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VCF and gVCF parser for C++ #18

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imedina opened this issue Nov 20, 2014 · 0 comments
Open

VCF and gVCF parser for C++ #18

imedina opened this issue Nov 20, 2014 · 0 comments
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@cyenyxe
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v2.0.0 development

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@imedina
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imedina commented Nov 20, 2014

Old Ragel VCF parser must be adapted to C++
@imedina imedina added this to the v2.0.0 development milestone Nov 20, 2014
@cyenyxe cyenyxe modified the milestone: v2.0.0 development Nov 28, 2014
cyenyxe pushed a commit that referenced this issue Dec 5, 2014
VCF ID column accepts semi-colons. #18 . Fixes #25
e659942
cyenyxe pushed a commit that referenced this issue Dec 5, 2014
Better parsing of chromosome field. #18
2d96767
cyenyxe pushed a commit that referenced this issue Dec 5, 2014
Improved support for structural variants with breakends (paired or si…
5bb622c 
…ngle). #18
cyenyxe pushed a commit that referenced this issue Dec 5, 2014
Accept slash in identifiers for INFO, PEDIGREE, and other meta tags. #18
cefc407
cyenyxe pushed a commit that referenced this issue Dec 5, 2014
Notifying all kind of errors in ALT metadata entries. #18
d5f62e8
cyenyxe pushed a commit that referenced this issue Dec 5, 2014
Notifying all kind of errors in FILTER metadata entries and all meta …
825c16b 
…ID subfields. #18
cyenyxe pushed a commit that referenced this issue Dec 5, 2014
Rule for URL parsing (maybe not the most strict, but works pretty wel…
f2fdea4 
…l). #18
cyenyxe pushed a commit that referenced this issue Dec 5, 2014
Notifying all kind of errors in assembly and pedigreeDB metadata entr…
fd0a705 
…ies. #18
cyenyxe pushed a commit that referenced this issue Dec 5, 2014
Notifying all kind of errors in FORMAT metadata entries. #18
292af77
cyenyxe pushed a commit that referenced this issue Dec 5, 2014
Notifying some errors in INFO metadata entries. #18
a7ff870
cyenyxe pushed a commit that referenced this issue Dec 12, 2014
Added ##contig meta entries to test associated rules. #18
ecd519a
cyenyxe pushed a commit that referenced this issue Jan 7, 2015
Notifying error when contig metadata does not fit ID+URL structure. #18
ed352e3
cyenyxe pushed a commit that referenced this issue Jan 7, 2015
Notifying all kind of errors in INFO metadata entries. #18
ec02745
cyenyxe pushed a commit that referenced this issue Jan 7, 2015
Notifying all kind of errors in SAMPLE metadata entries. #18
94b1742
cyenyxe pushed a commit that referenced this issue Jan 7, 2015
Notifying all kind of errors in PEDIGREE metadata entries. #18
50b144c
cyenyxe pushed a commit that referenced this issue Jan 7, 2015
Generic error messages for pedigreeDB and assembly metadata entries. #18
3a95d00
cyenyxe pushed a commit that referenced this issue Jan 7, 2015
Generic error messages for non-standard metadata entries. #18
6ab8c11
cyenyxe pushed a commit that referenced this issue Jan 7, 2015
Notify errors for CHROM, POS, ID, REF and ALT columns in a VCF record. …
88fd994 
…#18
cyenyxe pushed a commit that referenced this issue Jan 8, 2015
Notify errors for QUAL column in a VCF record. #18
218ccf9
cyenyxe pushed a commit that referenced this issue Jan 8, 2015
Notify errors for FILTER column in a VCF record. #18
33d92af
cyenyxe pushed a commit that referenced this issue Jan 8, 2015
Notify errors for FORMAT column in a VCF record. #18
84818a5
cyenyxe pushed a commit that referenced this issue Jan 8, 2015
Notify errors for samples in a VCF record, and also that GT must be i…
fe29e63 
…n FORMAT. #18
cyenyxe pushed a commit that referenced this issue Jan 8, 2015
Notify errors for standard tags in the INFO column from a VCF record. #…
2dbb774 
…18
cyenyxe pushed a commit that referenced this issue Jan 9, 2015
Notify errors for the header line and for custom INFO tags in from a …
7f7d877 
…VCF record. #18
cyenyxe pushed a commit that referenced this issue Jan 14, 2015
Metadata contig only mandatory field is ID. #18
a8d3b5a
cyenyxe pushed a commit that referenced this issue Jan 14, 2015
Removed redundant metadata error handling and basic VCF record token …
2b314ff 
…storage. #18
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