sra-toolkit 2.1.7a-1ubuntu2 / usr / lib / ncbi / schema / vdb.vschema

/*===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government have not placed any restriction on its use or reproduction.
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
*
*  Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/

/*==========================================================================
 * VDB external functions, formats and types
 */
version 1;

// built-in functions should be known to all
include 'vdb/built-in.vschema';


/*--------------------------------------------------------------------------
 * types
 */

/* text_token
 *  a vector describing tokens recognized within a text string
 *
 * COMPONENTS:
 *  0 - token id
 *  1 - token starting coordinate
 *  2 - token length
 */
typedef U16 text:token [ 3 ];


/*--------------------------------------------------------------------------
 * typesets
 */
typeset pack_set { B8, B16, B32, B64, integer_set };
typeset izip_set { integer_set };
typeset fzip_set { F32 };


/*--------------------------------------------------------------------------
 * formats
 */
fmtdef izip_fmt;
fmtdef fzip_fmt;
fmtdef rle_fmt;
fmtdef zlib_fmt;
fmtdef bzip2_fmt;


/*--------------------------------------------------------------------------
 * functions
 */

/* echo
 *  returns single or repeated constant value
 *
 *  "T" [ TYPE ] - type of constant data to return
 *
 *  "val" [ CONST ] - a data constant
 *
 *  "row_len" [ DATA, OPTIONAL ] - if omitted, "val" will be
 *  issued once and the resultant row-length will be the length
 *  of "val". otherwise, "val" will be repeated and/or truncated
 *  as necessary to produce a row-length equal to that of input.
 *
 * USAGE:
 *  to echo a single constant value
 *    U16 len = row_len ( col ) | < U16 > echo < 0 > ();
 *
 *  to create a row of repeated values
 *    ascii allN = < ascii > echo < 'N' > ( col );
 */
function < type T >
T echo #1.0 < T val > ( * any row_len )
    = vdb:echo;


/* exists
 *  returns constant or dynamic value if predicate input exists
 *
 *  "T" [ TYPE ] - type of data to return
 *
 *  "cval" [ CONST, OPTIONAL ] - a data constant. when present,
 *  the function will behave like "echo" ( see below )
 *
 *  "predicate" [ DATA ] - an input whose existence determines
 *  whether the function will operate or not.
 *
 *  "dval" [ DATA, OPTIONAL ] - data value, either passed through
 *  or used to determine a repeat count of "cval" ( see below )
 *
 * USAGE:
 *  when "cval" is omitted, "dval" must be present and will be
 *  passed through depending upon the existence of "predicate"
 *    U8 count = < U8 > exists ( col, count2 );
 *
 *  when "cval" is present, "dval" may be omitted, and "cval" will
 *  be passed through just like echo depending upon "predicate"
 *   U8 count = < U8 > exists < 2 > ( col2 ) | < U8 > echo < 1 > ();
 *
 *  when "cval" and "dval" are both present, the behavior is
 *  like echo, but gated with "predicate"
 *    ascii poly = < ascii > exists < 'a' > ( col, repeat );
 */
function < type T >
T exists #1.0 < * T cval > ( any predicate, * T dval )
    = vdb:exists;


/* map
 *  translate input elements
 *  behaves much like the Unix "tr" command
 *  except that charsets are not [currently] supported
 *
 *  "A" [ TYPE ] - input data type, e.g. "ascii"
 *
 *  "B" [ TYPE ] - output data type, e.g. "ascii" or "U8"
 *
 *  "from" [ CONST ] - set of key values.
 *
 *  "to" [ CONST ] - set of mapped values,
 *  where length ( from ) === length ( to )
 *
 *  "in" [ DATA ] - input data to be matched against keys
 *  in "from". also serves as source data when "src" is omitted
 *
 *  "src" [ DATA, OPTIONAL ] - source data to be edited by
 *  substituting "to" values when corresponding "in" value
 *  matches key in "from". if omitted, "in" is used.
 *
 * USAGE:
 *  to upper case letters from a given alphabet
 *    ascii upper = < ascii, ascii > map < 'acgtn', 'ACGTN' > ( in );
 *
 *  to translate from ascii to binary
 *    U8 bin = < ascii, U8 > map < 'ACGTN', [ 0, 1, 2, 3, 0 ] > ( in );
 *
 *  to alter certain values of a column based upon values in another
 *    U8 n_encoded = < ascii, U8 > map < 'N', 0 > ( read, quality );
 *
 * CAVEATS:
 *  the full canonical mode of operation uses separate inputs
 *  for key matching and output source.
 *
 *  when a single input is specified:
 *   - sizeof ( A ) must equal sizeof ( B )
 *   - A must be a proper subset of B -OR-
 *   - "from" keys must match every possible "in" value ( total substitution )
 */
function < type A, type B >
B map #1.0 < A from, B to > ( A in, * B src )
    = vdb:map;


