0df7d8fdb7c40a393e33791956a8c98ab460dead
markd
  Thu May 23 10:54:50 2019 -0700
import mouse GENCODE VM22 pre-release

diff --git src/hg/makeDb/outside/gencode/gencodeGenerateTrackDbs src/hg/makeDb/outside/gencode/gencodeGenerateTrackDbs
index b967853..81bf596 100755
--- src/hg/makeDb/outside/gencode/gencodeGenerateTrackDbs
+++ src/hg/makeDb/outside/gencode/gencodeGenerateTrackDbs
@@ -460,68 +460,68 @@
         "    {orgHgDb}.wgEncodeGencodeAttrsV{gencodeVer}.transcriptId  minCheck=0.63",
         "",
         "identifier wgEncodeGencodeRefSeqV{gencodeVer}",
         '"Link together Gencode RefSeq table with Attributes table"',
         "    {orgHgDb}.wgEncodeGencodeRefSeqV{gencodeVer}.transcriptId dupeOk",
         "    {orgHgDb}.wgEncodeGencodeAttrsV{gencodeVer}.transcriptId minCheck=0.05",
         "",
         "identifier wgEncodeGencodeRefSeqToRefGeneV{gencodeVer}",
         '"Link together Gencode RefSeq table with refGene track"',
         "    {orgHgDb}.wgEncodeGencodeRefSeqV{gencodeVer}.rnaAcc dupeOk chopAfter=.",
         "    {orgHgDb}.refGene.name minCheck=0.77",
         "",
         "identifier wgEncodeGencodeTagV{gencodeVer}",
         '"Link together Gencode Tag table with Attributes table"',
         "    {orgHgDb}.wgEncodeGencodeTagV{gencodeVer}.transcriptId dupeOk",
-        "    {orgHgDb}.wgEncodeGencodeAttrsV{gencodeVer}.transcriptId minCheck=0.373378",
+        "    {orgHgDb}.wgEncodeGencodeAttrsV{gencodeVer}.transcriptId minCheck=0.36",
         "    {orgHgDb}.wgEncodeGencodeRefSeqV{gencodeVer}.transcriptId minCheck=0.9",
         "",
         "identifier wgEncodeGencodeTranscriptSourceV{gencodeVer}",
         '"Link together Gencode Transcript Source table with Attributes table"',
         "    {orgHgDb}.wgEncodeGencodeTranscriptSourceV{gencodeVer}.transcriptId",
         "    {orgHgDb}.wgEncodeGencodeAttrsV{gencodeVer}.transcriptId",
         "",
         "identifier wgEncodeGencodeTranscriptSupportV{gencodeVer}",
         '"Link together Gencode Transcript Support table with Attributes table"',
         "    {orgHgDb}.wgEncodeGencodeTranscriptSupportV{gencodeVer}.transcriptId dupeOk",
         "    {orgHgDb}.wgEncodeGencodeAttrsV{gencodeVer}.transcriptId minCheck=0.20",
         "",
         "identifier wgEncodeGencodeTranscriptionSupportLevelV{gencodeVer}",
         '"Link together Gencode Transcription Support Level table with Attributes table"',
         "    {orgHgDb}.wgEncodeGencodeTranscriptionSupportLevelV{gencodeVer}.transcriptId dupeOk",
         "    {orgHgDb}.wgEncodeGencodeAttrsV{gencodeVer}.transcriptId minCheck=0.30",
         "",
         "identifier wgEncodeGencodeUniProtV{gencodeVer}",
         '"Link together Gencode UniProt Support table with Attributes table"',
         "    {orgHgDb}.wgEncodeGencodeUniProtV{gencodeVer}.transcriptId dupeOk",
-        "    {orgHgDb}.wgEncodeGencodeAttrsV{gencodeVer}.transcriptId minCheck=0.358209",
+        "    {orgHgDb}.wgEncodeGencodeAttrsV{gencodeVer}.transcriptId minCheck=0.35",
         "",
         "identifier wgEncodeGencodeAnnotationRemarkV{gencodeVer}",
         '"Link together Gencode Annotation Remark table with Attributes table"',
         "    {orgHgDb}.wgEncodeGencodeAnnotationRemarkV{gencodeVer}.transcriptId dupeOk",
         "    {orgHgDb}.wgEncodeGencodeAttrsV{gencodeVer}.transcriptId minCheck=0.10",
         "",
         "identifier wgEncodeGencodeEntrezGeneV{gencodeVer}",
         '"Link together Gencode UniProt Support table with Attributes table"',
         "    {orgHgDb}.wgEncodeGencodeEntrezGeneV{gencodeVer}.transcriptId dupeOk",
-        "    {orgHgDb}.wgEncodeGencodeEntrezGeneV{gencodeVer}.transcriptId minCheck=0.358209",
+        "    {orgHgDb}.wgEncodeGencodeEntrezGeneV{gencodeVer}.transcriptId minCheck=0.35",
     ""))
     yield forStd(params, (
         "identifier wgEncodeGencodeExonSupportV{gencodeVer}",
         '"Link together Gencode Exon Support table with Attributes table"',
         "    {orgHgDb}.wgEncodeGencodeExonSupportV{gencodeVer}.transcriptId dupeOk",
-        "    {orgHgDb}.wgEncodeGencodeAttrsV{gencodeVer}.transcriptId minCheck=0.95",
+        "    {orgHgDb}.wgEncodeGencodeAttrsV{gencodeVer}.transcriptId minCheck=0.90",
         ""))
     yield forBoth(params, (
         "# end Gencode V{gencodeVer}",
         ""))
 
 def hgSql(orgHgDb, sql):
     return subprocess.check_output(["hgsql", orgHgDb, "-Ne", sql]).split('\n')[0:-1]
 
 def gitAdd(fname):
     subprocess.check_call(["git", "add", fname])
 
 def getTransBioTypes(orgHgDb, gencodeVer):
     "obtain sorted list of transcript biotypes"
     return hgSql(orgHgDb, "SELECT DISTINCT(transcriptType) FROM wgEncodeGencodeAttrsV{} ORDER BY transcriptType".format(gencodeVer))