A 100 PASS . GT 0|0|1 0|1 4 | 1 61480 rs56992751 T A 100 PASS . GT 0 0|1 5 | --------------------------------------------------------------------------------