janxkoci · April 9, 2025 20:35 · janxkoci · Apr 9, 2025
diff --git a/bioawk_manual.txt b/bioawk_manual.txt
 AWK(1)                                         General Commands Manual                                         AWK(1)

 awk

 NAME
       awk - pattern-directed scanning and processing language

 SYNOPSIS
       awk [ -F fs ] [ -v var=value ] [ 'prog' | -f progfile ] [ file ...  ]

 DESCRIPTION
       Awk  scans each input file for lines that match any of a set of patterns specified literally in prog or in one
       or more files specified as -f progfile.  With each pattern there can be an associated action that will be per‐
       formed  when  a line of a file matches the pattern.  Each line is matched against the pattern portion of every
       pattern-action statement; the associated action is performed for each matched pattern.  The file name -  means
       the  standard  input.  Any file of the form var=value is treated as an assignment, not a filename, and is exe‐
       cuted at the time it would have been opened if it were a filename.  The option -v followed by var=value is  an
       assignment  to be done before prog is executed; any number of -v options may be present.  The -F fs option de‐
       fines the input field separator to be the regular expression fs.

       An input line is normally made up of fields separated by white space, or by regular expression FS.  The fields
       are  denoted $1, $2, ..., while $0 refers to the entire line.  If FS is null, the input line is split into one
       field per character.

       A pattern-action statement has the form

              pattern { action }

       A missing { action } means print the line; a missing pattern always matches.   Pattern-action  statements  are
       separated by newlines or semicolons.

       An action is a sequence of statements.  A statement can be one of the following:

              if( expression ) statement [ else statement ]
              while( expression ) statement
              for( expression ; expression ; expression ) statement
              for( var in array ) statement
              do statement while( expression )
              break
              continue
              { [ statement ... ] }
              expression              # commonly var = expression
              print [ expression-list ] [ > expression ]
              printf format [ , expression-list ] [ > expression ]
              return [ expression ]
              next                    # skip remaining patterns on this input line
              nextfile                # skip rest of this file, open next, start at top
              delete array[ expression ]# delete an array element
              delete array            # delete all elements of array
              exit [ expression ]     # exit immediately; status is expression

       Statements  are  terminated  by semicolons, newlines or right braces.  An empty expression-list stands for $0.
       String constants are quoted " ", with the usual C escapes recognized within.  Expressions take  on  string  or
       numeric  values as appropriate, and are built using the operators + - * / % ^ (exponentiation), and concatena‐
       tion (indicated by white space).  The operators ! ++ -- += -= *= /= %= ^= > >= < <= == != ?: are  also  avail‐
       able  in  expressions.  Variables may be scalars, array elements (denoted x[i]) or fields.  Variables are ini‐
       tialized to the null string.  Array subscripts may be any string, not necessarily numeric; this allows  for  a
       form  of associative memory.  Multiple subscripts such as [i,j,k] are permitted; the constituents are concate‐
       nated, separated by the value of SUBSEP.

       The print statement prints its arguments on the standard output (or on a file if >file or >>file is present or
       on  a  pipe if |cmd is present), separated by the current output field separator, and terminated by the output
       record separator.  file and cmd may be literal names or parenthesized expressions; identical string values  in
       different statements denote the same open file.  The printf statement formats its expression list according to
       the format (see printf(3)).  The built-in function close(expr) closes the file or  pipe  expr.   The  built-in
       function fflush(expr) flushes any buffered output for the file or pipe expr.

