dccdf29485000ddce07f65a431d52a51ffd158cf
braney
  Wed Nov 16 18:41:22 2016 -0800
add support for protein psls in bigPsl

diff --git src/hg/lib/bigPsl.as src/hg/lib/bigPsl.as
index 96b9911..a8c9bdd 100644
--- src/hg/lib/bigPsl.as
+++ src/hg/lib/bigPsl.as
@@ -1,33 +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 - 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)"
     string   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"
     )