beded063af0162677da2324db2f15ac8ada64936
braney
  Fri Jul 3 17:26:50 2020 -0700
add tiers to gencode file..  fix up filters.

diff --git src/hg/lib/gencodeBGP.as src/hg/lib/gencodeBGP.as
new file mode 100644
index 0000000..e74a968
--- /dev/null
+++ src/hg/lib/gencodeBGP.as
@@ -0,0 +1,34 @@
+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;        "Ensembl Id"
+   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;       "UCSC gene id"
+   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;    "Gene Symbol"
+   string geneName2;   "UniProt display ID"
+   string geneType;    "Gene type"
+
+# high level type of transcript (from gencodeAttrs)"
+   string transcriptClass; "Transcript Class"
+   string source; "Source of transcript (from gencodeTranscriptSource)"
+   string transcriptType; "BioType of transcript (from gencodeAttrs)"
+   string tag; "symbolic tags (from gencodeTags)"
+   string level;           "support level, tsl1 is strongest support, tsl5 weakest, NA means not analyzed (from gencodeTranscriptionSupportLevel)"
+# tier:  all, basic, canonical
+   string tier;   "Transcript Tier"
+   )
+