       The mathematical functions exp, log, sqrt, sin, cos, and atan2 are built in.  Other built-in functions:

       length the length of its argument taken as a string, or of $0 if no argument.

       rand   random number on (0,1)

       srand  sets seed for rand and returns the previous seed.

       int    truncates to an integer value

       substr(s, m, n)
              the n-character substring of s that begins at position m counted from 1.

       index(s, t)
              the position in s where the string t occurs, or 0 if it does not.

       match(s, r)
              the position in s where the regular expression r occurs, or 0 if it does not.  The variables RSTART and
              RLENGTH are set to the position and length of the matched string.

       split(s, a, fs)
              splits the string s into array elements a[1], a[2], ..., a[n], and returns n.  The separation  is  done
              with  the  regular expression fs or with the field separator FS if fs is not given.  An empty string as
              field separator splits the string into one array element per character.

       sub(r, t, s)
              substitutes t for the first occurrence of the regular expression r in the string s.  If s is not given,
              $0 is used.

       gsub   same as sub except that all occurrences of the regular expression are replaced; sub and gsub return the
              number of replacements.

       sprintf(fmt, expr, ... )
              the string resulting from formatting expr ...  according to the printf(3) format fmt

       system(cmd)
              executes cmd and returns its exit status

       tolower(str)
              returns a copy of str with all upper-case  characters  translated  to  their  corresponding  lower-case
              equivalents.

       toupper(str)
              returns  a  copy  of  str  with  all lower-case characters translated to their corresponding upper-case
              equivalents.

       The ``function'' getline sets $0 to the next input record from the current input file; getline <file  sets  $0
       to  the next record from file.  getline x sets variable x instead.  Finally, cmd | getline pipes the output of
       cmd into getline; each call of getline returns the next line of output from cmd.  In all  cases,  getline  re‐
       turns 1 for a successful input, 0 for end of file, and -1 for an error.

       Patterns  are arbitrary Boolean combinations (with ! || &&) of regular expressions and relational expressions.
       Regular expressions are as in egrep; see grep(1).  Isolated regular expressions in a pattern apply to the  en‐
       tire  line.  Regular expressions may also occur in relational expressions, using the operators ~ and !~.  /re/
       is a constant regular expression; any string (constant or variable) may be used as a regular  expression,  ex‐
       cept in the position of an isolated regular expression in a pattern.

       A  pattern  may  consist  of  two patterns separated by a comma; in this case, the action is performed for all
       lines from an occurrence of the first pattern though an occurrence of the second.

       A relational expression is one of the following:

              expression matchop regular-expression
              expression relop expression
              expression in array-name
              (expr,expr,...) in array-name

       where a relop is any of the six relational operators in C, and a matchop is either ~ (matches) or !~ (does not
       match).   A  conditional  is  an  arithmetic  expression, a relational expression, or a Boolean combination of
       these.

       The special patterns BEGIN and END may be used to capture control before the first input line is read and  af‐
       ter the last.  BEGIN and END do not combine with other patterns.

       Variable names with special meanings:

       CONVFMT
              conversion format used when converting numbers (default %.6g)

       FS     regular expression used to separate fields; also settable by option -Ffs.

       NF     number of fields in the current record

       NR     ordinal number of the current record

       FNR    ordinal number of the current record in the current file

       FILENAME
              the name of the current input file

       RS     input record separator (default newline)

       OFS    output field separator (default blank)

       ORS    output record separator (default newline)

       OFMT   output format for numbers (default %.6g)

       SUBSEP separates multiple subscripts (default 034)

       ARGC   argument count, assignable

       ARGV   argument array, assignable; non-null members are taken as filenames

       ENVIRON
              array of environment variables; subscripts are names.

       Functions may be defined (at the position of a pattern-action statement) thus:

              function foo(a, b, c) { ...; return x }

       Parameters  are passed by value if scalar and by reference if array name; functions may be called recursively.
       Parameters are local to the function; all other variables are global.  Thus local variables may be created  by
       providing excess parameters in the function definition.

 EXAMPLES
       length($0) > 72
              Print lines longer than 72 characters.

       { print $2, $1 }
              Print first two fields in opposite order.

       BEGIN { FS = ",[ \t]*|[ \t]+" }
             { print $2, $1 }
              Same, with input fields separated by comma and/or blanks and tabs.

