seqsero2: libs/sratoolkit.2.8.0-centos_linux64/schema/vdb/vdb.vschema annotate

annotate libs/sratoolkit.2.8.0-centos_linux64/schema/vdb/vdb.vschema @ 3:38ad1130d077 draft

planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

author	charles_s_test
date	Mon, 27 Nov 2017 11:21:07 -0500
parents
children

rev	line source
3 38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	1 /*===========================================================================
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	2 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	3 * PUBLIC DOMAIN NOTICE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	4 * National Center for Biotechnology Information
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	5 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	6 * This software/database is a "United States Government Work" under the
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	7 * terms of the United States Copyright Act. It was written as part of
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	8 * the author's official duties as a United States Government employee and
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	9 * thus cannot be copyrighted. This software/database is freely available
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	10 * to the public for use. The National Library of Medicine and the U.S.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	11 * Government have not placed any restriction on its use or reproduction.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	12 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	13 * Although all reasonable efforts have been taken to ensure the accuracy
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	14 * and reliability of the software and data, the NLM and the U.S.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	15 * Government do not and cannot warrant the performance or results that
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	16 * may be obtained by using this software or data. The NLM and the U.S.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	17 * Government disclaim all warranties, express or implied, including
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	18 * warranties of performance, merchantability or fitness for any particular
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	19 * purpose.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	20 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	21 * Please cite the author in any work or product based on this material.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	22 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	23 * ===========================================================================
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	24 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	25 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	26
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	27 /*==========================================================================
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	28 * VDB external functions, formats and types
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	29 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	30 version 1;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	31
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	32 // built-in functions should be known to all
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	33 include 'vdb/built-in.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	34
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	35
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	36 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	37 * types
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	38 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	39
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	40 /* text_token
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	41 * a vector describing tokens recognized within a text string
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	42 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	43 * COMPONENTS:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	44 * 0 - token id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	45 * 1 - token starting coordinate
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	46 * 2 - token length
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	47 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	48 typedef U16 text:token [ 3 ];
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	49
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	50
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	51 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	52 * typesets
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	53 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	54 typeset pack_set { B8, B16, B32, B64, integer_set };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	55 typeset izip_set { integer_set };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	56 typeset fzip_set { F32 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	57
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	58
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	59 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	60 * formats
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	61 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	62 fmtdef izip_fmt;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	63 fmtdef fzip_fmt;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	64 fmtdef rle_fmt;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	65 fmtdef zlib_fmt;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	66 fmtdef bzip2_fmt;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	67
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	68
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	69 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	70 * functions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	71 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	72
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	73 /* echo
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	74 * returns single or repeated constant value
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	75 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	76 * "T" [ TYPE ] - type of constant data to return
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	77 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	78 * "val" [ CONST ] - a data constant
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	79 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	80 * "row_len" [ DATA, OPTIONAL ] - if omitted, "val" will be
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	81 * issued once and the resultant row-length will be the length
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	82 * of "val". otherwise, "val" will be repeated and/or truncated
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	83 * as necessary to produce a row-length equal to that of input.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	84 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	85 * USAGE:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	86 * to echo a single constant value
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	87 * U16 len = row_len ( col ) \| < U16 > echo < 0 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	88 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	89 * to create a row of repeated values
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	90 * ascii allN = < ascii > echo < 'N' > ( col );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	91 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	92 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	93 T echo #1.0 < T val > ( * any row_len )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	94 = vdb:echo;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	95
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	96
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	97 /* exists
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	98 * returns constant or dynamic value if predicate input exists
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	99 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	100 * "T" [ TYPE ] - type of data to return
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	101 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	102 * "cval" [ CONST, OPTIONAL ] - a data constant. when present,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	103 * the function will behave like "echo" ( see below )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	104 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	105 * "predicate" [ DATA ] - an input whose existence determines
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	106 * whether the function will operate or not.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	107 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	108 * "dval" [ DATA, OPTIONAL ] - data value, either passed through
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	109 * or used to determine a repeat count of "cval" ( see below )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	110 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	111 * USAGE:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	112 * when "cval" is omitted, "dval" must be present and will be
