bdc95514b3e8856d9188ab3fb72b370d0fed94b9
baertsch
  Sun May 15 19:18:06 2011 -0700
changes to hgTracks, hgc, hgTrackUi, ucscRetroOrtho, ucscRetroInfo to change data structure and cart handling
diff --git src/hg/lib/ucscRetroInfo.as src/hg/lib/ucscRetroInfo.as
new file mode 100644
index 0000000..38c6509
--- /dev/null
+++ src/hg/lib/ucscRetroInfo.as
@@ -0,0 +1,57 @@
+table ucscRetroInfo
+"Retrogenes based on cDNA alignments that are expressed or processed pseudogenes."
+    (
+    string chrom;	"Reference sequence chromosome or scaffold col1"
+    uint chromStart;	"pseudogene alignment start position col2"
+    uint chromEnd;      "pseudogene alignment end position col3"
+    string name;        "Name of pseudogene col4"
+    uint score;         "score of pseudogene with gene col5"
+    char[2] strand;     "+ or -"
+    uint thickStart;    "Start of where display should be thick (start codon)"
+    uint thickEnd;      "End of where display should be thick (stop codon)"
+    uint reserved;      "Always zero for now"
+    int blockCount;     "Number of blocks"
+    int[blockCount] blockSizes; "Comma separated list of block sizes"
+    int[blockCount] chromStarts; "Start positions relative to chromStart"
+    int retroExonCount;	"number of exons in retroGene col13"
+    int axtScore;       "blastz score, parent mrna aligned to pseudogene col14"
+    string type;	"type of evidence col15"
+    string gChrom;	"Chromosome name col16"
+    int gStart;	        "gene alignment start position col17"
+    int gEnd;           "gene alignment end position col18"
+    char[2] gStrand;    "strand of gene col19"
+    uint parentSpliceCount;     "# of splice sites in parent gene col20"
+    uint geneOverlap;   "bases overlapping col21"
+    uint polyA;         "count of As in polyA col22"
+    int polyAstart;     "start of polyA, relative to end of pseudogene col23"
+    int exonCover;      "number of exons in Gene covered col24"
+    uint intronCount;   "number of introns in pseudogene col25"
+    uint bestAliCount;  "number of good mrnas aligning col26"
+    uint matches;       "matches + repMatches col27"
+    uint qSize;         "aligning bases in pseudogene col28"
+    uint qEnd;          "end of cdna alignment col29"
+    uint tReps;         "repeats in gene col30"
+    uint coverage;      "% of bases that align to gene col31"
+    int label;          "1=pseudogene,-1 not pseudogene -2 expressed retroGene col32"
+    uint milliBad;      "milliBad score, pseudogene aligned to genome col33"
+    uint oldScore;      "another heuristic col34"
+    int oldIntronCount; "old simple intron count col35"
+    int processedIntrons; "count of introns removed via retrotransposition col36"
+    int conservedSpliceSites; "conserved splice site count col37"
+    int maxOverlap ;    "largest overlap with another mrna col38"
+    string refSeq;	"Name of closest regSeq to gene col39"
+    int rStart;	        "refSeq alignment start position col40"
+    int rEnd;           "refSeq alignment end position col41"
+    string mgc;	        "Name of closest mgc to gene col42"
+    int mStart;	        "mgc alignment start position col43"
+    int mEnd;           "mgc alignment end position col44"
+    string kgName;	"Name of closest knownGene to gene col45"
+    int kStart;	        "kg alignment start position col46"
+    int kEnd;           "kg alignment end position col47"
+    string overName;	"name of overlapping mrna col48"
+    int overStart;	"overlapping mrna start position col49"
+    int overExonCover;  "count of overlapping mrna exons col50"
+    char[2] overStrand;  "strand of overlapping mrna col51"
+    float posConf;      "pvalue for positive col52"
+    uint polyAlen;      "length of polyA col53"
+    )