Avoid clearing ID/QUAL/FILTER/INFO fields when decomposing multi-alleleic

[chapmanb]

Adrian;
The latest fixes to decompose to pass along the FORMAT DP field (e51d17e) cleared all of the other variant fields, losing information like IDs, filters and quals and causing downstream errors (bcbio/bcbio-nextgen#744).
This avoids clearing these.

Here's a small test case that shows the problem.

##fileformat=VCFv4.1
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=GC,Number=1,Type=Integer,Description="GC content around the variant (see docs for window size details)">
##contig=<ID=1,length=249250621>
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  A   B
1   1460793 rs123   CTT CT,C    .   PASS    GC=40   GT  0|1 1|2
1   1460797 .   G   C,A .   PASS    GC=41   GT  0|1 1|2

Thanks much.

[atks]

ok, done. please update vt.

warm regards,

Adrian

On Tue, Feb 10, 2015 at 5:19 AM, Brad Chapman notifications@github.com
wrote:

Adrian;
The latest fixes to decompose to pass along the FORMAT DP field
(e51d17e
e51d17e
)
cleared all of the other variant fields, losing information like IDs,
filters and quals and causing downstream errors (
bcbio/bcbio-nextgen#744
bcbio/bcbio-nextgen#744).
This avoids clearing these.

Here's a small test case that shows the problem.

##fileformat=VCFv4.1
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=GC,Number=1,Type=Integer,Description="GC content around the variant (see docs for window size details)">
##contig=<ID=1,length=249250621>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
1 1460793 rs123 CTT CT,C . PASS GC=40 GT 0|1 1|2
1 1460797 . G C,A . PASS GC=41 GT 0|1 1|2

Thanks much.

You can view, comment on, or merge this pull request online at:

#6
Commit Summary

• Avoid clearing ID/QUAL/FILTER/INFO fields when decomposing
  multi-alleleic

File Changes

• M decompose.cpp https://github.com/atks/vt/pull/6/files#diff-0
  (1)

Patch Links:

• https://github.com/atks/vt/pull/6.patch
• https://github.com/atks/vt/pull/6.diff

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#6.