4a73fd653634412cc9ad0fc17aab320c3fb30be2
max
  Fri Aug 24 17:42:31 2018 -0700
making the wigToBigWig -clip option more tolerant to hg38 chroms with non-Hiram names, no redmine

diff --git src/utils/wigToBigWig/wigToBigWig.c src/utils/wigToBigWig/wigToBigWig.c
index 177a480..3402af8 100644
--- src/utils/wigToBigWig/wigToBigWig.c
+++ src/utils/wigToBigWig/wigToBigWig.c
@@ -28,31 +28,32 @@
   "or bedGraph format) to binary big wig format.\n"
   "usage:\n"
   "   wigToBigWig in.wig chrom.sizes out.bw\n"
   "Where in.wig is in one of the ascii wiggle formats, but not including track lines\n"
   "and chrom.sizes is a two-column file/URL: <chromosome name> <size in bases>\n"
   "and out.bw is the output indexed big wig file.\n"
   "If the assembly <db> is hosted by UCSC, chrom.sizes can be a URL like\n"
   "  http://hgdownload.soe.ucsc.edu/goldenPath/<db>/bigZips/<db>.chrom.sizes\n"
   "or you may use the script fetchChromSizes to download the chrom.sizes file.\n"
   "If not hosted by UCSC, a chrom.sizes file can be generated by running\n"
   "twoBitInfo on the assembly .2bit file.\n"
   "options:\n"
   "   -blockSize=N - Number of items to bundle in r-tree.  Default %d\n"
   "   -itemsPerSlot=N - Number of data points bundled at lowest level. Default %d\n"
   "   -clip - If set just issue warning messages rather than dying if wig\n"
-  "                  file contains items off end of chromosome.\n"
+  "                  file contains items off end of chromosome or chromosomes\n"
+  "                  that are not in the chrom.sizes file.\n"
   "   -unc - If set, do not use compression.\n"
   "   -fixedSummaries - If set, use a predefined sequence of summary levels.\n"
   "   -keepAllChromosomes - If set, store all chromosomes in b-tree."
   , bbiCurrentVersion, blockSize, itemsPerSlot
   );
 }
 
 static struct optionSpec options[] = {
    {"blockSize", OPTION_INT},
    {"itemsPerSlot", OPTION_INT},
    {"clip", OPTION_BOOLEAN},
    {"unc", OPTION_BOOLEAN},
    {"fixedSummaries", OPTION_BOOLEAN},
    {"keepAllChromosomes", OPTION_BOOLEAN},
    {NULL, 0},