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	113 * passed through depending upon the existence of "predicate"
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	114 * U8 count = < U8 > exists ( col, count2 );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	115 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	116 * when "cval" is present, "dval" may be omitted, and "cval" will
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	117 * be passed through just like echo depending upon "predicate"
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	118 * U8 count = < U8 > exists < 2 > ( col2 ) \| < U8 > echo < 1 > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	119 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	120 * when "cval" and "dval" are both present, the behavior is
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	121 * like echo, but gated with "predicate"
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	122 * ascii poly = < ascii > exists < 'a' > ( col, repeat );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	123 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	124 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	125 T exists #1.0 < * T cval > ( any predicate, * T dval )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	126 = vdb:exists;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	127
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	128
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	129 /* map
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	130 * translate input elements
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	131 * behaves much like the Unix "tr" command
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	132 * except that charsets are not [currently] supported
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	133 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	134 * "A" [ TYPE ] - input data type, e.g. "ascii"
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	135 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	136 * "B" [ TYPE ] - output data type, e.g. "ascii" or "U8"
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	137 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	138 * "from" [ CONST ] - set of key values.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	139 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	140 * "to" [ CONST ] - set of mapped values,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	141 * where length ( from ) === length ( to )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	142 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	143 * "in" [ DATA ] - input data to be matched against keys
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	144 * in "from". also serves as source data when "src" is omitted
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	145 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	146 * "src" [ DATA, OPTIONAL ] - source data to be edited by
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	147 * substituting "to" values when corresponding "in" value
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	148 * matches key in "from". if omitted, "in" is used.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	149 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	150 * USAGE:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	151 * to upper case letters from a given alphabet
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	152 * ascii upper = < ascii, ascii > map < 'acgtn', 'ACGTN' > ( in );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	153 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	154 * to translate from ascii to binary
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	155 * U8 bin = < ascii, U8 > map < 'ACGTN', [ 0, 1, 2, 3, 0 ] > ( in );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	156 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	157 * to alter certain values of a column based upon values in another
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	158 * U8 n_encoded = < ascii, U8 > map < 'N', 0 > ( read, quality );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	159 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	160 * CAVEATS:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	161 * the full canonical mode of operation uses separate inputs
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	162 * for key matching and output source.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	163 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	164 * when a single input is specified:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	165 * - sizeof ( A ) must equal sizeof ( B )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	166 * - A must be a proper subset of B -OR-
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	167 * - "from" keys must match every possible "in" value ( total substitution )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	168 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	169 function < type A, type B >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	170 B map #1.0 < A from, B to > ( A in, * B src )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	171 = vdb:map;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	172
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	173
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	174 /* clip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	175 * limit data values to given bounds
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	176 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	177 * "T" [ TYPE ] - input and output data type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	178 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	179 * "dim" [ CONST >= 1 ] - fixed dimension on
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	180 * input and output vectors
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	181 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	182 * "lower" [ CONST ] - lower bound, inclusive
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	183 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	184 * "upper" [ CONST ] - upper bounds, inclusive
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	185 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	186 * "in" [ DATA ] - data to be clipped
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	187 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	188 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	189 T clip #1.0 < T lower, T upper > ( T in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	190 = vdb:clip;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	191
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	192 function < type T, U32 dim >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	193 T [ dim ] vclip #1.0 < T lower, T upper > ( T [ dim ] in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	194 = vdb:clip;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	195
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	196
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	197 /* ceil
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	198 * round up to the nearest integer
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	199 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	200 * "in" [ DATA ] - data to be processed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	201 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	202 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	203 numeric_set ceil #1.0 ( float_set in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	204 = vdb:ceil;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	205
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	206 /* floor
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	207 * round down to the nearest integer
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	208 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	209 * "in" [ DATA ] - data to be processed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	210 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	211 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	212 numeric_set floor #1.0 ( float_set in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	213 = vdb:floor;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	214
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	215 /* round
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	216 * round to nearest integer away from zero
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	217 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	218 * "T" [ TYPE = { F32, F64 } ] - input and output data type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	219 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	220 * "in" [ DATA ] - data to be processed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	221 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	222 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	223 numeric_set round #1.0 ( float_set in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	224 = vdb:round;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	225
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	226 /* trunc
