Generic

Function: Deletes all overlapping self alignments.

Usage: pslDropOverlap in.psl out.psl

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

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

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

Usage: pslToBed psl bed

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: Convert ra file to table.

Usage: raToTab in.ra out.tab

Function: Lift PSLs from blat subrange alignments

Usage: pslLiftSubrangeBlat isPsl outPsl

Function: Convert psl records to chain records

Usage: pslToChain pslIn chainOut

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: Convert a GFF3 CIGAR file to a PSL file

Usage: gff3ToPsl mapFile inGff3 out.psl

Function: Convert blastz lav to psl format

Usage: lavToPsl in.lav out.psl

Function: Split a genome net file into chromosome net files

Usage: netSplit in.net outDir

Function: Find perfect matches in sequence.

Usage: oligoMatch oligos sequence output.bed

Function: Show size of various C types for reference

Usage: sizeof

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