Mercurial > repos > charles_s_test > seqsero2

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

/*==========================================================================
 * WGS Contig
 */
version 1;

include 'vdb/vdb.vschema';
include 'ncbi/ncbi.vschema';
include 'ncbi/seq.vschema';
include 'ncbi/spotname.vschema';
include 'ncbi/stats.vschema';


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

/* component_props
 *  a signed value describing contig or gap components of scaffolds, or
 *  gaps in contig sequences.
 *  Positive values refer to contigs and negatives describe gaps
 */
typedef I16 NCBI:WGS:component_props;

/* component description
 *  the sequencing status of the component
 *
 *  These typically correspond to keywords in the INSDC submission.
 *  Current acceptable values are:
 *    A           Active Finishing
 *    D           Draft HTG (often phase1 and phase2 are called Draft,
 *                whether or not they have the draft keyword).
 *    F           Finished HTG (phase3)
 *    G           Whole Genome Finishing
 *    O           Other sequence (typically means no HTG keyword)
 *    P           Pre Draft
 *    W           WGS contig
 */
const NCBI:WGS:component_props NCBI:WGS:component:WGS                  = 0;
const NCBI:WGS:component_props NCBI:WGS:component:ActiveFinishing      = 1;
const NCBI:WGS:component_props NCBI:WGS:component:DraftHTG             = 2;
const NCBI:WGS:component_props NCBI:WGS:component:FinishedHTG          = 3;
const NCBI:WGS:component_props NCBI:WGS:component:WholeGenomeFinishing = 4;
const NCBI:WGS:component_props NCBI:WGS:component:OtherSequence        = 5;
const NCBI:WGS:component_props NCBI:WGS:component:PreDraft             = 6;

/* strand
 *  specifies the orientation of the component relative to scaffold
 *  values given allow strand to be determined as "prop / 16"
 *  yielding:
 *    0           unknown orientation
 *    1           plus strand
 *    2           negative strand
 */
const NCBI:WGS:component_props NCBI:WGS:strand:plus                    = 16;
const NCBI:WGS:component_props NCBI:WGS:strand:minus                   = 32;


/* gap description
 *  These typically correspond to keywords in the INSDC submission.
 *  Current acceptable values are:
 *    N           gap with specified size
 *    U           gap of unknown size, defaulting to 100 bases.
 */
const NCBI:WGS:component_props NCBI:WGS:gap:known                      = -1;
const NCBI:WGS:component_props NCBI:WGS:gap:unknown                    = -2;

/* gap type
 *  scaffold          a gap between two sequence contigs in a scaffold
 *  contig            an unspanned gap between two sequence contigs
 *  centromere        a gap inserted for the centromere
 *  short_arm         a gap inserted at the start of an acrocentric chromosome
 *  heterochromatin   a gap inserted for an especially large region of heterochromatic sequence
 *  telomere          a gap inserted for the telomere
 *  repeat            an unresolvable repeat
 */
const NCBI:WGS:component_props NCBI:WGS:gap:scaffold                   = -4;
const NCBI:WGS:component_props NCBI:WGS:gap:contig                     = -8;
const NCBI:WGS:component_props NCBI:WGS:gap:centromere                 = -12;
const NCBI:WGS:component_props NCBI:WGS:gap:short_arm                  = -16;
const NCBI:WGS:component_props NCBI:WGS:gap:heterochromatin            = -20;
const NCBI:WGS:component_props NCBI:WGS:gap:telomere                   = -24;
const NCBI:WGS:component_props NCBI:WGS:gap:repeat                     = -28;

/* gap_linkage
 */
typedef I32 NCBI:WGS:gap_linkage;

