12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400
markd
  Wed Jan 27 17:49:12 2021 -0800
allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed

diff --git src/hg/utils/overlapSelect/usage.txt src/hg/utils/overlapSelect/usage.txt
index 6a8d35a..fcdb11b 100644
--- src/hg/utils/overlapSelect/usage.txt
+++ src/hg/utils/overlapSelect/usage.txt
@@ -1,36 +1,43 @@
 overlapSelect - Select records based on overlapping chromosome ranges.
 usage:
    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).
+          psl - PSL format (default for *.psl files).  Additional columns
+                are copied as-is.
+          pslq - PSL format, using query instead of target.  Additional columns
+                 are copied as-is.
+          genePred - genePred format (default for *.gp or *.genePred files).  Additional
+                     columns are copied as-is.
           bed - BED format (default for *.bed files).
-                If BED doesn't have blocks, the bed range is used. 
+                If BED doesn't have blocks, the bed range is used. If it has more
+                than 12 columns, the remainder of the columns are copied as-is.
+          bed3+ - BED format where only the first three columns are used as the
+                  range, the remainder are copied as-is.
+          bed6+ - BED format where only the first six columns are used as the
+                  range and strange, the remainder are copied as-is.
           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.