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	227 * round to the nearest integer not larger in absolute value
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	228 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	229 * "T" [ TYPE = { F32, F64 } ] - input and output data type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	230 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	231 * "in" [ DATA ] - data to be processed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	232 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	233 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	234 numeric_set trunc #1.0 ( float_set in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	235 = vdb:trunc;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	236
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	237
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	238 /* min
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	239 * return the minimum value of each element
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	240 * max
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	241 * return the maximum value of each element
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	242 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	243 * "T" [ TYPE ] - input and output data type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	244 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	245 * "a" [ DATA ] - first operand
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	246 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	247 * "b" [ DATA ] - second operand
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	248 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	249 * SYNOPSIS:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	250 * compares two inputs element by element
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	251 * returns min or max element of each
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	252 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	253 * USAGE:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	254 * intersections
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	255 * U32 left = < U32 > max ( left_a, left_b );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	256 * U32 right = < U32 > min ( right_a, right_b );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	257 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	258 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	259 T min #1.0 ( T a, T b )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	260 = vdb:min;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	261
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	262 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	263 T max #1.0 ( T a, T b )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	264 = vdb:max;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	265
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	266
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	267 /* sum
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	268 * return the sum of inputs
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	269 * diff
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	270 * return the difference of inputs
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	271 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	272 * "T" [ TYPE ] - input and output data type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	273 * must be member of numeric_set
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	274 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	275 * "k" [ CONST, DEFAULT 0 ] - optional constant
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	276 * to be added or subtracted
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	277 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	278 * "a" [ DATA ] - left-most operand
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	279 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	280 * "b" [ DATA ] - optional subtractand
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	281 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	282 * SYNOPSIS:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	283 * incorporates "k" into expression for every row
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	284 * returns sum or difference of inputs for all rows
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	285 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	286 * USAGE:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	287 * length of half-closed interval
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	288 * U32 len = < U32 > diff ( stop, start );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	289 * convert one-based coordinate to zero based
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	290 * U32 zero_based = < U32 > diff < 1 > ( one_based );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	291 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	292 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	293 T sum #1.0 < * T k > ( T a, ... )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	294 = vdb:sum;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	295
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	296 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	297 T diff #1.0 < * T k > ( T a * T b )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	298 = vdb:diff;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	299
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	300 /* deriv
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	301 * return the 1st derivative of an input row
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	302 * integral
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	303 * return the "integral" of an input row
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	304 * integral -> starts with 1st value
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	305 * integral_0 -> starts with 0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	306 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	307 * "T" [ TYPE ] - input and output data type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	308 * must be signed integer of any size
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	309 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	310 * "in" [ DATA ] - input to be modified
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	311 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	312 * SYNOPSIS:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	313 * derivative function is ( in [ i ] - in [ i - 1 ] )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	314 * for i = 0 .. length ( in ) - 1,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	315 * assuming in [ 0 - 1 ] = 0 ( i.e. leaves in [ 0 ] intact ).
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	316 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	317 * integral function is sum ( in [ 0 ] .. in [ i ] )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	318 * for i = 0 .. length ( in ) - 1.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	319 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	320 * integral_0 function is sum ( in [ 0 ] .. in [ i - 1 ] )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	321 * for i = 1 .. length ( in ) - 1,
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	322 * setting output [ 0 ] = 0.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	323 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	324 * USAGE:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	325 * "deriv" and "integral" are reciprocal functions.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	326 * the oddity is that "deriv" creates an output series
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	327 * with the same length as the input series, causing the
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	328 * first element of input to be copied to first element
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	329 * of output.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	330 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	331 * "integral_0" always creates an output with the first
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	332 * element being 0. the oddity here is again that the output
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	333 * series is the same length as the input, dropping the effect
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	334 * from the last element of input. its utility is primarily in
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	335 * operations such as creating absolute offsets from a series of
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	336 * lengths.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	337 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	338 * EXAMPLES:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	339 * given an input series ( 15, 17, 12, 315 ):
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	340 * "deriv" produces ( 15, 2, -5, 303 ) [ NOTICE first element ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	341 * integrating ( 15, 2, -5, 303 ):
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	342 * "integral" produces ( 15, 17, 12, 315 ), while
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	343 * "integral_0" produces ( 0, 15, 17, 12 ).