/* gap linkage and linkage evidence
 * There can be multiple linkage evidences or linkage with no evidence
 *
 *  paired-ends       paired sequences from the two ends of a DNA fragment
 *  align_genus       alignment to a reference genome within the same genus
 *  align_xgenus      alignment to a reference genome within another genus
 *  align_trnscpt     alignment to a transcript from the same species
 *  within_clone      sequence on both sides of the gap is derived from
 *                    the same clone, but the gap is not spanned by paired-ends
 *  clone_contig      linkage is provided by a clone contig in the tiling path
 *  map               linkage asserted using a non-sequence based map
 *                    such as RH, linkage, fingerprint or optical
 *  strobe            strobe sequencing (PacBio)
 *  unspecified
 *  pcr               PCR
 */
const NCBI:WGS:gap_linkage NCBI:WGS:gap:linkage:linked                 = 1;
const NCBI:WGS:gap_linkage NCBI:WGS:gap:linkage_evidence:paired_ends   = 2;
const NCBI:WGS:gap_linkage NCBI:WGS:gap:linkage_evidence:align_genus   = 4;
const NCBI:WGS:gap_linkage NCBI:WGS:gap:linkage_evidence:align_xgenus  = 8;
const NCBI:WGS:gap_linkage NCBI:WGS:gap:linkage_evidence:align_trnscpt = 16;
const NCBI:WGS:gap_linkage NCBI:WGS:gap:linkage_evidence:within_clone  = 32;
const NCBI:WGS:gap_linkage NCBI:WGS:gap:linkage_evidence:clone_contig  = 64;
const NCBI:WGS:gap_linkage NCBI:WGS:gap:linkage_evidence:map           = 128;
const NCBI:WGS:gap_linkage NCBI:WGS:gap:linkage_evidence:strobe        = 256;
const NCBI:WGS:gap_linkage NCBI:WGS:gap:linkage_evidence:unspecified   = 512;
const NCBI:WGS:gap_linkage NCBI:WGS:gap:linkage_evidence:pcr           = 1024;

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

/* tokenize_nuc_accession
 * tokenize_prot_accession
 *  scans name on input
 *  tokenizes into parts
 */
extern function text:token
    NCBI:WGS:tokenize_nuc_accession #1 ( ascii acc );
extern function text:token
    NCBI:WGS:tokenize_prot_accession #1 ( ascii acc );

const U16 NCBI:WGS:acc_token:unrecognized =  1;
const U16 NCBI:WGS:acc_token:prefix       =  2;
const U16 NCBI:WGS:acc_token:contig       =  3;


/* build_scaffold_read
 *  assembles contigs and gaps into a single row
 *  transcribes + strand contigs as they are,
 *  performs reverse complement of - strand contigs,
 *  fills gaps with stated number of N
 *
 * build_scaffold_quality
 *  assembles contig and gap qualities into a single row
 *  contig qualities are taken as they are,
 *  gap qualities are assigned a constant
 *
 *  "component_start" [ DATA ] - starting locations on each
 *   component or 0 for gaps. normal starting point is 0,
 *   but offsets are supported.
 *  NB - ONE-BASED COORDINATES
 *
 *  "component_len" [ DATA ] - length of contig sequence
 *   from component_start, or length of gap, projected onto
 *   scaffold at scaffold_start.
 *
 *  "component_props" [ DATA ] - see discussion of type
 *   distinguish between contigs and gaps, indicate strand
 *
 *  "component_id" [ DATA ] - foreign keys into SEQUENCE table
 *   row_len ( component_id ) == count-of-contigs ( component_props )
 */
extern function INSDC:4na:bin NCBI:WGS:build_scaffold_read #1
    ( INSDC:coord:one component_start, INSDC:coord:len component_len,
      NCBI:WGS:component_props component_props, I64 component_id );

extern function INSDC:quality:phred NCBI:WGS:build_scaffold_qual #1
    ( INSDC:coord:one component_start, INSDC:coord:len component_len,
      NCBI:WGS:component_props component_props, I64 component_id );


/* build_read_type
 *  generate standard SRA read type from component properties
 *  contigs are biological, gaps are technical
 *
 *  "component_props" [ DATA ] - see discussion of type
 *   distinguish between contigs and gaps, indicate strand
 */
extern function INSDC:SRA:xread_type
    NCBI:WGS:build_read_type #1 ( NCBI:WGS:component_props component_props );


/*--------------------------------------------------------------------------
 * nucleotide
 */
table NCBI:WGS:tbl:nucleotide #1.1
    = NCBI:tbl:base_space #2.0.3
    , NCBI:tbl:phred_quality #2.0.4
    , NCBI:SRA:tbl:stats #1.2.0
{
    /* ACCESSION
     *  [<opt-prefix>]<4-letter-prefix><2-digit-version><6-or-7-digit-contig>
     */
    extern column ascii ACCESSION = out_accession;
    extern column U32   ACC_VERSION = .ACC_VERSION | <U32> echo <1> ();

    // input
    ascii in_accession = ACCESSION;

    // parsed input
    text:token in_acc_token
        = NCBI:WGS:tokenize_nuc_accession ( in_accession );
    //  [<opt-prefix>]<4-letter-prefix><2-digit-version>
    ascii in_acc_prefix
        = extract_token < 0 > ( in_accession, in_acc_token );
    // <6-or-7-digit-contig>
    ascii in_contig_text
        = extract_token < 1 > ( in_accession, in_acc_token );
    U32 in_contig_len
        = row_len ( in_contig_text );
    U64 in_contig_bin
        = strtonum ( in_contig_text );

