diff bigPsl.as @ 0:f493979f1408 draft default tip

planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bigPsl.as	Wed Dec 21 12:13:04 2016 -0500
@@ -0,0 +1,33 @@
+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"
+
+    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"
+
+    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 "
+    )
+