0766f8ef11c8e73a7351fbbc5d5ae9f987941a54
angie
  Fri Mar 11 15:12:00 2011 -0800
Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/.
Test cases coming up...

diff --git src/oneShot/tabixFetch/tabixFetch.c src/oneShot/tabixFetch/tabixFetch.c
deleted file mode 100644
index 135f31e..0000000
--- src/oneShot/tabixFetch/tabixFetch.c
+++ /dev/null
@@ -1,114 +0,0 @@
-/* tabixFetch - Test lineFileOnTabix and lineFileSetTabixRegion (compare with cmd line tabix output). */
-#include "common.h"
-#include "linefile.h"
-#include "options.h"
-
-#ifdef USE_TABIX
-
-#include "sqlNum.h"
-#include "udc.h"
-#include "knetUdc.h"
-
-void usage()
-/* Explain usage and exit. */
-{
-errAbort(
-
-  "tabixFetch - Test lineFileOnTabix and lineFileSetTabixRegion (compare\n"
-  "             with command-line tabix output)\n"
-
-  "usage:\n"
-  "   tabixFetch fileOrUrl chrom:start-end\n"
-  "Fetch lines from the specified position range from a line-based file\n"
-  "with genomic positions that has been compressed and indexed by tabix.\n"
-  "This duplicates the fetching functionality of the tabix program -- it\n"
-  "was written solely to test lib/lineFile.c's tabix-wrapper mode.\n"
-  );
-}
-
-static struct optionSpec options[] = {
-   {NULL, 0},
-};
-
-#define BAD_POS_FORMAT "Expecting position format: chrom:N-M where N and M are integers.  " \
-		       "\"%s\" doesn't match."
-static void parsePosition(const char *position, char **retChrom, int *retStart, int *retEnd)
-/* Do we have a lib routine for this somewhere?  Too lazy to look. */
-{
-char *posDupe = cloneString(position);
-char *words[3];
-int wordCount = chopByChar(posDupe, ':', words, ArraySize(words));
-if (wordCount != 2)
-    errAbort(BAD_POS_FORMAT, position);
-*retChrom = posDupe;
-
-stripChar(words[1], ',');
-char *range = cloneString(words[1]);
-wordCount = chopByChar(range, '-', words, ArraySize(words));
-if (wordCount != 2)
-    errAbort(BAD_POS_FORMAT, position);
-*retStart = sqlUnsigned(words[0]);
-*retEnd = sqlUnsigned(words[1]);
-}
-
-void tabixFetch(char *fileOrUrl, char *position)
-/* tabixFetch - Test lineFileOnTabix and lineFileSetTabixRegion
- * (compare with cmd line tabix output). */
-{
-udcSetDefaultDir("/data/tmp/angie/udcCache");
-knetUdcInstall();
-struct lineFile *lf = lineFileOnTabix(fileOrUrl, TRUE);
-if (lf == NULL)
-    exit(1);
-int lineSize;
-char *line = NULL;
-boolean gotLine = FALSE;
-if (0)
-do
-    {
-    gotLine = lineFileNext(lf, &line, &lineSize);
-    puts(line);
-    }
-while (gotLine && (line[0] == '#' || isEmpty(line)));
-
-char *chrom = NULL;
-int start, end;
-parsePosition(position, &chrom, &start, &end);
-boolean success = lineFileSetTabixRegion(lf, chrom, start, end);
-if (!success)
-    printf("*** Could not set position to %s\n", position);
-else
-    {
-    printf("*** First (up to) 10 lines from query on %s:\n", position);
-    int i;
-    for (i=0;  i < 10;  i++)
-	{
-	if (lineFileNext(lf, &line, &lineSize))
-	    puts(line);
-	else break;
-	}
-    if (i == 0)
-	printf("*** No lines returned from query on %s\n", position);
-    }
-lineFileClose(&lf);
-}
-
-int main(int argc, char *argv[])
-/* Process command line. */
-{
-optionInit(&argc, argv, options);
-if (argc != 3)
-    usage();
-tabixFetch(argv[1], argv[2]);
-return 0;
-}
-
-#else // no USE_TABIX
-int main(int argc, char *argv[])
-/* Process command line. */
-{
-errAbort(COMPILE_WITH_TABIX, "tabixFetch");
-return 1;
-}
-
-#endif // no USE_TABIX