e98c85437ca0f563e15b62b624836938de72e339
max
  Thu May 22 09:13:08 2014 -0700
as long as we don't have bigPsl this is some replacement
diff --git src/hg/pslToBed/pslToBed.c src/hg/pslToBed/pslToBed.c
index 05a9471..8fb0fc0 100644
--- src/hg/pslToBed/pslToBed.c
+++ src/hg/pslToBed/pslToBed.c
@@ -6,36 +6,41 @@
 #include "options.h"
 
 
 void usage()
 /* print usage infomation and exit */
 {
 errAbort("pslToBed: tranform a psl format file to a bed format file.\n"
          "usage:\n"
          "    pslToBed psl bed\n"
 	 "options:\n"
 	 "    -cds=cdsFile\n"
 	 "cdsFile specifies a input cds tab-separated file which contains\n"
 	 "genbank-style CDS records showing cdsStart..cdsEnd\n"
 	 "e.g. NM_123456 34..305\n"
 	 "These coordinates are assumed to be in the query coordinate system\n"
-	 "of the psl, like those that are created from genePredToFakePsl\n");
+	 "of the psl, like those that are created from genePredToFakePsl\n"
+	 "    -posName\n"
+	 "write the full position in chrom:start-end format into the name field\n"
+	 "(can be used to create links to source position on details page)\n"
+         );
 
 } 
 
 static struct optionSpec options[] = {
    {"cds", OPTION_STRING},
+   {"posName", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 struct cds
 {
 int start, end;   // cds start and end 
 };
 
 static unsigned getTargetForQuery(struct psl *psl, int queryAddress)
 // get target address for query address from PSL
 {
 int  blockNum;
 
 for (blockNum=0; blockNum < psl->blockCount; blockNum++)
     {
@@ -81,40 +86,48 @@
 // we subtract one from start to convert to PSL coordinate system
 thickStart = getTargetForQuery(psl, cdsStart);
 
 // cdsEnd actually points to one base after the end, so
 // we translate the base address, then add one
 thickEnd = getTargetForQuery(psl, cdsEnd - 1) + 1;
 
 // if thickStart equals thickEnd, then there is no CDS
 if (thickStart == thickEnd)
     thickStart = thickEnd = 0;
 
 bed->thickStart = thickStart;
 bed->thickEnd = thickEnd;
 }
 
-void pslToBed(char *pslFile, char *bedFile, struct hash *cdsHash)
+void pslToBed(char *pslFile, char *bedFile, struct hash *cdsHash, bool doPosName)
 /* pslToBed -- tranform a psl format file to a bed format file */
 {
 struct lineFile *pslLf = pslFileOpen(pslFile);
 FILE *bedFh = mustOpen(bedFile, "w");
 struct psl *psl;
 
 while ((psl = pslNext(pslLf)) != NULL)
     {
     struct bed *bed = bedFromPsl(psl);
+    if (doPosName)
+        {
+        char *newName = needMem(512);
+        safef(newName, 512, "%s:%d-%d", psl->qName, psl->qStart, psl->qEnd);
+        freeMem(bed->name);
+        bed->name = newName;
+        }
+
     if (cdsHash)
 	{
 	struct cds *cds = hashFindVal(cdsHash, psl->qName);
 	if (cds == NULL)
 	    bed->thickStart = bed->thickEnd = bed->chromStart;
 	else
 	    setThick(psl, bed, cds);
 	}
     bedTabOutN(bed, 12, bedFh);
     bedFree(&bed);
     pslFree(&psl);
     }
 carefulClose(&bedFh);
 lineFileClose(&pslLf);
 }
@@ -137,25 +150,26 @@
     if (cds->start > cds->end)
 	errAbort("CDS start(%d) is before end(%d) on line %d",
 		cds->start, cds->end, lf->lineIx);
     hashAdd(hash, row[0], cds);
     }
 lineFileClose(&lf);
 return hash;
 }
 
 int main(int argc, char* argv[])
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 char *cdsFile = optionVal("cds", NULL);
+bool doPosName = optionExists("posName");
 struct hash *cdsHash = NULL;
 
 if (cdsFile != NULL)
     cdsHash = getCdsHash(cdsFile);
 
-pslToBed(argv[1], argv[2], cdsHash);
+pslToBed(argv[1], argv[2], cdsHash, doPosName);
 return 0;
 }