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* Add vCard with sample * Add sample + remove comment in yml * Add vCard grammar * Add id * Edit aliases * Add vcf to TSV + heuristics * Add test
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##fileformat=VCFv4.1 | ||
##source=Sniffles | ||
##fileDate=20190902 | ||
##contig=<ID=1,length=249250621> | ||
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##contig=<ID=GL000209.1,length=159169> | ||
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##contig=<ID=GL000213.1,length=164239> | ||
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##contig=<ID=GL000223.1,length=180455> | ||
##contig=<ID=GL000195.1,length=182896> | ||
##contig=<ID=GL000212.1,length=186858> | ||
##contig=<ID=GL000222.1,length=186861> | ||
##contig=<ID=GL000200.1,length=187035> | ||
##contig=<ID=GL000193.1,length=189789> | ||
##contig=<ID=GL000194.1,length=191469> | ||
##contig=<ID=GL000225.1,length=211173> | ||
##contig=<ID=GL000192.1,length=547496> | ||
##contig=<ID=NC_007605,length=171823> | ||
##contig=<ID=hs37d5,length=35477943> | ||
##ALT=<ID=DEL,Description="Deletion"> | ||
##ALT=<ID=DUP,Description="Duplication"> | ||
##ALT=<ID=INV,Description="Inversion"> | ||
##ALT=<ID=INVDUP,Description="InvertedDUP with unknown boundaries"> | ||
##ALT=<ID=TRA,Description="Translocation"> | ||
##ALT=<ID=INS,Description="Insertion"> | ||
##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation"> | ||
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant"> | ||
##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends"> | ||
##INFO=<ID=RE,Number=1,Type=Integer,Description="read support"> | ||
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> | ||
##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation"> | ||
##INFO=<ID=UNRESOLVED,Number=0,Type=Flag,Description="An insertion that is longer than the read and thus we cannot predict the full size."> | ||
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of the SV"> | ||
##INFO=<ID=REF_strand,Number=2,Type=Integer,Description="Length of the SV"> | ||
##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV"> | ||
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | ||
##INFO=<ID=SEQ,Number=1,Type=String,Description="Extracted sequence from the best representative read."> | ||
##INFO=<ID=STD_quant_start,Number=A,Type=Float,Description="STD of the start breakpoints across the reads."> | ||
##INFO=<ID=STD_quant_stop,Number=A,Type=Float,Description="STD of the stop breakpoints across the reads."> | ||
##INFO=<ID=Kurtosis_quant_start,Number=A,Type=Float,Description="Kurtosis value of the start breakpoints across the reads."> | ||
##INFO=<ID=Kurtosis_quant_stop,Number=A,Type=Float,Description="Kurtosis value of the stop breakpoints across the reads."> | ||
##INFO=<ID=SUPTYPE,Number=A,Type=String,Description="Type by which the variant is supported.(SR,ALN,NR)"> | ||
##INFO=<ID=STRANDS,Number=A,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> | ||
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency."> | ||
##INFO=<ID=ZMW,Number=A,Type=Integer,Description="Number of ZMWs (Pacbio) supporting SV."> | ||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference reads"> | ||
##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant reads"> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT alns_merged/hs37d5.all.md.bam | ||
1 10001 27885 N <INS> . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=1;END=10407;ZMW=4;STD_quant_start=0.500000;STD_quant_stop=78.452215;Kurtosis_quant_start=1.000000;Kurtosis_quant_stop=-1.530914;SVTYPE=INS;SUPTYPE=SR;SVLEN=406;STRANDS=-+;RE=4 GT:DR:DV ./.:.:4 | ||
1 10329 1 CCCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=1;END=10390;ZMW=21;STD_quant_start=0.316228;STD_quant_stop=3.794733;Kurtosis_quant_start=-0.866914;Kurtosis_quant_stop=-1.344369;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-61;STRANDS=+-;RE=21 GT:DR:DV ./.:.:21 | ||
