e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/utils/bigBedNamedItems/bigBedNamedItems.c src/utils/bigBedNamedItems/bigBedNamedItems.c
index 43f1702..7f91fb8 100644
--- src/utils/bigBedNamedItems/bigBedNamedItems.c
+++ src/utils/bigBedNamedItems/bigBedNamedItems.c
@@ -1,69 +1,72 @@
 /* bigBedNamedItems - Extract item(s) of given name(s) from bigBed. */
+
+/* Copyright (C) 2013 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "localmem.h"
 #include "udc.h"
 #include "bPlusTree.h"
 #include "bigBed.h"
 #include "obscure.h"
 #include "zlibFace.h"
 
 char *field = "name";
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bigBedNamedItems - Extract item of given name from bigBed\n"
   "usage:\n"
   "   bigBedNamedItems file.bb name output.bed\n"
   "options:\n"
   "   -nameFile - if set, treat name parameter as file full of space delimited names\n"
   "   -field=fieldName - use index on field name, default is \"name\"\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {"nameFile", OPTION_BOOLEAN},
    {"field", OPTION_STRING},
    {NULL, 0},
 };
 
 void bigBedNamedItems(char *bigBedFile, char *name, char *outFile)
 /* bigBedNamedItems - Extract item(s) of given name(s) from bigBed. */
 {
 struct bbiFile *bbi = bigBedFileOpen(bigBedFile);
 FILE *f = mustOpen(outFile, "w");
 struct lm *lm = lmInit(0);
 struct bigBedInterval *intervalList;
 int fieldIx;
 struct bptFile *bpt = bigBedOpenExtraIndex(bbi, field, &fieldIx);
 if (optionExists("nameFile"))
     {
     int wordCount = 0;
     char **words;
     char *buf;
     readAllWords(name, &words, &wordCount, &buf);
     intervalList = bigBedMultiNameQuery(bbi, bpt, fieldIx, words, wordCount, lm);
     }
 else
     {
     intervalList = bigBedNameQuery(bbi, bpt, fieldIx, name, lm);
     }
 bigBedIntervalListToBedFile(bbi, intervalList, f);
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 field = optionVal("field", field);
 bigBedNamedItems(argv[1], argv[2], argv[3]);
 return 0;
 }