a670673248a056c2026c04b8284a6640756e8870
kate
  Thu Feb 18 12:05:19 2016 -0800
Allow suppressing status messages from liftOver (with verbosity=0), but leave current behavior as default

diff --git src/hg/liftOver/liftOver.c src/hg/liftOver/liftOver.c
index 73bcba9..8d2c4cd 100644
--- src/hg/liftOver/liftOver.c
+++ src/hg/liftOver/liftOver.c
@@ -98,33 +98,33 @@
 }
 
 void liftOver(char *oldFile, char *mapFile, double minMatch, 
                 double minBlocks, int minSizeT, int minSizeQ,
                 int minChainT, int minChainQ, bool multiple, char *chainTable, 
                 char *newFile, char *unmappedFile)
 /* liftOver - Move annotations from one assembly to another. */
 {
 struct hash *chainHash = newHash(0);		/* Old chromosome name keyed, chromMap valued. */
 FILE *mapped = mustOpen(newFile, "w");
 FILE *unmapped = mustOpen(unmappedFile, "w");
 int errCt;
 
 if (!fileExists(oldFile))
     errAbort("Can't find file: %s\n", oldFile);
-fprintf(stderr, "Reading liftover chains\n");
+verbose(1, "Reading liftover chains\n");
 readLiftOverMap(mapFile, chainHash);
-fprintf(stderr, "Mapping coordinates\n");
+verbose(1, "Mapping coordinates\n");
 if (optionExists("gff"))
     {
     fprintf(stderr, "WARNING: -gff is not recommended.\nUse 'ldHgGene -out=<file.gp>' and then 'liftOver -genePred <file.gp>'\n");
     liftOverGff(oldFile, chainHash, minMatch, minBlocks, mapped, unmapped);
     }
 else if (optionExists("genePred"))
     liftOverGenePred(oldFile, chainHash, minMatch, minBlocks, fudgeThick,
                         mapped, unmapped);
 else if (optionExists("sample"))
     liftOverSample(oldFile, chainHash, minMatch, minBlocks, fudgeThick,
                         mapped, unmapped);
 else if (optionExists("pslT"))
     liftOverPsl(oldFile, chainHash, minMatch, minBlocks, fudgeThick,
                         mapped, unmapped);
 else if (optionExists("ends"))