1 10407 2 N CACCCTCACCCTCACCCTCACCCCCACCCCCACCCCCACCCCCACCCCCACCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=1;END=10461;ZMW=20;STD_quant_start=0.000000;STD_quant_stop=0.316228;Kurtosis_quant_start=-1.254650;Kurtosis_quant_stop=0.212091;SVTYPE=INS;SUPTYPE=AL;SVLEN=54;STRANDS=+-;RE=20 GT:DR:DV ./.:.:20 | ||
1 10862 3 N CAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGGGCCGGCGCAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=1;END=10996;ZMW=77;STD_quant_start=0.000000;STD_quant_stop=19.477382;Kurtosis_quant_start=-1.283652;Kurtosis_quant_stop=-2.008307;SVTYPE=INS;SUPTYPE=AL;SVLEN=47;STRANDS=+-;RE=77 GT:DR:DV ./.:.:77 | ||
1 136934 4 N CAAGGGGCTCGGGCTGACCTCTGTCCGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCGGGCTGACCTCTCTCAGTGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCACGCTGACCTCTGTCTGCGTGGGAGGGGCCGGTGTGAGACAAGGGGCTCGGGCTGACCTCTCTCAGCGTGGGAGGGGCCGGTGTGAGGCAAGGGGCTCGGGCTGACCTCTCTCAGCGTGGGAGGGGCCAGTGTGAGGCAAGGGCTCACACTGACCTCTCTCAGCATGGGAGGGGCCGGTGTGAGA . PASS PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=1;END=137227;ZMW=14;STD_quant_start=0.000000;STD_quant_stop=2.549510;Kurtosis_quant_start=2.193074;Kurtosis_quant_stop=2.855605;SVTYPE=INS;SUPTYPE=AL;SVLEN=293;STRANDS=+-;RE=14 GT:DR:DV ./.:.:14 | ||
1 533244 5 N CGGGTGCCATCTCAGCAGCTCACGGTGTGGAAACTGCGACACTCACGCGGGTGCCATCTCAGCAGCTCACGGTGTGGAAACTGCGACACTCACA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=1;END=533338;ZMW=3;STD_quant_start=27.135463;STD_quant_stop=25.980762;Kurtosis_quant_start=-0.000000;Kurtosis_quant_stop=0.000000;SVTYPE=INS;SUPTYPE=AL;SVLEN=94;STRANDS=+-;RE=3 GT:DR:DV ./.:.:3 | ||
1 545927 6 N TGCAGGAGAGGAGATGCCCAGGCCTGGCGGCCGGCGCACGCGGGTTCTCTGTGGCCAGCAGGCGGCGCTGCAGGAGAGGAGATGCCCAGGCCAGGCGGCCGGCGCACGCGGGTTCTCTGTGGCCAGCAGGCGGCGCTGCAGGAGAGGAGATGCCCAGGCCTGGCGGCCGGCGCACGCGGGTTCTCTGTGGCCAGCAGGCGGCGA . PASS PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=1;END=546131;ZMW=23;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=4.593400;Kurtosis_quant_stop=4.281659;SVTYPE=INS;SUPTYPE=AL;SVLEN=204;STRANDS=+-;RE=23 GT:DR:DV ./.:.:23 | ||
1 605031 7 N TACATGGAGGGGAACAACACACACCAGGGCCTCTCAGGGGGACAGGGGGTAGGAGACCATCAGGACAAACACGTGGATACATGGAGGGGAACAACACACACCAGGGCCTCTCAGGGGGACAGGGGGTAGGAGACCATCAGGACAAACACGTGGATACATGGAGGGGAACAACACACACCAGGGCCTCTCAGGGGGACAGGGGGTAGGAGACCATCAGGACAAACACGTGGG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=1;END=605262;ZMW=9;STD_quant_start=45.186035;STD_quant_stop=44.628093;Kurtosis_quant_start=2.035202;Kurtosis_quant_stop=1.944981;SVTYPE=INS;SUPTYPE=AL;SVLEN=231;STRANDS=+-;RE=9 GT:DR:DV ./.:.:9 | ||
1 662612 8 N GTGAGACAAGGGGCTCACGCTGACCTCTGTCCACGTGGGAGGGGCCGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=1;END=662661;ZMW=4;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=-nan;Kurtosis_quant_stop=-nan;SVTYPE=INS;SUPTYPE=AL;SVLEN=49;STRANDS=+-;RE=4 GT:DR:DV ./.:.:4 | ||
1 664891 9 GCAGGAGCTGGGCCTGGAGAGGCTGCAAAGAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=1;END=664923;ZMW=4;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=-nan;Kurtosis_quant_stop=-nan;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-32;STRANDS=+-;RE=4 GT:DR:DV ./.:.:4 | ||
1 725451 10 GGATGGGATGCGATGGGATGGGATGGGATGGGATGGGATGGGATGGGATGGATTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=1;END=725506;ZMW=3;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=-nan;Kurtosis_quant_stop=-nan;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-55;STRANDS=+-;RE=3 GT:DR:DV ./.:.:3 | ||
1 756259 11 N TCTACACTACCTGCCTGGCCAGCAGATCCACCCTGTCTACACTACCTGCCTGGGCAGTAGTTCCACGCAATCTCCCCTACCTGCCTCTCCAGCAGACCCGCCCTATCTATACTACTTGCCTGTCCAGCAGATCCACTCTATCTACACGACCTGCCTGTCCAGCAGATCCACCCTGTCTACACTACCTGCTTGTCCAGCAGGTCCACCCTGTCTATACTACCTGCCTGGCCAGTAGATCCACACTA . PASS PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=1;END=756504;ZMW=19;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=1.759442;Kurtosis_quant_stop=1.789241;SVTYPE=INS;SUPTYPE=AL;SVLEN=245;STRANDS=+-;RE=19 GT:DR:DV ./.:.:19 |