    // physical storage
    physical column < ascii > zip_encoding .ACC_PREFIX = in_acc_prefix;
    physical column < U32 > izip_encoding .ACC_CONTIG_LEN = in_contig_len;
    physical column < U64 > izip_encoding .ACC_CONTIG = in_contig_bin;
    physical column < U32 > izip_encoding .ACC_VERSION = ACC_VERSION; //needed to back-fill WGS data from ID where version may be > 1

    // output
    ascii out_acc_prefix
        = .ACC_PREFIX
        | < ascii > meta:read < 'ACC_PREFIX', true > ()
        ;
    U32 out_acc_contig_len
        = .ACC_CONTIG_LEN
        | < U32 > meta:value < 'ACC_CONTIG_LEN', true > ()
        ;
    U64 out_acc_contig
        = .ACC_CONTIG
        | ( U64 ) row_id ()
        ;
    ascii out_accession
        = sprintf < "%s%0*u" > ( out_acc_prefix, out_acc_contig_len, out_acc_contig );

    readonly column ascii ACC_PREFIX
        = .ACC_PREFIX
        | < ascii > meta:read < 'ACC_PREFIX', true > ()
        ;
    readonly column U32 ACC_CONTIG_LEN
        = .ACC_CONTIG_LEN
        | < U32 > meta:value < 'ACC_CONTIG_LEN', true > ()
        ;

    /* CONTIG_NAME
     *  principal name
     */
    extern column utf8 CONTIG_NAME
        = idx:text:project #1.0 < 'contig_name' > ( .CONTIG_NAME );

    physical column < utf8 > zip_encoding .CONTIG_NAME
        = idx:text:insert #1.0 < 'contig_name' > ( CONTIG_NAME );

    ascii out_contig_name = cast ( CONTIG_NAME );

    // NB - this is only useful if CONTIG_NAME is unique
    // or if clustered by CONTIG_NAME
    readonly column vdb:row_id_range CONTIG_NAME_ROW_RANGE
        = idx:text:lookup #1.0 < 'contig_name', 'NAME_QUERY' > ();

    /* EXTRA_SEQIDS
     *  pipe-separated list of additional names
     */
    extern column < ascii > zip_encoding EXTRA_SEQIDS;

    /* TITLE
     */
    extern column < ascii > zip_encoding TITLE;

    /* GI
     *  gi is indexed in a parallel table
     */
    extern column < NCBI:gi > izip_encoding GI;

    /* TAXID
     *  taxonomy id
     */
    extern column < NCBI:taxid > izip_encoding TAXID;

    /* GB_STATE
     *  genbank state
     */
    extern column < NCBI:gb_state > izip_encoding GB_STATE;

    /* DESCR
     *  ASN.1 description
     */
    extern column < NCBI:asn:binary > zip_encoding DESCR;

    /* ANNOT
     *  ASN.1 annotation
     */
    extern column < NCBI:asn:binary > zip_encoding ANNOT;

    /* GAP_START
     *  Starting position of a gap
     */
    extern column < INSDC:coord:zero > izip_encoding GAP_START;

    /* GAP_LEN
     *  Length of a gap
     */
    extern column < INSDC:coord:len > izip_encoding GAP_LEN;

    /* GAP_PROPS
     *  See description of type
     */
    extern column < NCBI:WGS:component_props > zip_encoding GAP_PROPS;

    /* GAP_LINKAGE
     *  See description of type
     */
    extern column < NCBI:WGS:gap_linkage> zip_encoding GAP_LINKAGE;


    ascii out_seqid_gi = sprintf < "gi|%u" > ( .GI );
    ascii out_seqid_gb = sprintf < "gb|%s.%u|" > ( out_accession, ACC_VERSION )
                       | sprintf < "gb|%s.1|" > ( out_accession );
    ascii out_seqid_gnl = sprintf < "gnl|WGS:%s|%s" > (.ACC_PREFIX, out_contig_name ) | <ascii> echo < '' > ();


    /* outputs to spotname */
    ascii out_seqid_name
        = sprintf < "%s|%s" > ( out_seqid_gi , out_seqid_gb )
		| sprintf < "%s" > ( out_seqid_gb );

    ascii out_spot_name = sprintf < "%s %s" > ( out_seqid_name, .TITLE );

    readonly column ascii SEQ_ID = out_seqid_name;
    readonly column ascii SEQ_ID_GNL = out_seqid_gnl;

