Generic

crTreeSearchBed
Function: Search a crTree indexed bed file and print all items that overlap query.
Usage: crTreeSearchBed file.bed index.cr chrom start end
faFilterN
Function: Get rid of sequences with too many N's
Usage: faFilterN in.fa out.fa maxPercentN
localtime
Function: Convert unix timestamp to date string
Usage: localtime
splitFile
Function: Split up a file
Usage: splitFile source linesPerFile outBaseName
headRest
Function: Return all *but* the first N lines of a file.
Usage: headRest count fileName
bedItemOverlapCount
Function: Count number of times a base is overlapped by theitems in a bed file. Output is bedGraph 4 to stdout.
Usage: sort bedFile.bed | bedItemOverlapCount [options] <database> stdin
checkAgpAndFa
Function: Take a .agp file and .fa file and ensure that they are in synch
Usage: checkAgpAndFa in.agp in.fa
chopFaLines
Function: Read in FA file with long lines and rewrite it with shorter lines
Usage: chopFaLines in.fa out.fa
chainSplit
Function: Split chains up by target or query sequence
Usage: chainSplit outDir inChain(s)
pslPartition
Function: Split PSL files into non-overlapping sets
Usage: pslPartition [options] pslFile outDircreated under outDir to prevent slow access to huge directories.
chainToAxt
Function: Convert from chain to axt file
Usage: chainToAxt in.chain tNibDirOr2bit qNibDirOr2bit out.axt
sqlToXml
Function: Dump out all or part of a relational database to XML, guidedby a dump specification. See sqlToXml.doc for additional information.
Usage: sqlToXml database dumpSpec.od output.xml
netChainSubset
Function: Create chain file with subset of chains that appear in the net
Usage: netChainSubset in.net in.chain out.chain
dbSnoop
Function: Produce an overview of a database.
Usage: dbSnoop database output
mrnaToGene
Function: Convert PSL alignments of mRNAs to gene annotations
Usage: mrnaToGene [options] psl genePredFile