Software Usage Function
mktime valid dates: 1970-01-01 00:00:00 to 2038-01-19 03:14:07 Convert date string to unix timestamp
positionalTblCheck positionalTblCheck db table positionalTblCheck - check that positional tables are sorted
bedCommonRegions bedCommonRegions file1 file2 file3 ... fileN Create a bed file (just bed3) that contains the regions common to all inputs.Regions are common only if exactly the same chromosome, starts, and end. Overlap is not enough. Each region must be in each input at most once. Output is stdout.
autoSql autoSql specFile outRoot {optional: -dbLink -withNull -json} Create SQL and C code for permanently storinga structure in database and loading it back into memorybased on a specification file
findMotif findMotif [options] -motif=<acgt...> sequence Find specified motif in sequence
pslxToFa pslxToFa in.psl out.fa Convert pslx (with sequence) to fasta file
toLower toLower inFile outFile Convert upper case to lower case in file. Leave other chars alone
aveCols aveCols file Average together columns
raToLines raToLines in.ra out.txt Output .ra file stanzas as single lines, with pipe-separated fields.
randomLines randomLines inFile count outFile Pick out random lines from file
bigWigCat bigWigCat ... Merge non-overlapping bigWig files
pigz pigz [options] [files ...] Compress files in parallel
gzip gzip [OPTION]... [FILE]... Compress FILEs (by default, compress FILES in-place).