/* clip
 *  limit data values to given bounds
 *
 *  "T" [ TYPE ] - input and output data type
 *
 *  "dim" [ CONST >= 1 ] - fixed dimension on
 *  input and output vectors
 *
 *  "lower" [ CONST ] - lower bound, inclusive
 *
 *  "upper" [ CONST ] - upper bounds, inclusive
 *
 *  "in" [ DATA ] - data to be clipped
 */
function < type T >
T clip #1.0 < T lower, T upper > ( T in )
    = vdb:clip;

function < type T, U32 dim >
T [ dim ] vclip #1.0 < T lower, T upper > ( T [ dim ] in )
    = vdb:clip;


/* ceil
 *  round up to the nearest integer
 *
 *  "in" [ DATA ] - data to be processed
 */
function
numeric_set ceil #1.0 ( float_set in )
    = vdb:ceil;

/* floor
 *  round down to the nearest integer
 *
 *  "in" [ DATA ] - data to be processed
 */
function
numeric_set floor #1.0 ( float_set in )
    = vdb:floor;

/* round
 *  round to nearest integer away from zero
 *
 *  "T" [ TYPE = { F32, F64 } ] - input and output data type
 *
 *  "in" [ DATA ] - data to be processed
 */
function
numeric_set round #1.0 ( float_set in )
    = vdb:round;

/* trunc
 *  round to the nearest integer not larger in absolute value
 *
 *  "T" [ TYPE = { F32, F64 } ] - input and output data type
 *
 *  "in" [ DATA ] - data to be processed
 */
function
numeric_set trunc #1.0 ( float_set in )
    = vdb:trunc;


/* min
 *  return the minimum value of each element
 * max
 *  return the maximum value of each element
 *
 *  "T" [ TYPE ] - input and output data type
 *
 *  "a" [ DATA ] - first operand
 *
 *  "b" [ DATA ] - second operand
 *
 * SYNOPSIS:
 *  compares two inputs element by element
 *  returns min or max element of each
 *
 * USAGE:
 *  intersections
 *    U32 left = < U32 > max ( left_a, left_b );
 *    U32 right = < U32 > min ( right_a, right_b );
 */
function < type T >
T min #1.0 ( T a, T b )
    = vdb:min;

function < type T >
T max #1.0 ( T a, T b )
    = vdb:max;


/* sum
 *  return the sum of inputs
 * diff
 *  return the difference of inputs
 *
 *  "T" [ TYPE ] - input and output data type
 *  must be member of numeric_set
 *
 *  "k" [ CONST, DEFAULT 0 ] - optional constant
 *  to be added or subtracted
 *
 *  "a" [ DATA ] - left-most operand
 *
 *  "b" [ DATA ] - optional subtractand
 *
 * SYNOPSIS:
 *  incorporates "k" into expression for every row
 *  returns sum or difference of inputs for all rows
 *
 * USAGE:
 *  length of half-closed interval
 *    U32 len = < U32 > diff ( stop, start );
 *  convert one-based coordinate to zero based
 *    U32 zero_based = < U32 > diff < 1 > ( one_based );
 */
function < type T >
T sum #1.0 < * T k > ( T a, ... )
    = vdb:sum;

function < type T >
T diff #1.0 < * T k > ( T a * T b )
    = vdb:diff;

/* deriv
 *  return the 1st derivative of an input row
 * integral
 *  return the integral of an input row
 *
 *  "T" [ TYPE ] - input and output data type
 *  must be signed integer of any size
 *
 *  "in" [ DATA ] - input to be modified
 *
 * SYNOPSIS:
 *  Takes/restores chained deltas of integer elements in a row
 *  Fist element is unmodified
 */

function < type T > T deriv #1.0  ( T in ) = vdb:deriv;
function < type T > T integral #1.0  ( T in ) = vdb:integral;


