src/hg/overlapSelect/usage.txt 1.12

Index: src/hg/overlapSelect/usage.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/overlapSelect/usage.txt,v
retrieving revision 1.11
retrieving revision 1.12
diff -b -B -U 1000000 -r1.11 -r1.12
--- src/hg/overlapSelect/usage.txt	14 Jan 2009 00:21:21 -0000	1.11
+++ src/hg/overlapSelect/usage.txt	30 Jan 2010 01:14:00 -0000	1.12
@@ -1,89 +1,88 @@
 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 - chrom, start, and end in specified
-              columns.
-            o chromCol,startCol,endCol,strandCol - chrom, start, end, and
-              strand in specified columns.
+            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,