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---|---|---|
@@ -0,0 +1,12 @@ | ||
##fileformat=VCFv4.2 | ||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> | ||
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> | ||
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> | ||
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | ||
##INFO=<ID=LV,Number=1,Type=Integer,Description="Level in the snarl tree (0=top level)"> | ||
##INFO=<ID=PS,Number=1,Type=String,Description="ID of variant corresponding to parent snarl"> | ||
##INFO=<ID=AT,Number=R,Type=String,Description="Allele Traversal as path in graph"> | ||
##contig=<ID=a,length=630> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b | ||
a 281 >1>9 AGCCGGGGCAGAAAGTTCTTCCTTGAATGTGGTCATCTGCATTTCAGCTCAGGAATCCTGCAAAAGACAG CTGTCTTTTGCAGGATTCCTGTGCTGAAATGCAGATGACCGCATTCAAGGAAGAACTATCTGCCCCGGCT 60.0 . AC=1;AF=1;AN=1;AT=>1>2>3>4>5>6>7>8>9,>1<8>10<6>11<4>12<2>9;NS=1;LV=0 GT 1 |
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@@ -0,0 +1,16 @@ | ||
BEGIN:VCARD | ||
VERSION:2.1 | ||
N:Gump;Forrest | ||
FN:Forrest Gump | ||
ORG:Bubba Gump Shrimp Co. | ||
TITLE:Shrimp Man | ||
PHOTO;GIF:http://www.example.com/dir_photos/my_photo.gif | ||
TEL;WORK;VOICE:(111) 555-1212 | ||
TEL;HOME;VOICE:(404) 555-1212 | ||
ADR;WORK:;;100 Waters Edge;Baytown;LA;30314;United States of America | ||
LABEL;WORK;ENCODING=QUOTED-PRINTABLE:100 Waters Edge=0D=0ABaytown, LA 30314=0D=0AUnited States of America | ||
ADR;HOME:;;42 Plantation St.;Baytown;LA;30314;United States of America | ||
LABEL;HOME;ENCODING=QUOTED-PRINTABLE:42 Plantation St.=0D=0ABaytown, LA 30314=0D=0AUnited States of America | ||
EMAIL;PREF;INTERNET:[email protected] | ||
REV:20080424T195243Z | ||
END:VCARD |
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@@ -0,0 +1,34 @@ | ||
BEGIN:VCARD | ||
VERSION:4.0 | ||
ADR;TYPE=work:pobox;apt;street;city;state;zipcode;country | ||
ANNIVERSARY:19960415 | ||
BDAY:--0203 | ||
CALADRURI:http://example.com/calendar/jdoe | ||
CALURI;MEDIATYPE=text/calendar:ftp://ftp.example.com/calA.ics | ||
CLIENTPIDMAP:1;urn:uuid:3df403f4-5924-4bb7-b077-3c711d9eb34b | ||
EMAIL;TYPE=work:[email protected] | ||
FBURL;MEDIATYPE=text/calendar:ftp://example.com/busy/project-a.ifb | ||
FN:J. Doe | ||
GENDER:M;Fellow | ||
GEO:geo:37.386013\,-122.082932 | ||
IMPP;PREF=1:xmpp:[email protected] | ||
KEY:http://www.example.com/keys/jdoe.cer | ||
KIND:individual | ||
LANG;PREF=1:fr | ||
LOGO:http://www.example.com/pub/logos/abccorp.jpg | ||
MEMBER:urn:uuid:03a0e51f-d1aa-4385-8a53-e29025acd8af | ||
N:Stevenson;John;Philip,Paul;Dr.;Jr.,M.D.,A.C.P. | ||
NICKNAME;TYPE=work:Boss | ||
NOTE:This fax number is operational 0800 to 1715 EST\, Mon-Fri | ||
ORG:ABC\, Inc.;North American Division;Marketing | ||
PHOTO:http://www.example.com/pub/photos/jqpublic.gif | ||
RELATED;TYPE=friend:urn:uuid:f81d4fae-7dec-11d0-a765-00a0c91e6bf6 | ||
REV:19951031T222710Z | ||
ROLE:Project Leader | ||
SOUND:CID:[email protected] | ||
SOURCE:ldap://ldap.example.com/cn=Babs%20Jensen\,%20o=Babsco\,%20c=US | ||
TEL;VALUE=uri;TYPE=home:tel:+33-01-23-45-67 | ||
TITLE:Research Scientist | ||
TZ;VALUE=utc-offset:-0500 | ||
XML:<html xmlns="http://www.w3.org/1999/xhtml"></html> | ||
END:VCARD |
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Submodule vscode-vcard
added at
875ceb
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@@ -0,0 +1,21 @@ | ||
--- | ||
name: vscode-vcard | ||
version: 875ceb468d7042685faa3a8f0db3bef3a3a1aaac | ||
type: git_submodule | ||
homepage: https://github.com/cstrachan88/vscode-vcard.git | ||
license: mit | ||
licenses: | ||
- sources: LICENSE.txt | ||
text: |- | ||
The MIT License | ||
Copyright 2019 Courtney Strachan | ||
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: | ||
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. | ||
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. | ||
- sources: README.md | ||
text: This project is licensed under the [MIT License](LICENSE.txt). | ||
notices: [] |