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/txgToAgx/txgToAgx.c src/hg/txGraph/txgToAgx/txgToAgx.c
index cbe5bd7..ca15ff1 100644
--- src/hg/txGraph/txgToAgx/txgToAgx.c
+++ src/hg/txGraph/txgToAgx/txgToAgx.c
@@ -1,134 +1,134 @@
 /* txgToAgx - Convert from txg (txGraph) format to agx (altGraphX). */
 
 /* 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(
   "txgToAgx - Convert from txg (txGraph) format to agx (altGraphX)\n"
   "usage:\n"
   "   txgToAgx in.txg out.agx\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 struct altGraphX *txGraphToAltGraphX(struct txGraph *tx)
 /* Copy transcription graph to altSpliceX format. */
 {
 /* Allocate struct and deal with easy fields. */
 struct altGraphX *ag;
 AllocVar(ag);
 ag->tName = cloneString(tx->tName);
 ag->tStart = tx->tStart;
 ag->tEnd = tx->tEnd;
 ag->name = cloneString(tx->name);
 ag->id = 0;
 ag->strand[0] = tx->strand[0];
 
 /* Deal with vertices. */
 int vertexCount = ag->vertexCount = tx->vertexCount;
 AllocArray(ag->vTypes, vertexCount);
 AllocArray(ag->vPositions, vertexCount);
 int i;
 for (i=0; i<vertexCount; ++i)
     {
     struct txVertex *v = &tx->vertices[i];
     ag->vTypes[i] = v->type;
     ag->vPositions[i] = v->position;
     }
 
 /* Deal with edges. */
 int edgeCount = ag->edgeCount = tx->edgeCount;
 AllocArray(ag->edgeStarts, edgeCount);
 AllocArray(ag->edgeEnds, edgeCount);
 AllocArray(ag->edgeTypes, edgeCount);
 struct txEdge *edge;
 for (edge = tx->edgeList, i=0; edge != NULL; edge = edge->next, ++i)
     {
     assert(i < edgeCount);
     ag->edgeStarts[i] = edge->startIx;
     ag->edgeEnds[i] = edge->endIx;
     ag->edgeTypes[i] = edge->type;
     }
 
 /* Deal with evidence inside of edges. */
 for (edge = tx->edgeList; edge != NULL; edge = edge->next)
     {
     struct evidence *ev;
     AllocVar(ev);
     int *mrnaIds = AllocArray(ev->mrnaIds, edge->evCount);
     int i;
     struct txEvidence *txEv;
     for (txEv = edge->evList, i=0; txEv != NULL; txEv = txEv->next, ++i)
         {
 	assert(i < edge->evCount);
 	struct txSource *source = &tx->sources[txEv->sourceId];
 	char *sourceType = source->type;
 	if (sameString(sourceType, "refSeq") || sameString(sourceType, "mrna") || sameString(sourceType, "est"))
 	    {
 	    mrnaIds[ev->evCount] = txEv->sourceId;
 	    ev->evCount += 1;
 	    }
         }
     slAddHead(&ag->evidence, ev);
     }
 slReverse(&ag->evidence);
 
 /* Convert sources into mrnaRefs. */
 int sourceCount = ag->mrnaRefCount = tx->sourceCount;
 AllocArray(ag->mrnaRefs, sourceCount);
 int sourceIx;
 for (sourceIx=0; sourceIx<sourceCount; ++sourceIx)
     {
     struct txSource *source = &tx->sources[sourceIx];
     ag->mrnaRefs[sourceIx] = cloneString(source->accession);
     }
 
 /* Deal with tissues and libs by just making arrays of all zero. */
 AllocArray(ag->mrnaTissues, tx->sourceCount);
 AllocArray(ag->mrnaLibs, tx->sourceCount);
 return ag;
 }
 
 void txgToAgx(char *inTxg, char *outAgx)
 /* txgToAgx - Convert from txg (txGraph) format to agx (altGraphX). */
 {
 struct lineFile *lf = lineFileOpen(inTxg, TRUE);
 char *row[TXGRAPH_NUM_COLS];
 FILE *f = mustOpen(outAgx, "w");
 
 while (lineFileRow(lf, row))
     {
     struct txGraph *txg = txGraphLoad(row);
     verbose(2, "loaded txGraph %s\n", txg->name);
     struct altGraphX *agx = txGraphToAltGraphX(txg);
     altGraphXTabOut(agx, f);
     altGraphXFree(&agx);
     txGraphFree(&txg);
     }
 
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 txgToAgx(argv[1], argv[2]);
 return 0;
 }