b95ff3835509b242bd9007ba55c4f60c1022da47
markd
  Thu Dec 30 14:58:16 2010 -0800
moved to programs to hg/utils, fixed build of distributed utilities
diff --git src/hg/overlapSelect/usage.txt src/hg/overlapSelect/usage.txt
deleted file mode 100644
index a51d91c..0000000
--- src/hg/overlapSelect/usage.txt
+++ /dev/null
@@ -1,88 +0,0 @@
-overlapSelect [options] selectFile inFile outFile
-
-Select records based on overlapping chromosome ranges.  The ranges are
-specified in the selectFile, with each block specifying a range.
-Records are copied from the inFile to outFile based on the selection
-criteria.  Selection is based on blocks or exons rather than entire
-range.
-
-Options starting with -select* apply to selectFile and those starting
-with -in* apply to inFile.
-
-Options:
-  -selectFmt=fmt - specify selectFile format:
-          psl - PSL format (default for *.psl files).
-          pslq - PSL format, using query instead of target
-          genePred - genePred format (default for *.gp or
-                     *.genePred files).
-          bed - BED format (default for *.bed files).
-                If BED doesn't have blocks, the bed range is used. 
-          chain - chain file format (default from .chain files)
-          chainq - chain file format, using query instead of target
-  -selectCoordCols=spec - selectFile is tab-separate with coordinates
-       as described by spec, which is one of:
-            o chromCol - chrom in this column followed by start and end.
-            o chromCol,startCol,endCol,strandCol,name - chrom, start, end, and
-              strand in specified columns. Columns can be omitted from the end
-              or left empty to not specify.
-          NOTE: column numbers are zero-based
-  -selectCds - Use only CDS in the selectFile
-  -selectRange - Use entire range instead of blocks from records in
-          the selectFile.
-  -inFmt=fmt - specify inFile format, same values as -selectFmt.
-  -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
-      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
-      by other criteria.
-  -overlapSimilarity=0.0 - minimum fraction of inFile and select records that
-      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
-      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.
-  -statsOutputBoth - like -statsOutput, however output all selectFile and
-      inFile records, including those that are not overlapped.
-  -mergeOutput - output file with be a merge of the input file with the
-      selectFile records that selected it.  The format is
-         inRec<tab>selectRec.
-      if multiple select records hit, inRec is repeated. This will increase
-      the memory required. Not supported with -nonOverlapping or -aggregate.
-  -idOutput - output a tab-separated file of pairs of
-         inId selectId
-      with -aggregate, only a single column of inId is written
-  -dropped=file  - output rows that were dropped to this file.
-  -verbose=n - verbose > 1 prints some details,