/* delta
 *  return the 1st derivative of a whole blob
 * undelta
 *  return the integral of a whole blob
 *
 *  "T" [ TYPE ] - input and output data type
 *  must be signed integer of any size
 *
 *  "in" [ DATA ] - input to be modified
 *
 * SYNOPSIS:
 *  similar to deriv/integral but operates on full blob
 */

function < type T > T delta #1.0  ( T in ) = vdb:delta;
function < type T > T undelta #1.0  ( T in ) = vdb:undelta;


/* outlier_encode
 *  removes a given outlier from a data series
 * outlier_decode
 *  removes the effect of outlier_encode
 *
 *  "T" [ TYPE ] - input and output data type
 *  must be an integer of any size
 *
 *  "in" [ DATA ] - input to be modified
 *
 * SYNOPSIS:
 *  The encode replaces every element that is equal to the
 *  outlier with (the value of the previous element) * 2 + 1
 *  and the remaining elements are replaced with their value * 2.
 */

function < type T > T outlier_encode #1.0 < T outlier > ( T in ) = vdb:outlier_encode;
function < type T > T outlier_decode #1.0 < T outlier > ( T in ) = vdb:outlier_decode;

/* add_row_id
 *  return the sum of an input and its row-id
 * sub_row_id
 *  return the difference of an input and its row-id
 *
 *  "T" [ TYPE ] - input and output data type
 *  must be member of numeric_set
 *
 *  "in" [ DATA ] - input to be modified
 *
 * SYNOPSIS:
 *  adjusts for relationship between input and row-id
 *  used primarily to reduce serial ids to constants
 */
function < type T >
T add_row_id #1.0 ( T in )
    = vdb:add_row_id;

function < type T >
T sub_row_id #1.0 ( T in )
    = vdb:sub_row_id;


/* cut
 *  extract one or more elements from input vector
 *  to form an output vector of equal or less dimension
 *
 *  "T" [ TYPE ] - base element type to be processed
 *
 *  "idx" [ CONST ] - mandatory initial element index
 *  count of parameters must equal dimension of output type
 *
 *  "in" [ DATA ] - source of input vectors where the vector
 *  element type is known, but any dimension is accepted.
 *
 * USAGE:
 *  extracting a single channel from a 4 channel vector
 *    F32 [ 4 ] vect ...
 *    F32 chan = < F32 > cut < 0 > ( vect );
 *
 *  extracting multiple channels
 *    U8 [ 16 ] in ...
 *    U8 [ 3 ] out = < U8 > cut < 5, 1, 3 > ( in );
 *
 *  reversing channels
 *    I16 [ 2 ] norm ...
 *    I16 [ 2 ] rev = < I16 > cut < 1, 0 > ( norm );
 */
function < type T >
T [ * ] cut #1.0 < U32 idx, ... > ( T [ * ] in )
    = vdb:cut;


/* paste
 *  combine all elements of all inputs into a single vector
 *  output dimension is sum of all input dimensions after type normalization
 *
 *  "T" [ TYPE ] - base element type to be processed
 *
 *  "in" [ DATA ] - first of an arbitrary number of columns
 *  the total of input elements produces an output of "T [ total ]"
 */
function < type T >
T [ * ] paste #1.0 ( T [ * ] in, ... )
    = vdb:paste;


/* vec_sum
 *  compute the sum of all the elements of the input vector
 *
 *  "T" [ TYPE ] - base element type to be processed
 *
 *  "in" [ DATA ] - the input
 */
function < type T >
T vec_sum #1.0 ( T [ * ] in )
    = vdb:vec_sum;


/* checksum
 *  compute a checksum ( hash ) of all of the input bytes
 *  to be used in a trigger production
 *
 *  "node" [ CONST ] - path to metadata node where checksum
 *   will be stored.
 *
 *  "algorithm" [ CONST ] - type of checksum to perform:
 *    'crc-32'  # match against POSIX cksum
 *    'md5'     #  "   "  md5sum
 *    'sha-1'   #  "   "  sha1sum
 *    'sha-256' #  "   "  sha256sum
 *    'sha-384' #  "   "  sha384sum
 *    'sha-512' #  "   "  sha512sum
 *
 *  "in" [ DATA ] - the octet-stream to be checksummed
 */
function
bool checksum #1.0 < ascii node, ascii algorithm > ( B8 in )
    = vdb:checksum;