            { s += $1 }
       END  { print "sum is", s, " average is", s/NR }
              Add up first column, print sum and average.

       /start/, /stop/
              Print all lines between start/stop pairs.

       BEGIN     {    # Simulate echo(1)
            for (i = 1; i < ARGC; i++) printf "%s ", ARGV[i]
            printf "\n"
            exit }

 BIOAWK EXTENSIONS
       Bioawk  adds a new -c fmt option that specifies the input format. The behavior of bioawk may vary depending on
       the value of fmt.  When fmt is header or hdr, bioawk parses named columns.  It  automatically  adds  variables
       whose  names  are taken from the first line and values from the column index. Special characters are converted
       to a underscore. When fmt is sam, vcf, bed or gff, it sets predefined column names. Users may  check  out  the
       predefined column names by -c help.  When fmt is fastx, bioawk will parse the input FASTA or FASTQ file into a
       TAB-delimited format first with each line consisting of sequence name, sequence,  quality  and  comments,  and
       then sets column names. Note that when -c fmt is in use, the input file can be optionally gzip'ed.

       Bioawk also adds more built-in functions:

       reverse(s)
              reverse string s

       revcomp(s)
              reverse complement a nucleotide string s in the IUB encoding.

       trimq(qual, beg, end, param)
              trim  quality  string  qual  in  the  Sanger  scale using Richard Mott's algorithm (used in Phred). The
              0-based beginning and ending positions are written to beg and end,  respectively.  The  last  arguement
              param is the single parameter used in the algorithm, which is optional and defaults 0.05.

       and(x, y)
              bit AND operation (& in C)

       or(x, y)
              bit OR operation (| in C)

       xor(x, y)
              bit XOR operation (^ in C)

 SEE ALSO
       lex(1), sed(1)
       A.  V.  Aho,  B.  W.  Kernighan,  P.  J. Weinberger, The AWK Programming Language, Addison-Wesley, 1988.  ISBN
       0-201-07981-X

 BUGS
       There are no explicit conversions between numbers and strings.  To force an expression to be treated as a num‐
       ber add 0 to it; to force it to be treated as a string concatenate "" to it.
       The scope rules for variables in functions are a botch; the syntax is worse.

                                                                                                               AWK(1)
	AWK(1) General Commands Manual AWK(1)

	awk

	NAME
	awk - pattern-directed scanning and processing language

	SYNOPSIS
	awk [ -F fs ] [ -v var=value ] [ 'prog' \| -f progfile ] [ file ... ]

	DESCRIPTION
	Awk scans each input file for lines that match any of a set of patterns specified literally in prog or in one
	or more files specified as -f progfile. With each pattern there can be an associated action that will be per‐
	formed when a line of a file matches the pattern. Each line is matched against the pattern portion of every
	pattern-action statement; the associated action is performed for each matched pattern. The file name - means
	the standard input. Any file of the form var=value is treated as an assignment, not a filename, and is exe‐
	cuted at the time it would have been opened if it were a filename. The option -v followed by var=value is an
	assignment to be done before prog is executed; any number of -v options may be present. The -F fs option de‐
	fines the input field separator to be the regular expression fs.

	An input line is normally made up of fields separated by white space, or by regular expression FS. The fields
	are denoted $1, $2, ..., while $0 refers to the entire line. If FS is null, the input line is split into one
	field per character.

	A pattern-action statement has the form

	pattern { action }

	A missing { action } means print the line; a missing pattern always matches. Pattern-action statements are
	separated by newlines or semicolons.

