Generic

Function: Program to create random fasta records

Usage: faRandomize [-seed=N] in.fa randomized.fa

Function: Convert file to C strings

Usage: stringify [options] in.txt

Function: Convert seconds since 1970 to time and date

Usage: tickToDate ticks

Function: Deletes all overlapping self alignments.

Usage: pslDropOverlap in.psl out.psl

Function: Generate structures code and parser for XML file from DTD-like spec

Usage: autoXml file.dtdx root

Function: Calculate GC Percentage in 20kb windows

Usage: hgGcPercent [options] database nibDir

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

Usage: bedGeneParts part in.bed out.bed

Function: Split a genome net file into chromosome net files

Usage: netSplit in.net outDir

Function: Query the trackDb system using SQL syntax.

Usage: tdbQuery sqlStatement

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: Validate genePred files or tables

Usage: genePredCheck [options] fileTbl ..

Function: Convert a GFF3 CIGAR file to a PSL file

Usage: gff3ToPsl mapFile inGff3 out.psl

Function: Try to fetch url with multiple connections

Usage: paraFetch N R URL {outPath}