Generic

netSyntenic
Function: Add synteny info to net.
Usage: netSyntenic in.net out.net
checkHgFindSpec
Function: Test and describe search specs in hgFindSpec tables.
Usage: checkHgFindSpec database [options | termToSearch]
catDir
Function: catDir - concatenate files in directory to stdout.For those times when too many files for cat to handle.
Usage: catDir dir(s)
catUncomment
Function: catUncomment - Concatenate input removing lines that start with '#'Output goes to stdout
Usage: catUncomment file(s)
maskOutFa
Function: Produce a masked .fa file given an unmasked .fa anda RepeatMasker .out file, or a .bed file to mask on.
Usage: maskOutFa in.fa maskFile out.fa.masked
genePredSingleCover
Function: Create single-coverage genePred files
Usage: genePredSingleCover [options] inGenePred outGenePred
hgsqldump
Function: Execute mysqldump using passwords from .hg.conf
Usage: hgsqldump [OPTIONS] database [tables]
wigEncode
Function: Convert Wiggle ascii data to binary format
Usage: wigEncode [options] wigInput wigFile wibFile
netClass
Function: Add classification info to net
Usage: netClass [options] in.net tDb qDb out.net
colTransform
Function: colTransform - Add and/or multiply column by constant.
Usage: colTransform column input.tab addFactor mulFactor output.tab
faCmp
Function: Compare two fasta files
Usage: faCmp [options] a.fa b.fa
chainPreNet
Function: Remove chains that don't have a chance of being netted
Usage: chainPreNet in.chain target.sizes query.sizes out.chain
faFilterN
Function: Get rid of sequences with too many N's
Usage: faFilterN in.fa out.fa maxPercentN
pslReps
Function: Analyse repeats and generate genome wide bestalignments from a sorted set of local alignments
Usage: pslReps in.psl out.psl out.psr
nibFrag
Function: Extract part of a nib file as .fa (all bases/gaps lower case by default)
Usage: nibFrag [options] file.nib start end strand out.fa