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,