314b81670d2d1446d4da81108ac0ce2a72fc569d
markd
  Fri Jan 6 15:32:57 2017 -0800
bigTransMap hgc working

diff --git src/hg/lib/bigTransMap.as src/hg/lib/bigTransMap.as
new file mode 100644
index 0000000..5d9087d
--- /dev/null
+++ src/hg/lib/bigTransMap.as
@@ -0,0 +1,47 @@
+table bigTransMap
+"bigPsl derived pairwise alignment with additional information"
+    (
+    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), faction identity * 1000"
+    char[1] strand;     "+ or - indicates whether the query aligns to the + or - strand on the reference"
+    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"
+
+    uint    oChromStart;"Start position in other chromosome"
+    uint    oChromEnd;  "End position in other chromosome"
+    char[1] oStrand;    "+ or -, - means that psl was reversed into BED-compatible coordinates" 
+    uint    oChromSize; "Size of other chromosome."
+    int[blockCount] oChromStarts; "Start positions relative to oChromStart or from oChromStart+oChromSize depending on strand"
+
+    lstring  oSequence;  "Sequence on other chrom (or edit list, or empty)"
+    lstring  oCDS;       "CDS in NCBI format"
+
+    uint    chromSize;"Size of target chromosome"
+
+    uint match;        "Number of bases matched."
+    uint misMatch; " Number of bases that don't match "
+    uint repMatch; " Number of bases that match but are part of repeats "
+    uint nCount;   " Number of 'N' bases "
+    uint seqType;    "0=empty, 1=nucleotide, 2=amino_acid"
+    string srcDb;   "source organism database names"
+    string srcChrom;  "source organism chromosome name"
+    uint srcChromStart; "start position in source chromosome"
+    uint srcChromEnd; "end position in source chromosome"
+    uint srcScore;    "source source (faction identity * 1000)
+    uint srcAligned;   "fraction of source aligned (faction identity * 1000)
+    string geneName;  "gene name"
+    string geneId;  "gene identifier"
+    string geneType; "type of gene"
+    string transcriptType; "type of transcript"
+    string chainType;  "type of chains used for mapping"
+    string commonName; "common organism name"
+    string orgAbbrev;  "organism abbreviation"
+    )
+