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	344 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	345 * generating starting offsets from a series of lengths ( 15, 17, 12, 315 ):
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	346 * "integral_0" produces ( 0, 15, 32, 44 ) which can be used
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	347 * to accompany the input series for starts and lengths.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	348 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	349
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	350 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	351 T deriv #1.0 ( T in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	352 = vdb:deriv;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	353 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	354 T integral #1.0 ( T in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	355 = vdb:integral;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	356 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	357 T integral_0 #1.1 ( T in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	358 = vdb:integral_0;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	359
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	360 /* delta
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	361 * return the 1st derivative of a whole blob
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	362 * undelta
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	363 * return the integral of a whole blob
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	364 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	365 * "T" [ TYPE ] - input and output data type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	366 * must be signed integer of any size
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	367 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	368 * "in" [ DATA ] - input to be modified
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	369 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	370 * SYNOPSIS:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	371 * similar to deriv/integral but operates on full blob
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	372 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	373
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	374 function < type T > T delta #1.0 ( T in ) = vdb:delta;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	375 function < type T > T undelta #1.0 ( T in ) = vdb:undelta;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	376
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	377
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	378 /* outlier_encode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	379 * removes a given outlier from a data series
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	380 * outlier_decode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	381 * removes the effect of outlier_encode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	382 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	383 * "T" [ TYPE ] - input and output data type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	384 * must be an integer of any size
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	385 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	386 * "in" [ DATA ] - input to be modified
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	387 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	388 * SYNOPSIS:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	389 * The encode replaces every element that is equal to the
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	390 * outlier with (the value of the previous element) * 2 + 1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	391 * and the remaining elements are replaced with their value * 2.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	392 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	393
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	394 function < type T > T outlier_encode #1.0 < T outlier > ( T in ) = vdb:outlier_encode;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	395 function < type T > T outlier_decode #1.0 < T outlier > ( T in ) = vdb:outlier_decode;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	396
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	397 /* add_row_id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	398 * return the sum of an input and its row-id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	399 * sub_row_id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	400 * return the difference of an input and its row-id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	401 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	402 * "T" [ TYPE ] - input and output data type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	403 * must be member of numeric_set
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	404 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	405 * "in" [ DATA ] - input to be modified
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	406 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	407 * SYNOPSIS:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	408 * adjusts for relationship between input and row-id
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	409 * used primarily to reduce serial ids to constants
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	410 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	411 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	412 T add_row_id #1.0 ( T in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	413 = vdb:add_row_id;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	414
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	415 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	416 T sub_row_id #1.0 ( T in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	417 = vdb:sub_row_id;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	418
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	419
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	420 /* cut
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	421 * extract one or more elements from input vector
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	422 * to form an output vector of equal or less dimension
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	423 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	424 * "T" [ TYPE ] - base element type to be processed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	425 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	426 * "idx" [ CONST ] - mandatory initial element index
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	427 * count of parameters must equal dimension of output type
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	428 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	429 * "in" [ DATA ] - source of input vectors where the vector
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	430 * element type is known, but any dimension is accepted.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	431 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	432 * USAGE:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	433 * extracting a single channel from a 4 channel vector
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	434 * F32 [ 4 ] vect ...
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	435 * F32 chan = < F32 > cut < 0 > ( vect );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	436 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	437 * extracting multiple channels
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	438 * U8 [ 16 ] in ...
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	439 * U8 [ 3 ] out = < U8 > cut < 5, 1, 3 > ( in );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	440 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	441 * reversing channels
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	442 * I16 [ 2 ] norm ...
