Generic

Function: Split a genome net file into chromosome net files

Usage: netSplit in.net outDir

Function: Convert a GFF3 CIGAR file to a PSL file

Usage: gff3ToPsl mapFile inGff3 out.psl

Function: Load a generic bed file into database

Usage: hgLoadBed database track files(s).bed

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

Function: Little command line calculator

Usage: calc this + that * theOther / (a + b)

Function: Drop tables from a database older than specified N hours

Usage: dbTrash -age=N [-drop] [-historyToo] [-db=<DB>] [-verbose=N]

Function: Try to fetch url with multiple connections

Usage: paraFetch N R URL {outPath}

Function: Convert unix timestamp to date string

Usage: gmtime

Function: Convert lower case to upper case in file. Leave other chars alone

Usage: toUpper inFile outFile

Function: Load a wiggle track definition into database

Usage: hgLoadWiggle [options] database track files(s).wig

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

Function: Validate genePred files or tables

Usage: genePredCheck [options] fileTbl ..

Function: Lift PSLs from blat subrange alignments

Usage: pslLiftSubrangeBlat isPsl outPsl

Function: Concatenate psl files

Usage: pslCat file(s)

Function: It merges two or more .clstr files. The cluster orders need to be identical.

Usage: clstr_merge.pl db2new.clstr db3new.clstr > db23new.clstr