bd1404d9126eb1575ed20098204038364ea90308
kent
  Tue Mar 5 10:04:23 2013 -0800
Big bed extra indexes seem to work now.  Code still needs a little polish and testing.
diff --git src/utils/bigBedNamedItems/bigBedNamedItems.c src/utils/bigBedNamedItems/bigBedNamedItems.c
index c7c0ebf..43f1702 100644
--- src/utils/bigBedNamedItems/bigBedNamedItems.c
+++ src/utils/bigBedNamedItems/bigBedNamedItems.c
@@ -27,42 +27,43 @@
 
 /* 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;
-struct bptFile *bpt = bigBedOpenExtraIndex(bbi, field);
+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, words, wordCount, lm);
+    intervalList = bigBedMultiNameQuery(bbi, bpt, fieldIx, words, wordCount, lm);
     }
 else
     {
-    intervalList = bigBedNameQuery(bbi, bpt, name, lm);
+    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;
 }