src/hg/lib/genbankTables.as 1.6

Index: src/hg/lib/genbankTables.as
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/genbankTables.as,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/hg/lib/genbankTables.as	23 Jan 2007 19:15:24 -0000	1.5
+++ src/hg/lib/genbankTables.as	7 Jul 2009 18:05:11 -0000	1.6
@@ -1,72 +1,58 @@
 table gbCharacteristic
 "Characteristics of GenBank sequences referenced in the gbCdnaInfo table"
    (
    int    id;              "Unique id of characteristic (referenced by mrna table)"
    string name;            "Characteristic/value"
    int 	  crc;             "Cyclic redundancy check (performance optimization for loading tables)"
    )
 
 table gbLoaded
 "Release, updates and partitions loaded (cached to speed up loading process)"
     (
     enum srcDb;		"Source database: 'GenBank' or 'RefSeq'"
     enum type;		"Full length ('mRNA') or EST ('EST')"
     string loadRelease;	"release version that was loaded"
     string loadUpdate;	"update that was loaded (date or 'full')"
     string accPrefix;   "first two characters of accessions (or empty)"
     timestamp time;	"time that this entry was inserted"
     boolean extFileUpdated;	"true if extFile has been updated"
     )
 
-table gbSeq
-"GenBank sequence metadata"
-    (
-    uint id;		"ID/index"
-    string acc;		"GenBank accession"
-    short version;	"GenBank version number suffix"
-    uint size;		"number of bases in sequence"
-    uint gbExtFile;	"ID/index of sequence file record in gbExtFile table"
-    long file_offset;	"byte offset in sequence file"
-    uint file_size;	"byte length of sequence in sequence file"
-    enum type;		"Full length ('mRNA') or EST ('EST')"
-    enum srcDb;		"Source database: 'GenBank' or 'RefSeq'"
-    )
-
 table gbStatus
 "GenBank version info for alignments in the database"
     (
     string acc;		"GenBank accession"
     short version;	"GenBank version number suffix"
     date modDate;	"last modified date"
     enum type;		"Full length ('mRNA') or EST ('EST')"
     enum srcDb;		"Source database: 'GenBank' or 'RefSeq'"
     enum orgCat;	"Organism category: this ('native') or other ('xeno')"
     uint gbSeq;		"ID/index in gbSeq table"
     uint numAligns;	"number of alignments of the accession"
     string seqRelease;	"release version where the sequence was obtained"
     string seqUpdate;	"update where sequence was obtained (date or 'full')"
     string metaRelease;	"release version where the metadata was obtained"
     string metaUpdate;	"update where metadata was obtained (date or 'full')"
     string extRelease;	"release version containing the external file"
     string extUpdate;	"update containing the external file (date or 'full')"
     timestamp time;	"time that this entry was inserted"
     )
 
 table mgcFullStatus
 "Status of full-CDS MGC clones"
     (
     uint imageId;	"IMAGE ID for clone"
     enum status;	"MGC status code: ('unpicked','candidate','picked','notBack','noDecision','fullLength','fullLengthShort','fullLengthSynthetic','incomplete','chimeric','frameShift','contaminated','retainedIntron','mixedWells','noGrowth','noInsert','no5est','microDel','artifact','noPolyATail','cantSequence','inconsistentWithGene')"
     enum state;		"MGC state code: ('unpicked', 'pending', 'fullLength', 'problem')"
     string acc;		"GenBank accession"
     string organism;	"organism code"
     string geneName;	"RefSeq accession for gene, if available"
     )
 
 table refSeqSummary
 "Summary or completeness info for RefSeqs (when given in comments)"
     (
     string mrnaAcc;	"NM_* RefSeq mRNA accession"
     enum completeness;	"'Complete5End', 'Complete3End', 'FullLength', 'IncompleteBothEnds', 'Incomplete5End', 'Incomplete3End', 'Partial', 'Unknown'"
     string summary;	"Summary comments"
     )