458a5bb9b8a7f91f4a85a9a65432627bc7dfcf6c
markd
  Thu Jan 27 18:08:54 2022 -0800
fixed confusing usage message per user complaint

diff --git src/hg/utils/overlapSelect/usage.txt src/hg/utils/overlapSelect/usage.txt
index fcdb11b..f48b74e 100644
--- src/hg/utils/overlapSelect/usage.txt
+++ src/hg/utils/overlapSelect/usage.txt
@@ -42,46 +42,46 @@
   -inCoordCols=spec - inFile is tab-separate with coordinates specified by
       spec, in format described above.
   -inCds - Use only CDS in the inFile
   -inRange - Use entire range instead of blocks of records in the inFile.
   -nonOverlapping - select non-overlapping instead of overlapping records
   -strand - must be on the same strand to be considered overlapping
   -oppositeStrand - must be on the opposite strand to be considered overlapping
   -excludeSelf - don't compare records with the same coordinates and name.
       Warning: using only one of -inCds or -selectCds will result in different
       coordinates for the same record.
   -idMatch - only select overlapping records if they have the same id
   -aggregate - instead of computing overlap bases on individual select entries, 
       compute it based on the total number of inFile bases overlap by selectFile
       records. -overlapSimilarity and -mergeOutput will not work with
       this option.
-  -overlapThreshold=0.0 - minimum fraction of an inFile record that
+  -overlapThreshold=N - minimum fraction of an inFile record that
       must be overlapped by a single select record to be considered
       overlapping.  Note that this is only coverage by a single select
-      record, not total coverage.
-  -overlapThresholdCeil=1.1 - select only inFile records with less than
-      this amount of overlap with a single record, provided they are selected
+      record, not total coverage.  Default is 0.0.
+  -overlapThresholdCeil=N - select only inFile records with less than
+      this fraction of overlap with a single record, provided they are selected
       by other criteria.
-  -overlapSimilarity=0.0 - minimum fraction bases in inFile and selectFile
+  -overlapSimilarity=N - minimum fraction bases in inFile and selectFile
       records that overlap the same genomic locations.  This is computed
       by (2*overlapBase)/(inFileBase+selectFileBases).
       Note that this is only coverage by a single select record and this
       is bidirectional inFile and selectFile must overlap by this
       amount.  A value of 1.0 will select identical records (or CDS if
       both CDS options are specified.  Not currently supported with
-      -aggregate.
-  -overlapSimilarityCeil=1.1 - select only inFile records with less than this
+      -aggregate.   Default is 0.0.
+  -overlapSimilarityCeil=N - select only inFile records with less than this
       amount of similarity with a single record. provided they are selected by
       other criteria.
   -overlapBases=-1 - minimum number of bases of overlap, < 0 disables.
   -statsOutput - output overlap statistics instead of selected records. 
       If no overlap criteria is specified, all overlapping entries are
       reported, Otherwise only the pairs passing the criteria are
       reported. This results in a tab-separated file with the columns:
          inId selectId inOverlap selectOverlap overBases
       Where inOverlap is the fraction of the inFile record overlapped by
       the selectFile record and selectOverlap is the fraction of the
       select record overlap by inFile records.  With -aggregate, output
       is:
          inId inOverlap inOverBases inBases
   -statsOutputAll - like -statsOutput, however output all inFile records,
       including those that are not overlapped.