4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/txGraph/agxToTxg/agxToTxg.c src/hg/txGraph/agxToTxg/agxToTxg.c
index 0731a37..4f11d89 100644
--- src/hg/txGraph/agxToTxg/agxToTxg.c
+++ src/hg/txGraph/agxToTxg/agxToTxg.c
@@ -1,116 +1,116 @@
 /* agxToTxg - Convert from old altGraphX format to newer txGraph format.. */
 
 /* Copyright (C) 2007 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "altGraphX.h"
 #include "txGraph.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "agxToTxg - Convert from old altGraphX format to newer txGraph format.\n"
   "usage:\n"
   "   agxToTxg in.agx out.txg\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 struct txGraph *txgFromAltGraphX(struct altGraphX *ag)
 /* Create txGraph that is as nearly possible the same ag altGraphX */
 {
 struct txGraph *txg;
 AllocVar(txg);
 txg->tName = cloneString(ag->tName);
 txg->tStart = ag->tStart;
 txg->tEnd = ag->tEnd;
 txg->name = cloneString(ag->name);
 txg->strand[0] = ag->strand[0];
 
 /* Deal with vertices. */
 int vertexCount = txg->vertexCount = ag->vertexCount;
 AllocArray(txg->vertices, vertexCount);
 int i;
 for (i=0; i<vertexCount; ++i)
     {
     struct txVertex *v = &txg->vertices[i];
     v->type = ag->vTypes[i];
     v->position = ag->vPositions[i];
     }
 
 /* Deal with edges. */
 int edgeCount = txg->edgeCount = ag->edgeCount;
 struct evidence *agEv = ag->evidence;
 for (i=0; i<edgeCount; ++i, agEv=agEv->next)
     {
     struct txEdge *e;
     AllocVar(e);
     e->startIx = ag->edgeStarts[i];
     e->endIx = ag->edgeEnds[i];
     e->type = ag->edgeTypes[i];
     slAddHead(&txg->edgeList, e);
 
     /* Deal with evidence. */
     int j;
     e->evCount = agEv->evCount;
     for (j=0; j<agEv->evCount; ++j)
         {
 	struct txEvidence *ev;
 	AllocVar(ev);
 	ev->sourceId = agEv->mrnaIds[j];
 	ev->start = txg->vertices[e->startIx].position;
 	ev->end = txg->vertices[e->endIx].position;
 	slAddHead(&e->evList, ev);
 	}
     slReverse(&e->evList);
     }
 slReverse(&txg->edgeList);
 
 /* Deal with sources. */
 int sourceCount = txg->sourceCount = ag->mrnaRefCount;
 AllocArray(txg->sources, sourceCount);
 for (i=0; i<sourceCount; ++i)
     {
     char *acc = ag->mrnaRefs[i];
     char *type = (startsWith("NM_", acc) ? "refSeq" : "mrna");
     struct txSource *source = &txg->sources[i];
     source->accession = cloneString(acc);
     source->type = cloneString(type);
     }
 return txg;
 }
 
 void agxToTxg(char *inAgx, char *outTxg)
 /* agxToTxg - Convert from old altGraphX format to newer txGraph format.. */
 {
 struct lineFile *lf = lineFileOpen(inAgx, TRUE);
 FILE *f = mustOpen(outTxg, "w");
 char *row[ALTGRAPHX_NUM_COLS];
 while (lineFileRow(lf, row))
     {
     struct altGraphX *ag = altGraphXLoad(row);
     struct txGraph *txg = txgFromAltGraphX(ag);
     txGraphTabOut(txg, f);
     altGraphXFree(&ag);
     }
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 agxToTxg(argv[1], argv[2]);
 return 0;
 }