a303141f78d58be17a8ceedf12293a64a86ea15b
hartera
  Fri Apr 19 15:57:55 2013 -0700
Removed oldScore column as no longer used. Renamed oldIntronCount as alignGapCount and modified description.
diff --git src/hg/lib/ucscRetroInfo.as src/hg/lib/ucscRetroInfo.as
index 38c6509..016a073 100644
--- src/hg/lib/ucscRetroInfo.as
+++ src/hg/lib/ucscRetroInfo.as
@@ -1,57 +1,56 @@
 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"
+    int alignGapCount; "simple intron count col34"
+    int processedIntrons; "count of introns removed via retrotransposition col35"
+    int conservedSpliceSites; "conserved splice site count col36"
+    int maxOverlap ;    "largest overlap with another mrna col37"
+    string refSeq;	"Name of closest regSeq to gene col38"
+    int rStart;	        "refSeq alignment start position col39"
+    int rEnd;           "refSeq alignment end position col40"
+    string mgc;	        "Name of closest mgc to gene col41"
+    int mStart;	        "mgc alignment start position col42"
+    int mEnd;           "mgc alignment end position col43"
+    string kgName;	"Name of closest knownGene to gene col44"
+    int kStart;	        "kg alignment start position col45"
+    int kEnd;           "kg alignment end position col46"
+    string overName;	"name of overlapping mrna col47"
+    int overStart;	"overlapping mrna start position col48"
+    int overExonCover;  "count of overlapping mrna exons col49"
+    char[2] overStrand;  "strand of overlapping mrna col50"
+    float posConf;      "pvalue for positive col51"
+    uint polyAlen;      "length of polyA col52"
     )