Generic

validateFiles
Function: Validates the format of different genomic files.Exits with a zero status for no errors detected and non-zero for errors.Uses filename 'stdin' to read from stdin.Automatically decompresses Files in .gz, .bz2, .zip, .Z format.Accepts multiple input files of the same type.Writes Error messages to stderr
Usage: validateFiles -chromInfo=FILE -options -type=FILE_TYPE file1 [file2 [...]]
pslToBed
Function: pslToBed: tranform a psl format file to a bed format file.
Usage: pslToBed psl bed
hgLoadOut
Function: Load RepeatMasker .out files into database
Usage: hgLoadOut database file(s).out
raToTab
Function: Convert ra file to table.
Usage: raToTab in.ra out.tab
genePredHisto
Function: Get data for generating histograms from a genePred file.
Usage: genePredHisto [options] what genePredFile histoOut
oligoMatch
Function: Find perfect matches in sequence.
Usage: oligoMatch oligos sequence output.bed
pslToChain
Function: Convert psl records to chain records
Usage: pslToChain pslIn chainOut
sizeof
Function: Show size of various C types for reference
Usage: sizeof
lavToPsl
Function: Convert blastz lav to psl format
Usage: lavToPsl in.lav out.psl
qacAgpLift
Function: Use AGP to combine per-scaffold qac into per-chrom qac.
Usage: qacAgpLift scaffoldToChrom.agp scaffolds.qac chrom.qac
autoDtd
Function: Give this a XML document to look at and it will come up with a DTDto describe it.
Usage: autoDtd in.xml out.dtd out.stats
calc
Function: Little command line calculator
Usage: calc this + that * theOther / (a + b)
chainAntiRepeat
Function: Get rid of chains that are primarily the results of repeats and degenerate DNA
Usage: chainAntiRepeat tNibDir qNibDir inChain outChain
gff3ToPsl
Function: Convert a GFF3 CIGAR file to a PSL file
Usage: gff3ToPsl mapFile inGff3 out.psl
toUpper
Function: Convert lower case to upper case in file. Leave other chars alone
Usage: toUpper inFile outFile