4e6512b9b01495cb58e13d6b5a2245c3a28cd4d2
max
  Tue Aug 13 14:13:44 2024 -0700
mention the PSL filter commands on the blat output page, email from someone

diff --git src/blat/blat.c src/blat/blat.c
index 9f712ae..919b957 100644
--- src/blat/blat.c
+++ src/blat/blat.c
@@ -141,30 +141,33 @@
   "                  requiring high %%ID. Query sizes must not exceed %d.\n"
   "   -out=type      Controls output file format.  Type is one of:\n"
   "                    psl - Default.  Tab-separated format, no sequence\n"
   "                    pslx - Tab-separated format with sequence\n"
   "                    axt - blastz-associated axt format\n"
   "                    maf - multiz-associated maf format\n"
   "                    sim4 - similar to sim4 format\n"
   "                    wublast - similar to wublast format\n"
   "                    blast - similar to NCBI blast format\n"
   "                    blast8- NCBI blast tabular format\n"
   "                    blast9 - NCBI blast tabular format with comments\n"
   "   -fine          For high-quality mRNAs, look harder for small initial and\n"
   "                  terminal exons.  Not recommended for ESTs.\n"
   "   -maxIntron=N  Sets maximum intron size. Default is %d.\n"
   "   -extendThroughN  Allows extension of alignment through large blocks of Ns.\n"
+  "\n"
+  "  To filter PSL files to the best hits (e.g. minimum ID > 90%% or 'only best match'),\n"
+  "  you can use the commands pslReps, pslCDnaFilter or pslUniq.\n"
   , gfVersion, MAXSINGLEPIECESIZE, ffIntronMaxDefault
   );
 exit(-1);
 }
 
 
 struct optionSpec options[] = {
    {"t", OPTION_STRING},
    {"q", OPTION_STRING},
    {"prot", OPTION_BOOLEAN},
    {"ooc", OPTION_STRING},
    {"tileSize", OPTION_INT},
    {"stepSize", OPTION_INT},
    {"oneOff", OPTION_INT},
    {"minMatch", OPTION_INT},