    /* outputs to spotdesc */
    // INSDC:coord:len in_read_len  = (INSDC:coord:len) row_len ( in_2na_bin );
    INSDC:coord:len  out_read_len = (INSDC:coord:len) row_len ( out_2na_bin );
    INSDC:coord:len  trim_len = (INSDC:coord:len) row_len ( out_2na_bin );
    INSDC:coord:zero out_read_start = <INSDC:coord:zero> echo < 0 > ();
    INSDC:coord:zero trim_start = <INSDC:coord:zero> echo < 0 > ();
    INSDC:SRA:read_filter out_rd_filter = < INSDC:SRA:read_filter > echo < SRA_READ_FILTER_PASS > ();
    INSDC:SRA:xread_type  out_read_type = < INSDC:SRA:xread_type > echo < SRA_READ_TYPE_BIOLOGICAL > ();
    // help trigger statistics
    INSDC:SRA:xread_type  _alt_in_read_type = < INSDC:SRA:xread_type > echo < SRA_READ_TYPE_BIOLOGICAL > ();
    INSDC:coord:len       _alt_in_read_len  = (INSDC:coord:len) row_len ( in_2na_bin );

    ascii out_label = < ascii > echo < "contig" > ();
    INSDC:coord:len out_label_len = < INSDC:coord:len > echo < 6 > ();
    INSDC:coord:zero out_label_start = < INSDC:coord:zero > echo < 0 > ();

    INSDC:SRA:platform_id out_platform = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
};


/*--------------------------------------------------------------------------
 * protein
 *  contig
 */
table NCBI:WGS:tbl:protein #1
    = NCBI:tbl:protein #1.0.0
{
    /* ACCESSION
     *  [<opt-prefix>]<4-letter-prefix><2-digit-version><6-or-7-digit-contig>
     */
    extern column ascii ACCESSION = out_accession;

    // input
    ascii in_accession = ACCESSION;

    // parsed input
    text:token in_acc_token
        = NCBI:WGS:tokenize_prot_accession ( in_accession );
    //  [<opt-prefix>]<4-letter-prefix><2-digit-version>
    ascii in_acc_prefix
        = extract_token < 0 > ( in_accession, in_acc_token );
    // <6-or-7-digit-contig>
    ascii in_contig_text
        = extract_token < 1 > ( in_accession, in_acc_token );
    U32 in_contig_len
        = row_len ( in_contig_text );
    I64 in_contig_bin
        = strtonum ( in_contig_text );

    // physical storage
    physical column < ascii > zip_encoding .ACC_PREFIX = in_acc_prefix;
    physical column < U32 > izip_encoding .ACC_CONTIG_LEN = in_contig_len;
    physical column < U64 > izip_encoding .ACC_CONTIG = in_contig_bin;

    // output
    ascii out_acc_prefix
        = .ACC_PREFIX
        | < ascii > meta:read < 'ACC_PREFIX', true > ()
        ;
    U32 out_acc_contig_len
        = .ACC_CONTIG_LEN
        | < U32 > meta:value < 'ACC_CONTIG_LEN', true > ()
        ;
    U64 out_acc_contig
        = .ACC_CONTIG
        | ( U64 ) row_id ()
        ;
    ascii out_accession
        = sprintf < "%s%0*u" > ( out_acc_prefix, out_acc_contig_len, out_acc_contig );

    /* TITLE
     */
    extern column < ascii > zip_encoding TITLE;

    /* GI
     *  gi is indexed in a parallel table
     */
    extern column < NCBI:gi > izip_encoding GI;

    /* GB_STATE
     *  genbank state
     */
    extern column < NCBI:gb_state > izip_encoding GB_STATE;

    /* DESCR
     *  ASN.1 description
     */
    extern column < NCBI:asn:binary > zip_encoding DESCR;

    /* ANNOT
     *  ASN.1 annotation
     */
    extern column < NCBI:asn:binary > zip_encoding ANNOT;

    /* outputs to spotname */
    ascii out_seqid_name = sprintf < "TBD" > ( .ACC_PREFIX, out_accession );
    ascii out_spot_name = sprintf < "%s %s" > ( out_seqid_name, .TITLE );

    /* TBD
     *  need to create an extension to NCBI:tbl:protein
     *  that satisfies fastq-dump requirements for READ and QUALITY
     */
};