/* md5sum
 *  compute an md5 checksum of all of the input bytes
 */
function
bool md5sum #1.0 < ascii node > ( B8 in )
{
    return checksum < node, 'md5' > ( in );
}


/* pack
 *  packs words into bit-aligned units
 *  words are expected in architecture native byte-order
 *  and returned in "big-bit-endian" order
 *
 *  the packed size is determined by the dimension of the
 *  left-hand assignment value.
 *
 *  "in" [ DATA ] - B8, B16, B32 or B64 data
 */
function
B1 [ * ] pack #1.0 ( pack_set in )
    = vdb:pack;


/* unpack
 *  unpacks bit-aligned units into words
 *  input is expected in "big-bit-endian" order
 *  and returned in architecture native byte-order
 *
 *  the unpacked type is determined from the left-hand
 *  assignment value.
 *
 *  "in" [ DATA ] - B[1]..B[64]
 */
function
pack_set unpack #1.0 ( B1 [ * ] in )
    = vdb:unpack;


/* izip
 * iunzip
 *  integer compression
 */
function
izip_fmt izip #2.1 ( izip_set in )
    = vdb:izip;

function
izip_set iunzip #2.1 ( izip_fmt in )
    = vdb:iunzip;

physical < type T >
T izip_encoding #1.0
{
    decode { return ( T ) iunzip ( @ ); }
    encode { return izip ( @ ); }
};


/* fzip
 * funzip
 *  floating point compression
 *
 *  "mantissa" [ CONST ] - the number of mantissa bits
 *  to preserve
 */
function
fzip_fmt fzip #1.0 < U32 mantissa > ( fzip_set in )
    = vdb:fzip;

function
fzip_set funzip #1.0 ( fzip_fmt in )
    = vdb:funzip;

physical < type T >
T fzip_encoding #1.0 < U32 mantissa >
{
    decode { return funzip ( @ ); }
    encode { return fzip < mantissa > ( @ ); }
};


/* rlencode
 * rldecode
 *  run-length encoding
 */
function
rle_fmt rlencode #1.0 ( any in )
    = vdb:rlencode;

function
any rldecode #1.0 ( rle_fmt in )
    = vdb:rldecode;


/* zip
 * unzip
 *  run things through zlib
 *
 *  "strategy" [ CONST, OPTIONAL ] - set the compression strategy
 *
 *  "level" [ CONST, OPTIONAL ] - set the amount of compression
 *  from 0..9 ( none to best compression ), or use -1 for zlib
 *  default behavior.
 */

// zlib strategy
const I32 Z_FILTERED            =  1;
const I32 Z_HUFFMAN_ONLY        =  2;
const I32 Z_RLE                 =  3;
const I32 Z_DEFAULT_STRATEGY    =  0;

// zlib level
const I32 Z_NO_COMPRESSION      =  0;
const I32 Z_BEST_SPEED          =  1;
const I32 Z_BEST_COMPRESSION    =  9;
const I32 Z_DEFAULT_COMPRESSION = -1;

function
zlib_fmt zip #1.0 < * I32 strategy, I32 level > ( any in )
    = vdb:zip;

function
any unzip #1.0 ( zlib_fmt in )
    = vdb:unzip;

physical < type T >
T zip_encoding #1.0 < * I32 strategy, I32 level >
{
    decode { return unzip ( @ ); }
    encode { return zip < strategy, level > ( @ ); }
};

physical
bool bool_encoding #1.0
{
    decode
    {
        B1 bit = unzip ( @ );
        return ( bool ) unpack ( bit );
    }

    encode
    {
        U8 lim = < U8 > clip < 0, 1 > ( @ );
        B1 bit = pack ( lim );
        return zip < Z_RLE, Z_BEST_SPEED > ( bit );
    }
}

physical < type T >
T delta_izip_encoding #1.0
{
    decode
    {
        T dlt = iunzip ( @ );
        return < T > undelta ( dlt );
    }

    encode
    {
        T dlt = <T> delta ( @ );
        return izip ( dlt );
    }
}
physical < type T >
T delta_zip_encoding #1.0
{
    decode
    {
        T dlt = unzip ( @ );
        return < T > undelta ( dlt );
    }

    encode
    {
        T dlt = <T> delta ( @ );
        return zip < Z_RLE, Z_BEST_SPEED > ( dlt );
    }
}

