dcd4d579f74a2af013fbfe9c8c81c31b2962b0c9
max
  Mon Jun 4 16:38:42 2018 -0700
CIRM: small changes to cdwMakePairedEndQa and related tools to make debugging of problems
easier next time.

diff --git src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c
index 1bf7081..77a9c3f 100644
--- src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c
+++ src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c
@@ -29,30 +29,31 @@
  * sometimes varied when dealing with compressed input files, and this would break the
  * correspondence between read pairs, so now the estimate is always 1/10. */
 
 int sampleSize = 100000;
 int seed = 0;
 boolean smallOk = FALSE;
 boolean json = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "fastqStatsAndSubsample v2 - Go through a fastq file doing sanity checks and collecting stats\n"
   "and also producing a smaller fastq out of a sample of the data.  The fastq input may be\n"
   "compressed with gzip or bzip2.\n"
+  "Paired-end samples: run on both files, the seed is fixed so it will chose the paired reads\n")
   "usage:\n"
   "   fastqStatsAndSubsample in.fastq out.stats out.fastq\n"
   "options:\n"
   "   -sampleSize=N - default %d\n"
   "   -seed=N - Use given seed for random number generator.  Default %d.\n"
   "   -smallOk - Not an error if less than sampleSize reads.  out.fastq will be entire in.fastq\n"
   "   -json - out.stats will be in json rather than text format\n"
   "Use /dev/null for out.fastq and/or out.stats if not interested in these outputs\n"
   , sampleSize, seed
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {"sampleSize", OPTION_INT},