f5c9593440ecc2d53a2c7467968b599a9958efc4
braney
  Thu Mar 19 11:32:48 2015 -0700
first cut at bigPsl format

diff --git src/hg/lib/bigPsl.as src/hg/lib/bigPsl.as
new file mode 100644
index 0000000..16df4e5
--- /dev/null
+++ src/hg/lib/bigPsl.as
@@ -0,0 +1,34 @@
+table bigPsl
+"bigPsl pairwise alignment"
+   (
+   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)"
+   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  oChrom;     "Other chromosome in the alignment"
+   uint    oChromStart;"Start position in other chromosome"
+   uint    oChromEnd;  "End position in other chromosome"
+   char[1] oStrand;    "+ or - for other strand"
+   uint    oChromSize; "Size of other chromosome."
+   int[blockCount] oChromStarts; "Start positions relative to oChromStart"
+
+   uint  match;        "Number of bases matched."
+   uint matches;       "Number of matching bases that aren't repeats."
+   uint misMatches;    "Number of bases that don't match."
+   uint repMatches;    "Number of matching bases that are part of repeats."
+   uint nCount;        "Number of 'N' bases."
+   uint qNumInsert;    "Number of inserts in query."
+   uint qBaseInsert;   "Number of bases inserted into query."
+   uint tNumInsert;    "Number of inserts in target."
+   uint tBaseInsert;   "Number of bases inserted into target."
+   )
+