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	443 * I16 [ 2 ] rev = < I16 > cut < 1, 0 > ( norm );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	444 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	445 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	446 T [ * ] cut #1.0 < U32 idx, ... > ( T [ * ] in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	447 = vdb:cut;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	448
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	449
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	450 /* paste
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	451 * combine all elements of all inputs into a single vector
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	452 * output dimension is sum of all input dimensions after type normalization
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	453 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	454 * "T" [ TYPE ] - base element type to be processed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	455 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	456 * "in" [ DATA ] - first of an arbitrary number of columns
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	457 * the total of input elements produces an output of "T [ total ]"
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	458 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	459 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	460 T [ * ] paste #1.0 ( T [ * ] in, ... )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	461 = vdb:paste;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	462
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	463
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	464 /* vec_sum
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	465 * compute the sum of all the elements of the row
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	466 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	467 * "T" [ TYPE ] - base element type to be processed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	468 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	469 * "in" [ DATA ] - the input
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	470 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	471 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	472 T vec_sum #1.0 ( T [ * ] in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	473 = vdb:vec_sum;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	474
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	475 /* vec_sum
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	476 * compute the sum of all the elements of the input vector
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	477 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	478 * "T" [ TYPE ] - base element type to be processed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	479 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	480 * "in" [ DATA ] - the input
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	481 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	482 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	483 T fixed_vec_sum #1.0 ( T [ * ] in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	484 = vdb:fixed_vec_sum;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	485
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	486
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	487 /* checksum
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	488 * compute a checksum ( hash ) of all of the input bytes
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	489 * to be used in a trigger production
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	490 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	491 * "node" [ CONST ] - path to metadata node where checksum
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	492 * will be stored.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	493 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	494 * "algorithm" [ CONST ] - type of checksum to perform:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	495 * 'crc-32' # match against POSIX cksum
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	496 * 'md5' # " " md5sum
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	497 * 'sha-1' # " " sha1sum
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	498 * 'sha-256' # " " sha256sum
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	499 * 'sha-384' # " " sha384sum
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	500 * 'sha-512' # " " sha512sum
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	501 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	502 * "in" [ DATA ] - the octet-stream to be checksummed
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	503 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	504 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	505 bool checksum #1.0 < ascii node, ascii algorithm > ( B8 in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	506 = vdb:checksum;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	507
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	508 /* md5sum
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	509 * compute an md5 checksum of all of the input bytes
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	510 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	511 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	512 bool md5sum #1.0 < ascii node > ( B8 in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	513 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	514 return checksum < node, 'md5' > ( in );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	515 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	516
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	517
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	518 /* pack
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	519 * packs words into bit-aligned units
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	520 * words are expected in architecture native byte-order
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	521 * and returned in "big-bit-endian" order
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	522 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	523 * the packed size is determined by the dimension of the
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	524 * left-hand assignment value.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	525 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	526 * "in" [ DATA ] - B8, B16, B32 or B64 data
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	527 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	528 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	529 B1 [ * ] pack #1.0 ( pack_set in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	530 = vdb:pack;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	531
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	532
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	533 /* unpack
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	534 * unpacks bit-aligned units into words
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	535 * input is expected in "big-bit-endian" order
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	536 * and returned in architecture native byte-order
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	537 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	538 * the unpacked type is determined from the left-hand
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	539 * assignment value.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	540 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	541 * "in" [ DATA ] - B[1]..B[64]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	542 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	543 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	544 pack_set unpack #1.0 ( B1 [ * ] in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	545 = vdb:unpack;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	546
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	547
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	548 /* izip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	549 * iunzip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	550 * integer compression
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	551 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	552 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	553 izip_fmt izip #2.1 ( izip_set in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	554 = vdb:izip;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	555
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	556 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	557 izip_set iunzip #2.1 ( izip_fmt in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	558 = vdb:iunzip;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	559
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	560 physical < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	561 T izip_encoding #1.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	562 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	563 decode { return ( T ) iunzip ( @ ); }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	564 encode { return izip ( @ ); }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	565 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	566
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	567
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	568 /* fzip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	569 * funzip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	570 * floating point compression
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	571 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	572 * "mantissa" [ CONST ] - the number of mantissa bits
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	573 * to preserve
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	574 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	575 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	576 fzip_fmt fzip #1.0 < U32 mantissa > ( fzip_set in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	577 = vdb:fzip;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	578
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	579 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	580 fzip_set funzip #1.0 ( fzip_fmt in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	581 = vdb:funzip;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	582