/*--------------------------------------------------------------------------
 * gi_idx
 *  gi is row-id
 */
table NCBI:WGS:tbl:gi_idx #1
{
    /* NUC_ROW_ID
     *  row-id in nucleotide table
     */
    extern column < I64 > izip_encoding NUC_ROW_ID;

    /* PROT_ROW_ID
     *  row-id in protein table
     */
    extern column < I64 > izip_encoding PROT_ROW_ID;
};


/*--------------------------------------------------------------------------
 * scaffold
 *  records AGP data
 */
table NCBI:WGS:tbl:scaffold #1
{
    /* SCAFFOLD_NAME
     *  This is the identifier for the object being assembled.
     *  This can be a chromosome, scaffold or contig.
     *  If an accession.version identifier is not used to describe
     *  the object the naming convention is to precede chromosome numbers
     *  (e.g. chr1) and linkage group numbers  (e.g. LG3).
     *  Contigs or scaffolds may have any identifier that is unique
     *  within the assembly
     */
    extern column utf8 SCAFFOLD_NAME
        = out_scaffold_name;
    extern column ascii SCAFFOLD_NAME = cast (out_scaffold_name);
    utf8 out_scaffold_name
        = idx:text:project #1.0 < 'scaffold_name' > ( .SCAFFOLD_NAME );
    physical column < utf8 > zip_encoding .SCAFFOLD_NAME
        = idx:text:insert #1.0 < 'scaffold_name' > ( SCAFFOLD_NAME );

    /* COMPONENT_START
     *  starting position within the component sequence
     */
    extern column < INSDC:coord:one > izip_encoding COMPONENT_START;

    /* COMPONENT_LEN
     *  length of the component/gap projected onto the scaffold
     */
    extern column < INSDC:coord:len > izip_encoding COMPONENT_LEN;

    /* COMPONENT_PROPS
     *  see description of type
     */
    extern column < NCBI:WGS:component_props > zip_encoding COMPONENT_PROPS;

    /* COMPONENT_ID
     *  one row-id for each non-gap component
     */
    extern column < I64 > izip_encoding COMPONENT_ID;

    /* COMPONENT_LINKAGE
     *  see description of type
     *  one row-id for each gap component
     */
    extern column < NCBI:WGS:gap_linkage > zip_encoding COMPONENT_LINKAGE;
}

table NCBI:WGS:view:scaffold #1 = NCBI:WGS:tbl:scaffold #1
{
    /* ACCESSION
     *  scaffold accession
     */
    readonly column ascii ACCESSION
        = out_accession;
    I64 scaffold_row_id
        = row_id ();
    I64 acc_row_id
        = < I64 > echo < 1 > ();
    ascii acc_prefix
        = < ascii > simple_sub_select < 'SEQUENCE', 'ACC_PREFIX' > ( acc_row_id );
    U32 acc_contig_len
        = < U32 > simple_sub_select < 'SEQUENCE', 'ACC_CONTIG_LEN' > ( acc_row_id );
    ascii out_accession
        = sprintf < "%sS%0*d" > ( acc_prefix, acc_contig_len, scaffold_row_id );

    /* READ
     *  base space construction of entire scaffold
     */

    // construct the read from contigs and gaps
    INSDC:4na:bin out_4na_bin = NCBI:WGS:build_scaffold_read
        ( .COMPONENT_START, .COMPONENT_LEN, .COMPONENT_PROPS, .COMPONENT_ID );

    // various READ columns
    default readonly column INSDC:dna:text READ
        = < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( out_4na_bin );
    readonly column INSDC:4na:bin READ
        = out_4na_bin;
    readonly column INSDC:4na:packed READ
        = pack ( out_4na_bin );
    readonly column INSDC:x2na:bin READ
        = out_x2na_bin;
    INSDC:x2na:bin out_x2na_bin
        = < INSDC:4na:bin, INSDC:x2na:bin > map < INSDC:4na:map:BINSET, [ 4,0,1,4,2,4,4,4,3,4,4,4,4,4,4,4 ] > ( out_4na_bin );
    readonly column INSDC:2na:bin READ
        = out_2na_bin;
    INSDC:2na:bin out_2na_bin
        = < INSDC:x2na:bin, INSDC:2na:bin > map < INSDC:x2na:map:BINSET, [ 0, 1, 2, 3, 0 ] > ( out_x2na_bin );
    readonly column INSDC:2na:packed READ
        = pack ( out_2na_bin );