	An action is a sequence of statements. A statement can be one of the following:

	if( expression ) statement [ else statement ]
	while( expression ) statement
	for( expression ; expression ; expression ) statement
	for( var in array ) statement
	do statement while( expression )
	break
	continue
	{ [ statement ... ] }
	expression # commonly var = expression
	print [ expression-list ] [ > expression ]
	printf format [ , expression-list ] [ > expression ]
	return [ expression ]
	next # skip remaining patterns on this input line
	nextfile # skip rest of this file, open next, start at top
	delete array[ expression ]# delete an array element
	delete array # delete all elements of array
	exit [ expression ] # exit immediately; status is expression

	Statements are terminated by semicolons, newlines or right braces. An empty expression-list stands for $0.
	String constants are quoted " ", with the usual C escapes recognized within. Expressions take on string or
	numeric values as appropriate, and are built using the operators + - * / % ^ (exponentiation), and concatena‐
	tion (indicated by white space). The operators ! ++ -- += -= *= /= %= ^= > >= < <= == != ?: are also avail‐
	able in expressions. Variables may be scalars, array elements (denoted x[i]) or fields. Variables are ini‐
	tialized to the null string. Array subscripts may be any string, not necessarily numeric; this allows for a
	form of associative memory. Multiple subscripts such as [i,j,k] are permitted; the constituents are concate‐
	nated, separated by the value of SUBSEP.

	The print statement prints its arguments on the standard output (or on a file if >file or >>file is present or
	on a pipe if \|cmd is present), separated by the current output field separator, and terminated by the output
	record separator. file and cmd may be literal names or parenthesized expressions; identical string values in
	different statements denote the same open file. The printf statement formats its expression list according to
	the format (see printf(3)). The built-in function close(expr) closes the file or pipe expr. The built-in
	function fflush(expr) flushes any buffered output for the file or pipe expr.

	The mathematical functions exp, log, sqrt, sin, cos, and atan2 are built in. Other built-in functions:

	length the length of its argument taken as a string, or of $0 if no argument.

	rand random number on (0,1)

	srand sets seed for rand and returns the previous seed.

	int truncates to an integer value

	substr(s, m, n)
	the n-character substring of s that begins at position m counted from 1.

	index(s, t)
	the position in s where the string t occurs, or 0 if it does not.

	match(s, r)
	the position in s where the regular expression r occurs, or 0 if it does not. The variables RSTART and
	RLENGTH are set to the position and length of the matched string.

	split(s, a, fs)
	splits the string s into array elements a[1], a[2], ..., a[n], and returns n. The separation is done
	with the regular expression fs or with the field separator FS if fs is not given. An empty string as
	field separator splits the string into one array element per character.

	sub(r, t, s)
	substitutes t for the first occurrence of the regular expression r in the string s. If s is not given,
	$0 is used.

	gsub same as sub except that all occurrences of the regular expression are replaced; sub and gsub return the
	number of replacements.

	sprintf(fmt, expr, ... )
	the string resulting from formatting expr ... according to the printf(3) format fmt

	system(cmd)
	executes cmd and returns its exit status

	tolower(str)
	returns a copy of str with all upper-case characters translated to their corresponding lower-case
	equivalents.

	toupper(str)
	returns a copy of str with all lower-case characters translated to their corresponding upper-case
	equivalents.

	The ``function'' getline sets $0 to the next input record from the current input file; getline <file sets $0
	to the next record from file. getline x sets variable x instead. Finally, cmd \| getline pipes the output of
	cmd into getline; each call of getline returns the next line of output from cmd. In all cases, getline re‐
	turns 1 for a successful input, 0 for end of file, and -1 for an error.

	Patterns are arbitrary Boolean combinations (with ! \|\| &&) of regular expressions and relational expressions.
	Regular expressions are as in egrep; see grep(1). Isolated regular expressions in a pattern apply to the en‐
	tire line. Regular expressions may also occur in relational expressions, using the operators ~ and !~. /re/
	is a constant regular expression; any string (constant or variable) may be used as a regular expression, ex‐
	cept in the position of an isolated regular expression in a pattern.

	A pattern may consist of two patterns separated by a comma; in this case, the action is performed for all
	lines from an occurrence of the first pattern though an occurrence of the second.