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	583 physical < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	584 T fzip_encoding #1.0 < U32 mantissa >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	585 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	586 decode { return funzip ( @ ); }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	587 encode { return fzip < mantissa > ( @ ); }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	588 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	589
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	590
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	591 /* rlencode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	592 * rldecode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	593 * run-length encoding
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	594 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	595 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	596 rle_fmt rlencode #1.0 ( any in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	597 = vdb:rlencode;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	598
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	599 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	600 any rldecode #1.0 ( rle_fmt in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	601 = vdb:rldecode;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	602
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	603
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	604 /* zip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	605 * unzip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	606 * run things through zlib
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	607 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	608 * "strategy" [ CONST, OPTIONAL ] - set the compression strategy
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	609 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	610 * "level" [ CONST, OPTIONAL ] - set the amount of compression
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	611 * from 0..9 ( none to best compression ), or use -1 for zlib
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	612 * default behavior.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	613 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	614
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	615 // zlib strategy
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	616 const I32 Z_FILTERED = 1;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	617 const I32 Z_HUFFMAN_ONLY = 2;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	618 const I32 Z_RLE = 3;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	619 const I32 Z_DEFAULT_STRATEGY = 0;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	620
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	621 // zlib level
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	622 const I32 Z_NO_COMPRESSION = 0;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	623 const I32 Z_BEST_SPEED = 1;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	624 const I32 Z_BEST_COMPRESSION = 9;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	625 const I32 Z_DEFAULT_COMPRESSION = -1;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	626
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	627 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	628 zlib_fmt zip #1.0 < * I32 strategy, I32 level > ( any in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	629 = vdb:zip;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	630
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	631 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	632 any unzip #1.0 ( zlib_fmt in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	633 = vdb:unzip;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	634
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	635 physical < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	636 T zip_encoding #1.0 < * I32 strategy, I32 level >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	637 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	638 decode { return unzip ( @ ); }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	639 encode { return zip < strategy, level > ( @ ); }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	640 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	641
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	642 physical
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	643 bool bool_encoding #1.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	644 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	645 decode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	646 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	647 B1 bit = unzip ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	648 return ( bool ) unpack ( bit );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	649 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	650
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	651 encode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	652 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	653 U8 lim = < U8 > clip < 0, 1 > ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	654 B1 bit = pack ( lim );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	655 return zip < Z_RLE, Z_BEST_SPEED > ( bit );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	656 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	657 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	658
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	659 physical < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	660 T delta_izip_encoding #1.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	661 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	662 decode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	663 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	664 T dlt = iunzip ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	665 return < T > undelta ( dlt );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	666 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	667
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	668 encode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	669 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	670 T dlt = <T> delta ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	671 return izip ( dlt );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	672 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	673 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	674 physical < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	675 T delta_zip_encoding #1.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	676 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	677 decode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	678 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	679 T dlt = unzip ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	680 return < T > undelta ( dlt );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	681 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	682
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	683 encode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	684 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	685 T dlt = <T> delta ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	686 return zip < Z_RLE, Z_BEST_SPEED > ( dlt );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	687 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	688 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	689 physical < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	690 T delta_average_zip_encoding #1.0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	691 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	692 decode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	693 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	694 delta_averaged_fmt t = unzip ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	695 return undelta_average ( t );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	696 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	697
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	698 encode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	699 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	700 delta_averaged_fmt t = delta_average ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	701 return zip < Z_RLE, Z_BEST_SPEED > ( t );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	702 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	703 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	704
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	705 /* bzip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	706 * bunzip
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	707 * run things through bzip2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	708 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	709 * "blockSize100k" [ CONST, OPTIONAL ] - set the compression workspace size
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	710 * from 1..9 inclusive, produces a workspace of blockSize100K * 100000 bytes
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	711 * default is 5
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	712 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	713 * "workFactor" [ CONST, OPTIONAL ] - set compression level
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	714 * from 0..250 inclusive, where 0 means bzip2 default, currently 30
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	715 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	716
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	717 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	718 bzip2_fmt bzip #1.0 < * U32 blockSize100k, U32 workFactor > ( any in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	719 = vdb:bzip;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	720
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	721 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	722 any bunzip #1.0 ( bzip2_fmt in )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	723 = vdb:bunzip;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	724
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	725 physical < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	726 T bzip_encoding #1.0 < * U32 blockSize100k, U32 workFactor >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	727 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	728 decode { return bunzip ( @ ); }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	729 encode { return bzip < blockSize100k, workFactor > ( @ ); }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	730 };
