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 @@ -1,99 +1,99 @@ 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). 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 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. -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. -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,