/* bzip
 * bunzip
 *  run things through bzip2
 *
 *  "blockSize100k" [ CONST, OPTIONAL ] - set the compression workspace size
 *  from 1..9 inclusive, produces a workspace of blockSize100K * 100000 bytes
 *  default is 5
 *
 *  "workFactor" [ CONST, OPTIONAL ] - set compression level
 *  from 0..250 inclusive, where 0 means bzip2 default, currently 30
 */

function
bzip2_fmt bzip #1.0 < * U32 blockSize100k, U32 workFactor > ( any in )
    = vdb:bzip;

function
any bunzip #1.0 ( bzip2_fmt in )
    = vdb:bunzip;

physical < type T >
T bzip_encoding #1.0 < * U32 blockSize100k, U32 workFactor >
{
    decode { return bunzip ( @ ); }
    encode { return bzip < blockSize100k, workFactor > ( @ ); }
};


/* simple_sub_select
 *  project a column from another table within database
 *
 *  "T" [ TYPE ] - data type of column
 *   must be compatible with source column
 *
 *  "tbl" [ CONST ] - name of table within parent
 *
 *  "col" [ CONST ] - column spec, i.e. simple name or
 *   typed name spec
 *
 *  "row" [ DATA ] - row to select
 *
 *  "idx" [ DATA ] - one-based indexing of what element to pick, defaults to all if not given
 */
function < type T >
T simple_sub_select #1.0 < ascii tbl, ascii col > ( I64 row *  I32 idx )
    = vdb:simple_sub_select_1;


/* extract_token
 *  extract a textual token from an input string
 *
 *  "idx" [ CONST ] - a zero-based index of the token
 *  if value < row_len ( tok ), then the substring of
 *  indexed token is returned. otherwise, returns empty.
 *
 *  "str" [ DATA ] - input text. type must be compatible with
 *  output production, meaning types must be same, or ascii input
 *  with utf8 output.
 *
 *  "tok" [ DATA ] - results of tokenizing "str"
 */
function
text_set extract_token #1.0 < U32 idx > ( text_set str, text:token tok )
    = vdb:extract_token;


/* strtonum
 *  convert string to number
 *
 *  "radix" [ CONST, DEFAULT 10 ]
 *   if not specified, or if given as 0, the default will be 10
 *   unless the string begins with "0x" or "0X", in which case radix will be 16
 *   octal is NOT inferred ( i.e. leading "0" does not imply octal )
 *
 *  "str" [ DATA ] - text to be converted
 */
function
numeric_set strtonum #1.0 < * U32 radix > ( text_set str )
    = vdb:strtonum;


/* sprintf
 *  formatted print to a string
 *
 *  formatting rules differ somewhat from C sprintf:
 *
 *    '%' [ <flags> ] [ <field-width> ] [ ':' <index-range> ] [ '.' <precision> ] <storage-class>
 *
 *  where:
 *
 *    flags
 *        = ' '           : prepend space to a numeral if it does not have a sign
 *        | '+'           : always produce a sign on numeric conversion
 *        | '-'           : left-align parameter within field
 *        | '0'           : left-pad with zeroes rather than spaces
 *        | '#'           : use "alternate" representation
 *        | ','           : produce comma-separated triples
 *        ;
 *
 *    field-width
 *        = DECIMAL       : a base-10 numeral
 *        | '*'           : take field width from args
 *        ;
 *
 *    index-range
 *        = index
 *        | index '-' index
 *        ;
 *
 *    index
 *        = DECIMAL       : a base-10 numeral
 *        | '$'           : last vector element
 *        | '*'           : take index from args
 *        ;
 *
 *    precision
 *        = DECIMAL       : a base-10 numeral
 *        | '*'           : take precision from args
 *        ;
 *
 *    storage-class
 *        = 'd' | 'i'     : general decimal integer
 *        | 'u'           : decimal unsigned integer
 *        | 'x'           : lower-case hex
 *        | 'X'           : upper-case hex
 *        | 'o'           : octal
 *        | 'b'           : binary
 *        | 'f'           : floating point
 *        | 'e'           : scientific notation
 *        | 'g'           : general floating point
 *        | 'c' | 's'     : character
 *        ;
 *
 *
 *  "fmt" [ CONST ] - constant format string
 *
 *  "p1" [ DATA ] - first param
 *  this and any subsequent params must correspond to format
 */
function
text_set sprintf #1.0 < ascii fmt > ( any p1, ... )
    = vdb:sprintf;