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	731
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	732
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	733 /* simple_sub_select
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	734 * project a column from another table within database
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	735 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	736 * "T" [ TYPE ] - data type of column
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	737 * must be compatible with source column
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	738 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	739 * "tbl" [ CONST ] - name of table within parent
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	740 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	741 * "col" [ CONST ] - column spec, i.e. simple name or
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	742 * typed name spec
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	743 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	744 * "row" [ DATA ] - row to select
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	745 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	746 * "idx" [ DATA ] - one-based indexing of what element to pick, defaults to all if not given
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	747 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	748 function < type T >
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	749 T simple_sub_select #1.0 < ascii tbl, ascii col > ( I64 row * I32 idx )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	750 = vdb:simple_sub_select_1;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	751
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	752
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	753 /* extract_token
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	754 * extract a textual token from an input string
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	755 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	756 * "idx" [ CONST ] - a zero-based index of the token
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	757 * if value < row_len ( tok ), then the substring of
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	758 * indexed token is returned. otherwise, returns empty.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	759 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	760 * "str" [ DATA ] - input text. type must be compatible with
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	761 * output production, meaning types must be same, or ascii input
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	762 * with utf8 output.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	763 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	764 * "tok" [ DATA ] - results of tokenizing "str"
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	765 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	766 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	767 text_set extract_token #1.0 < U32 idx > ( text_set str, text:token tok )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	768 = vdb:extract_token;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	769
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	770
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	771 /* strtonum
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	772 * convert string to number
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	773 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	774 * "radix" [ CONST, DEFAULT 10 ]
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	775 * if not specified, or if given as 0, the default will be 10
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	776 * unless the string begins with "0x" or "0X", in which case radix will be 16
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	777 * octal is NOT inferred ( i.e. leading "0" does not imply octal )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	778 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	779 * "str" [ DATA ] - text to be converted
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	780 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	781 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	782 numeric_set strtonum #1.0 < * U32 radix > ( text_set str )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	783 = vdb:strtonum;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	784
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	785
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	786 /* sprintf
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	787 * formatted print to a string
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	788 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	789 * formatting rules differ somewhat from C sprintf:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	790 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	791 * '%' [ <flags> ] [ <field-width> ] [ '.' <precision> ] [ ':' <index> ] <storage-class>
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	792 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	793 * where:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	794 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	795 * flags
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	796 * = ' ' : prepend space to a numeral if it does not have a sign
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	797 * \| '+' : always produce a sign on numeric conversion
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	798 * \| '-' : left-align parameter within field
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	799 * \| '0' : left-pad with zeroes rather than spaces
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	800 * \| '#' : use "alternate" representation
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	801 * \| ',' : produce comma-separated triples
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	802 * ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	803 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	804 * field-width
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	805 * = DECIMAL : a base-10 numeral
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	806 * \| '*' : take field width from args
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	807 * ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	808 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	809 * precision
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	810 * = DECIMAL : a base-10 numeral
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	811 * \| '*' : take precision from args
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	812 * \| : an empty precision means 0
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	813 * ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	814 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	815 * index
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	816 * = idx : a single, zero-based vector element
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	817 * \| idx '-' idx : a fully-closed, zero-based interval
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	818 * \| idx '/' len : a start index plus length
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	819 * ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	820 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	821 * idx
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	822 * = DECIMAL : an unsigned base-10 numeral
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	823 * \| '*' : take index from args
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	824 * \| '$' : last element in cell
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	825 * \| : an empty index means 0 or $
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	826 * ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	827 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	828 * len
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	829 * = DECIMAL : a base-10 numeral
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	830 * \| '*' : take length from args
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	831 * \| '$' : row-length of ( cell )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	832 * \| : an empty length means $
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	833 * ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	834 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	835 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	836 * storage-class
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	837 * = 'd' \| 'i' : general decimal integer
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	838 * \| 'u' : decimal unsigned integer
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	839 * \| 'x' : lower-case hex
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	840 * \| 'X' : upper-case hex
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	841 * \| 'o' : octal
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	842 * \| 'b' : binary
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	843 * \| 'f' : floating point
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	844 * \| 'e' : scientific notation
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	845 * \| 'g' : general floating point
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	846 * \| 'c' \| 's' : character
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	847 * ;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	848 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	849 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	850 * "fmt" [ CONST ] - constant format string, adhering to
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	851 * the description above
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	852 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	853 * "p1" [ DATA ] - first param
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	854 * this and any subsequent params must correspond to format
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	855 * in type/position/number.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	856 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	857 function
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	858 text_set sprintf #1.0 < ascii fmt > ( any p1, ... )
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: diff changeset	859 = vdb:sprintf;

Mercurial > repos > charles_s_test > seqsero2

annotate libs/sratoolkit.2.8.0-centos_linux64/schema/vdb/vdb.vschema @ 3:38ad1130d077 draft