    /* CSREAD
     *  base space converted to color space
     */
    default readonly column INSDC:color:text CSREAD
        = < INSDC:x2cs:bin, INSDC:color:text > map <  INSDC:x2cs:map:BINSET, INSDC:x2cs:map:CHARSET > ( out_x2cs_bin );
    readonly column INSDC:x2cs:bin CSREAD
        = out_x2cs_bin;
    INSDC:x2cs:bin out_x2cs_bin
        = NCBI:color_from_dna ( out_x2na_bin, out_read_start, .COMPONENT_LEN, out_cs_key, out_color_matrix );
    readonly column INSDC:2cs:bin CSREAD
        = out_2cs_bin;
    INSDC:2cs:bin out_2cs_bin
        = < INSDC:x2cs:bin, INSDC:2cs:bin > map < INSDC:x2cs:map:BINSET, [ 0, 1, 2, 3, 0 ] > ( out_x2cs_bin );
    readonly column INSDC:2cs:packed CSREAD
        = pack ( out_2cs_bin );

    /* CS_NATIVE
     *  is color-space the native sequence space
     */
    readonly column bool CS_NATIVE
        = < bool > echo < false > ();

    /* CS_KEY
     *  leading call given in base-space
     */
    readonly column INSDC:dna:text CS_KEY
        = out_cs_key;
    INSDC:dna:text out_cs_key
        = < INSDC:dna:text > echo < 'T' > ( .COMPONENT_LEN );

    /* COLOR_MATRIX
     *  matrix used for color-space conversions
     */
    readonly column U8 COLOR_MATRIX
        = out_color_matrix;
    U8 out_color_matrix
        = < U8 > echo < INSDC:color:default_matrix > ();


    /* QUALITY
     *  base or color call qualities
     */
    INSDC:quality:phred out_qual_phred = NCBI:WGS:build_scaffold_qual
        ( .COMPONENT_START, .COMPONENT_LEN, .COMPONENT_PROPS, .COMPONENT_ID );

    // PHRED is default
    default readonly column INSDC:quality:phred QUALITY
        = out_qual_phred;

    // textual encodings
    readonly column INSDC:quality:text:phred_33 QUALITY
        = ( INSDC:quality:text:phred_33 ) < B8 > sum < 33 > ( out_qual_phred );
    readonly column INSDC:quality:text:phred_64 QUALITY
        = ( INSDC:quality:text:phred_64 ) < B8 > sum < 64 > ( out_qual_phred );


    /* PLATFORM
     *  sequencing platform, if known
     */
    INSDC:SRA:platform_id out_platform
        = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
    readonly column INSDC:SRA:platform_id PLATFORM
        = out_platform;

    /* SPOT_ID
     *  support for libsra
     */
    INSDC:SRA:spotid_t out_spot_id
        = cast ( scaffold_row_id );
    readonly column INSDC:SRA:spotid_t SPOT_ID
        = out_spot_id;

    /* NAME
     *  spot name
     */
    readonly column ascii NAME
        = out_scaffold_name;

    /* SPOT_LEN
     * TRIM_START
     * TRIM_LEN
     *  spot descriptor
     */
    readonly column INSDC:coord:len SPOT_LEN
        = out_spot_len;
    INSDC:coord:len out_spot_len
        = < INSDC:coord:len > vec_sum ( .COMPONENT_LEN );
    readonly column INSDC:coord:zero TRIM_START
        = < INSDC:coord:zero > echo < 0 > ();
    readonly column INSDC:coord:len TRIM_LEN
        = out_spot_len;


    /* READ_START
     * READ_LEN
     * READ_TYPE
     *  read descriptor portion
     */
    readonly column INSDC:coord:zero READ_START
        = out_read_start;
    INSDC:coord:zero out_read_start
        = ( INSDC:coord:zero ) < U32 > integral ( .COMPONENT_LEN );
    readonly column INSDC:coord:len READ_LEN
        = .COMPONENT_LEN;
    readonly column INSDC:SRA:xread_type READ_TYPE
        = out_read_type;
    INSDC:SRA:xread_type out_read_type
        = NCBI:WGS:build_read_type ( .COMPONENT_PROPS );
}


/*--------------------------------------------------------------------------
 * contig
 */
database NCBI:WGS:db:contig #1.1
{
    table NCBI:WGS:tbl:nucleotide SEQUENCE;
    table NCBI:WGS:tbl:protein PROTEIN;
    table NCBI:WGS:tbl:gi_idx GI_IDX;
    table NCBI:WGS:view:scaffold SCAFFOLD;
};
author	charles_s_test
date	Mon, 27 Nov 2017 11:21:07 -0500
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