db42a8012f0dad34f7dbe68a948970d3a17e1524
angie
  Mon Oct 26 09:38:10 2020 -0700
hashTwoColumnFile expects whitespace-sep not tab-sep -- update usage message for {phylo,vcf}RenameAndPrune.

diff --git src/hg/utils/vcfRenameAndPrune/vcfRenameAndPrune.c src/hg/utils/vcfRenameAndPrune/vcfRenameAndPrune.c
index 04071cf..61a4240 100644
--- src/hg/utils/vcfRenameAndPrune/vcfRenameAndPrune.c
+++ src/hg/utils/vcfRenameAndPrune/vcfRenameAndPrune.c
@@ -1,34 +1,34 @@
 /* vcfRenameAndPrune - Rename or remove samples from VCF with genotypes. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "obscure.h"
 #include "options.h"
 #include "vcf.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "vcfRenameAndPrune - Rename samples in VCF; if new name not found, remove sample.\n"
   "usage:\n"
-  "   vcfRenameAndPrune vcfIn.vcf[.gz] renaming.tab vcfOut.vcf\n"
+  "   vcfRenameAndPrune vcfIn.vcf[.gz] renaming.txt vcfOut.vcf\n"
 //  "options:\n"
 //  "   -xxx=XXX\n"
-  "renaming.tab has two columns: old name (must uniquely match some sample\n"
-  "named in #CHROM header line) and new name.\n"
+  "renaming.txt has two whitespace-separated columns: old name (must uniquely match\n"
+  "some sample named in #CHROM header line) and new name.\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 void vcfRenameAndPrune(char *vcfInFile, char *renamingFile, char *vcfOutFile)
 /* vcfRenameAndPrune - Rename or remove samples from VCF with genotypes. */
 {
 struct hash *renaming = hashTwoColumnFile(renamingFile);
 struct lineFile *lf = lineFileOpen(vcfInFile, TRUE);
 FILE *outF = mustOpen(vcfOutFile, "w");
 int headerColCount = 0;