Generic

netToBed
Function: Convert target coverage of net to a bed file.
Usage: netToBed in.net out.bed
blastXmlToPsl
Function: Convert blast XML output to PSLs
Usage: blastXmlToPsl [options] blastXml psl
liftUp
Function: Change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf.bscore .tab .gdup .axt .chain .net, genePred, .wab, .bed, or .bed8 files toparent coordinate system.
Usage: liftUp [-type=.xxx] destFile liftSpec how sourceFile(s)
splitFileByColumn
Function: Split text input into files named by column value
Usage: splitFileByColumn source outDir
addCols
Function: Sum columns in a text file.
Usage: addCols <fileName>
faToTab
Function: Convert fa file to tab separated file
Usage: faToTab infileName outFileName
linesToRa
Function: Generate .ra format from lines with pipe-separated fields
Usage: linesToRa in.txt out.ra
axtToPsl
Function: Convert axt to psl format
Usage: axtToPsl in.axt tSizes qSizes out.psl
hubCheck
Function: hubCheck - Check a track data hub for integrity.
Usage: hubCheck http://yourHost/yourDir/hub.txt
pslSelect
Function: Select records from a PSL file.
Usage: pslSelect [options] inPsl outPsl
pslFilter
Function: Filter out psl file
Usage: pslFilter in.psl out.psl
makeTableList
Function: makeTableList - create/recreate tableList tables (cache of SHOW TABLES)
Usage: makeTableList [assemblies]
pslSwap
Function: Swap target and query in psls
Usage: pslSwap [options] inPsl outPsl
chromGraphToBin
Function: Make binary version of chromGraph.
Usage: chromGraphToBin in.tab out.chromGraph
featureBits
Function: Correlate tables via bitmap projections.
Usage: featureBits database table(s)