Generic

chainMergeSort
Function: Combine sorted files into larger sorted file
Usage: chainMergeSort file(s)
pslMap
Function: Map PSLs alignments to new targets using alignments ofthe old target to the new target. Given inPsl and mapPsl, wherethe target of inPsl is the query of mapPsl, create a new PSLwith the query of inPsl aligned to all the targets of mapPsl.If inPsl is a protein to nucleotide alignment and mapPsl is anucleotide to nucleotide alignment, the resulting alignment isnucleotide to nucleotide alignment of a hypothetical mRNA thatwould code for the protein. This is useful as it gives basealignments of spliced codons. A chain file may be used insteadmapPsl.
Usage: pslMap [options] inPsl mapFile outPsl
clstr_merge.pl
Function: It merges two or more .clstr files. The cluster orders need to be identical.
Usage: clstr_merge.pl db2new.clstr db3new.clstr > db23new.clstr
pslToChain
Function: Convert psl records to chain records
Usage: pslToChain pslIn chainOut
wordLine
Function: Chop up words by white space and output them with oneword to each line.
Usage: wordLine inFile(s)
chainAntiRepeat
Function: Get rid of chains that are primarily the results of repeats and degenerate DNA
Usage: chainAntiRepeat tNibDir qNibDir inChain outChain
dbTrash
Function: Drop tables from a database older than specified N hours
Usage: dbTrash -age=N [-drop] [-historyToo] [-db=<DB>] [-verbose=N]
gmtime
Function: Convert unix timestamp to date string
Usage: gmtime
paraFetch
Function: Try to fetch url with multiple connections
Usage: paraFetch N R URL {outPath}
rmFaDups
Function: Remove duplicate records in FA file
Usage: rmFaDup oldName.fa newName.fa
stringify
Function: Convert file to C strings
Usage: stringify [options] in.txt
validateFiles
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 [...]]
netFilter
Function: Filter out parts of net. What passesfilter goes to standard output. Note a net is arecursive data structure. If a parent fails to passthe filter, the children are not even considered.
Usage: netFilter in.net(s)
countChars
Function: Count the number of occurences of a particular char
Usage: countChars char file(s)
oligoMatch
Function: Find perfect matches in sequence.
Usage: oligoMatch oligos sequence output.bed