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Function: Program to create random fasta records
Usage: faRandomize [-seed=N] in.fa randomized.fa
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Function: Convert file to C strings
Usage: stringify [options] in.txt
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Function: Convert seconds since 1970 to time and date
Usage: tickToDate ticks
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Function: Deletes all overlapping self alignments.
Usage: pslDropOverlap in.psl out.psl
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Function: Generate structures code and parser for XML file from DTD-like spec
Usage: autoXml file.dtdx root
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Function: Calculate GC Percentage in 20kb windows
Usage: hgGcPercent [options] database nibDir
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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 [...]]
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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
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Function: Given a bed, spit out promoter, first exon, or all introns.
Usage: bedGeneParts part in.bed out.bed
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Function: Split a genome net file into chromosome net files
Usage: netSplit in.net outDir
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Function: Query the trackDb system using SQL syntax.
Usage: tdbQuery sqlStatement
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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
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Function: Validate genePred files or tables
Usage: genePredCheck [options] fileTbl ..
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Function: Convert a GFF3 CIGAR file to a PSL file
Usage: gff3ToPsl mapFile inGff3 out.psl
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Function: Try to fetch url with multiple connections
Usage: paraFetch N R URL {outPath}