	A relational expression is one of the following:

	expression matchop regular-expression
	expression relop expression
	expression in array-name
	(expr,expr,...) in array-name

	where a relop is any of the six relational operators in C, and a matchop is either ~ (matches) or !~ (does not
	match). A conditional is an arithmetic expression, a relational expression, or a Boolean combination of
	these.

	The special patterns BEGIN and END may be used to capture control before the first input line is read and af‐
	ter the last. BEGIN and END do not combine with other patterns.

	Variable names with special meanings:

	CONVFMT
	conversion format used when converting numbers (default %.6g)

	FS regular expression used to separate fields; also settable by option -Ffs.

	NF number of fields in the current record

	NR ordinal number of the current record

	FNR ordinal number of the current record in the current file

	FILENAME
	the name of the current input file

	RS input record separator (default newline)

	OFS output field separator (default blank)

	ORS output record separator (default newline)

	OFMT output format for numbers (default %.6g)

	SUBSEP separates multiple subscripts (default 034)

	ARGC argument count, assignable

	ARGV argument array, assignable; non-null members are taken as filenames

	ENVIRON
	array of environment variables; subscripts are names.

	Functions may be defined (at the position of a pattern-action statement) thus:

	function foo(a, b, c) { ...; return x }

	Parameters are passed by value if scalar and by reference if array name; functions may be called recursively.
	Parameters are local to the function; all other variables are global. Thus local variables may be created by
	providing excess parameters in the function definition.

	EXAMPLES
	length($0) > 72
	Print lines longer than 72 characters.

	{ print $2, $1 }
	Print first two fields in opposite order.

	BEGIN { FS = ",[ \t]*\|[ \t]+" }
	{ print $2, $1 }
	Same, with input fields separated by comma and/or blanks and tabs.

	{ s += $1 }
	END { print "sum is", s, " average is", s/NR }
	Add up first column, print sum and average.

	/start/, /stop/
	Print all lines between start/stop pairs.

	BEGIN { # Simulate echo(1)
	for (i = 1; i < ARGC; i++) printf "%s ", ARGV[i]
	printf "\n"
	exit }

	BIOAWK EXTENSIONS
	Bioawk adds a new -c fmt option that specifies the input format. The behavior of bioawk may vary depending on
	the value of fmt. When fmt is header or hdr, bioawk parses named columns. It automatically adds variables
	whose names are taken from the first line and values from the column index. Special characters are converted
	to a underscore. When fmt is sam, vcf, bed or gff, it sets predefined column names. Users may check out the
	predefined column names by -c help. When fmt is fastx, bioawk will parse the input FASTA or FASTQ file into a
	TAB-delimited format first with each line consisting of sequence name, sequence, quality and comments, and
	then sets column names. Note that when -c fmt is in use, the input file can be optionally gzip'ed.

	Bioawk also adds more built-in functions:

	reverse(s)
	reverse string s

	revcomp(s)
	reverse complement a nucleotide string s in the IUB encoding.

	trimq(qual, beg, end, param)
	trim quality string qual in the Sanger scale using Richard Mott's algorithm (used in Phred). The
	0-based beginning and ending positions are written to beg and end, respectively. The last arguement
	param is the single parameter used in the algorithm, which is optional and defaults 0.05.

	and(x, y)
	bit AND operation (& in C)

	or(x, y)
	bit OR operation (\| in C)

	xor(x, y)
	bit XOR operation (^ in C)

	SEE ALSO
	lex(1), sed(1)
	A. V. Aho, B. W. Kernighan, P. J. Weinberger, The AWK Programming Language, Addison-Wesley, 1988. ISBN
	0-201-07981-X

	BUGS
	There are no explicit conversions between numbers and strings. To force an expression to be treated as a num‐
	ber add 0 to it; to force it to be treated as a string concatenate "" to it.
	The scope rules for variables in functions are a botch; the syntax is worse.

	AWK(1)