808fa9a4c306d2d85df51d5c7c8ea9976a0fb0f1
max
  Thu Apr 30 11:41:48 2020 -0700
adding genbankToBigGenePred tool, right now only for wuhCor1 assembly, but possibly useful elsewhere, as per emails with Braney

diff --git src/hg/lib/genbankBigGenePred.as src/hg/lib/genbankBigGenePred.as
new file mode 100644
index 0000000..7c16ec4
--- /dev/null
+++ src/hg/lib/genbankBigGenePred.as
@@ -0,0 +1,31 @@
+table bigGenePred
+"bigGenePred gene models"
+(
+   string chrom;       "Reference sequence chromosome or scaffold"
+   uint   chromStart;  "Start position in chromosome"
+   uint   chromEnd;    "End position in chromosome"
+   string name;        "Name or ID of item, ideally both human readable and unique"
+   uint score;         "Score (0-1000)"
+   char[1] strand;     "+ or - for strand"
+   uint thickStart;    "Start of where display should be thick (start codon)"
+   uint thickEnd;      "End of where display should be thick (stop codon)"
+   uint reserved;       "RGB value (use R,G,B string in input file)"
+   int blockCount;     "Number of blocks"
+   int[blockCount] blockSizes; "Comma separated list of block sizes"
+   int[blockCount] chromStarts; "Start positions relative to chromStart"
+   string name2;       "Alternative/human readable name"
+   string cdsStartStat; "Status of CDS start annotation (none, unknown, incomplete, or complete)"
+   string cdsEndStat;   "Status of CDS end annotation (none, unknown, incomplete, or complete)"
+   int[blockCount] exonFrames; "Exon frame {0,1,2}, or -1 if no frame for exon"
+   string type;        "Transcript type"
+   string geneName;    "Primary identifier for gene"
+   string geneName2;   "Alternative/human readable gene name"
+   string geneType;    "Gene type"
+   string note;    "Notes"
+   string product;    "Protein Product"
+   string geneId;    "NCBI Gene ID"
+   lstring _cdnaSeq;    "cDNA Sequence"
+   lstring _cdnaPsl;    "cDNA to genome PSL alignment (or empty)"
+   lstring _protSeq;    "Protein Sequence"
+   lstring _protPsl;    "protein to cDNA PSL alignment (or empty)"
+)