Generic

faRandomize
Function: Program to create random fasta records
Usage: faRandomize [-seed=N] in.fa randomized.fa
stringify
Function: Convert file to C strings
Usage: stringify [options] in.txt
tickToDate
Function: Convert seconds since 1970 to time and date
Usage: tickToDate ticks
pslDropOverlap
Function: Deletes all overlapping self alignments.
Usage: pslDropOverlap in.psl out.psl
autoXml
Function: Generate structures code and parser for XML file from DTD-like spec
Usage: autoXml file.dtdx root
hgGcPercent
Function: Calculate GC Percentage in 20kb windows
Usage: hgGcPercent [options] database nibDir
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 [...]]
validateManifest
Function: Validates the ENCODE3 manifest.txt file. Calls validateFiles on each file in the manifest.Exits with a zero status for no errors detected and non-zero for errors. Writes Error messages to stderr
Usage: validateManifest
bedGeneParts
Function: Given a bed, spit out promoter, first exon, or all introns.
Usage: bedGeneParts part in.bed out.bed
netSplit
Function: Split a genome net file into chromosome net files
Usage: netSplit in.net outDir
tdbQuery
Function: Query the trackDb system using SQL syntax.
Usage: tdbQuery sqlStatement
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
genePredCheck
Function: Validate genePred files or tables
Usage: genePredCheck [options] fileTbl ..
gff3ToPsl
Function: Convert a GFF3 CIGAR file to a PSL file
Usage: gff3ToPsl mapFile inGff3 out.psl
paraFetch
Function: Try to fetch url with multiple connections
Usage: paraFetch N R URL {outPath}