Generic

Function: Find perfect matches in sequence.

Usage: oligoMatch oligos sequence output.bed

Function: pslToBed: tranform a psl format file to a bed format file.

Usage: pslToBed psl bed

Function: Given a bed, spit out promoter, first exon, or all introns.

Usage: bedGeneParts part in.bed out.bed

Function: Deletes all overlapping self alignments.

Usage: pslDropOverlap in.psl out.psl

Function: Convert blastz lav to psl format

Usage: lavToPsl in.lav out.psl

Function: Load RepeatMasker .out files into database

Usage: hgLoadOut database file(s).out

Function: Convert from uncompressed to compressedquality score format.

Usage: qaToQac in.qa out.qac

Function: Convert ra file to table.

Usage: raToTab in.ra out.tab

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 [...]]

Function: Get data for generating histograms from a genePred file.

Usage: genePredHisto [options] what genePredFile histoOut

Function: Convert psl records to chain records

Usage: pslToChain pslIn chainOut

Function: Use AGP to combine per-scaffold qac into per-chrom qac.

Usage: qacAgpLift scaffoldToChrom.agp scaffolds.qac chrom.qac

Function: Get rid of chains that are primarily the results of repeats and degenerate DNA

Usage: chainAntiRepeat tNibDir qNibDir inChain outChain

Function: Show size of various C types for reference

Usage: sizeof

Function: Concatenate xml files together, stuffing all records inside a single outer tag.

Usage: xmlCat XXX