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/cirm/cdw/lib/cdwBamFileFromRa.c src/hg/cirm/cdw/lib/cdwBamFileFromRa.c
index 25d8055..4c083d1 100644
--- src/hg/cirm/cdw/lib/cdwBamFileFromRa.c
+++ src/hg/cirm/cdw/lib/cdwBamFileFromRa.c
@@ -1,210 +1,210 @@
 /* Parser to read in a cdwBamFile from a ra file where tags in ra file correspond to fields in a
  * struct. This program was generated by raToStructGen. */
 
 /* Copyright (C) 2014 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 "obscure.h"
 #include "sqlNum.h"
 #include "sqlList.h"
 #include "ra.h"
 #include "raToStruct.h"
 #include "cdw.h"
 
 struct raToStructReader *cdwBamFileRaReader()
 /* Make a raToStructReader for cdwBamFile */
 {
 static char *fields[] = {
     "isPaired",
     "isSortedByTarget",
     "readCount",
     "readBaseCount",
     "mappedCount",
     "uniqueMappedCount",
     "readSizeMean",
     "readSizeStd",
     "readSizeMin",
     "readSizeMax",
     "u4mReadCount",
     "u4mUniquePos",
     "u4mUniqueRatio",
     "targetBaseCount",
     "targetSeqCount",
     };
 static char *requiredFields[] = {
     "isPaired",
     "isSortedByTarget",
     "readCount",
     "readBaseCount",
     "mappedCount",
     "uniqueMappedCount",
     "readSizeMean",
     "readSizeStd",
     "readSizeMin",
     "readSizeMax",
     "u4mReadCount",
     "u4mUniquePos",
     "u4mUniqueRatio",
     "targetBaseCount",
     "targetSeqCount",
     };
 return raToStructReaderNew("cdwBamFile", ArraySize(fields), fields, ArraySize(requiredFields), requiredFields);
 }
 
 
 struct cdwBamFile *cdwBamFileFromNextRa(struct lineFile *lf, struct raToStructReader *reader)
 /* Return next stanza put into an cdwBamFile. */
 {
 enum fields
     {
     isPairedField,
     isSortedByTargetField,
     readCountField,
     readBaseCountField,
     mappedCountField,
     uniqueMappedCountField,
     readSizeMeanField,
     readSizeStdField,
     readSizeMinField,
     readSizeMaxField,
     u4mReadCountField,
     u4mUniquePosField,
     u4mUniqueRatioField,
     targetBaseCountField,
     targetSeqCountField,
     };
 if (!raSkipLeadingEmptyLines(lf, NULL))
     return NULL;
 
 struct cdwBamFile *el;
 AllocVar(el);
 
 bool *fieldsObserved = reader->fieldsObserved;
 bzero(fieldsObserved, reader->fieldCount);
 
 char *tag, *val;
 while (raNextTagVal(lf, &tag, &val, NULL))
     {
     struct hashEl *hel = hashLookup(reader->fieldIds, tag);
     if (hel != NULL)
         {
 	int id = ptToInt(hel->val);
 	if (fieldsObserved[id])
 	     errAbort("Duplicate tag %s line %d of %s\n", tag, lf->lineIx, lf->fileName);
 	fieldsObserved[id] = TRUE;
 	switch (id)
 	    {
 	    case isPairedField:
 	        {
 	        el->isPaired = sqlSigned(val);
 		break;
 	        }
 	    case isSortedByTargetField:
 	        {
 	        el->isSortedByTarget = sqlSigned(val);
 		break;
 	        }
 	    case readCountField:
 	        {
 	        el->readCount = sqlLongLong(val);
 		break;
 	        }
 	    case readBaseCountField:
 	        {
 	        el->readBaseCount = sqlLongLong(val);
 		break;
 	        }
 	    case mappedCountField:
 	        {
 	        el->mappedCount = sqlLongLong(val);
 		break;
 	        }
 	    case uniqueMappedCountField:
 	        {
 	        el->uniqueMappedCount = sqlLongLong(val);
 		break;
 	        }
 	    case readSizeMeanField:
 	        {
 	        el->readSizeMean = sqlDouble(val);
 		break;
 	        }
 	    case readSizeStdField:
 	        {
 	        el->readSizeStd = sqlDouble(val);
 		break;
 	        }
 	    case readSizeMinField:
 	        {
 	        el->readSizeMin = sqlSigned(val);
 		break;
 	        }
 	    case readSizeMaxField:
 	        {
 	        el->readSizeMax = sqlSigned(val);
 		break;
 	        }
 	    case u4mReadCountField:
 	        {
 	        el->u4mReadCount = sqlSigned(val);
 		break;
 	        }
 	    case u4mUniquePosField:
 	        {
 	        el->u4mUniquePos = sqlSigned(val);
 		break;
 	        }
 	    case u4mUniqueRatioField:
 	        {
 	        el->u4mUniqueRatio = sqlDouble(val);
 		break;
 	        }
 	    case targetBaseCountField:
 	        {
 	        el->targetBaseCount = sqlLongLong(val);
 		break;
 	        }
 	    case targetSeqCountField:
 	        {
 	        el->targetSeqCount = sqlUnsigned(val);
 		break;
 	        }
 	    default:
 	        internalErr();
 		break;
 	    }
 	}
     }
 
 raToStructReaderCheckRequiredFields(reader, lf);
 return el;
 }
 
 struct cdwBamFile *cdwBamFileLoadRa(char *fileName)
 /* Return list of all cdwBamFile in ra file. */
 {
 struct raToStructReader *reader = cdwBamFileRaReader();
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 struct cdwBamFile *el, *list = NULL;
 while ((el = cdwBamFileFromNextRa(lf, reader)) != NULL)
     slAddHead(&list, el);
 slReverse(&list);
 lineFileClose(&lf);
 raToStructReaderFree(&reader);
 return list;
 }
 
 struct cdwBamFile *cdwBamFileOneFromRa(char *fileName)
 /* Return cdwBamFile in file and insist there be exactly one record. */
 {
 struct cdwBamFile *one = cdwBamFileLoadRa(fileName);
 if (one == NULL)
     errAbort("No data in %s", fileName);
 if (one->next != NULL)
     errAbort("Multiple records in %s", fileName);
 return one;
 }