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@nalinigans nalinigans commented Jan 27, 2025

If vcfheader.vcf exists in the workspace, genomicsdb_query with --list-fields options lists the Description in addition to reporting the Field, Class, Type and Length.
e.g.

./genomicsdb_query -w <ws> --list-fields
Field                Class      Type       Length     Description
-----                -----      ----       ------     -----------
PASS                 FILTER     Integer    1          "All filters passed"
q10                  FILTER     Integer    1          "Quality below 10"
s50                  FILTER     Integer    1          "Less than 50\% \of samples have data"
NS                   INFO       Integer    1          "Number of Samples With Data"
DP                   INFO       Integer    1          "Total Depth"
AF                   INFO       Float      A          "Allele Frequency"
AA                   INFO       String     var        "Ancestral Allele"
DB                   INFO       Flag       1          "dbSNP membership
H2                   INFO       Flag       1          "HapMap2 membership"
GT                   FORMAT     Integer    PP         "Genotype"
VAF                  FORMAT     Float      1          "Variant Allele Fraction"
VP                   FORMAT     Integer    1          "Variant Priority or clinical significance"
...

as against

./genomicsdb_query -w <ws_without_vcfheader_vcf> --list-fields
Field                Class      Type       Length
-----                -----      ----       ------
GQ                   FORMAT     Integer    1
GT                   FORMAT     Integer    PP
BAF                  FORMAT     Float      1
LRR                  FORMAT     Float      1
MIN_DP               FORMAT     Integer    1
PGT                  FORMAT     String     VAR
PID                  FORMAT     String     VAR
PL                   FORMAT     Integer    G
RGQ                  FORMAT     Integer    1
SB                   FORMAT     Integer    4
DS                   FORMAT     Float      1
HDS                  FORMAT     Float      2
...

Nalini Ganapati added 2 commits January 27, 2025 08:40
…plate header files are present in the workspace
@nalinigans nalinigans requested a review from mlathara January 27, 2025 19:04
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lgtm

@nalinigans nalinigans merged commit 69ae32f into develop Jan 29, 2025
17 checks passed
@nalinigans nalinigans deleted the ng_fields_01272025 branch January 29, 2025 23:15
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2 participants