/*===========================================================================
*
*                            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.
*
* ===========================================================================
*
*/
#include <klib/log.h>
#include <klib/out.h>
#include <klib/container.h>
#include <klib/text.h>
#include <kapp/main.h>

#include <sra/sradb.h>
#include <sra/types.h>
#include <sra/fastq.h>

#include <os-native.h>
#include <sysalloc.h>

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <errno.h>
#include <strtol.h>

#include "core.h"
#include "debug.h"

#define DATABUFFERINITSIZE 10240

typedef struct TAlignedRegion_struct
{
    const char* name;
    uint32_t name_len;
    /* 1-based, 0 - means not set */
    uint64_t from;
    uint64_t to;
} TAlignedRegion;


typedef struct TMatepairDistance_struct
{
    uint64_t from;
    uint64_t to;
} TMatepairDistance;


struct FastqArgs_struct
{
    bool is_platform_cs_native;

    int maxReads;
    bool skipTechnical;

    uint32_t minReadLen;
    bool applyClip;
    bool dumpOrigFmt;
    bool dumpBase;
    bool dumpCs;
    bool readIds;
    bool SuppressQualForCSKey;      /* added Jan 15th 2014 ( a new fastq-variation! ) */
    int offset;
    bool qual_filter;
    bool qual_filter1;
    const char* b_deffmt;
    SLList* b_defline;
    const char* q_deffmt;
    SLList* q_defline;
    const char *desiredCsKey;
    bool split_files;
    bool split_3;
    bool split_spot;
    uint64_t fasta;
    const char* file_extension;
    bool aligned;
    bool unaligned;
    TAlignedRegion* alregion;
    uint32_t alregion_qty;
    bool mp_dist_unknown;
    TMatepairDistance* mp_dist;
    uint32_t mp_dist_qty;
} FastqArgs;


typedef enum DefNodeType_enum
{
    DefNode_Unknown = 0,
    DefNode_Text = 1,
    DefNode_Optional,
    DefNode_Accession,
    DefNode_SpotId,
    DefNode_SpotName,
    DefNode_SpotGroup,
    DefNode_SpotLen,
    DefNode_ReadId,
    DefNode_ReadName,
    DefNode_ReadLen,
    DefNode_Last
} DefNodeType;


typedef struct DefNode_struct
{
    SLNode node;
    DefNodeType type;
    union
    {
        SLList* optional;
        char* text;
    } data;
} DefNode;


typedef struct DeflineData_struct
{
    rc_t rc;
    bool optional;
    union
    {
        spotid_t* id;
        struct
        {
            const char* s;
            size_t sz;
        } str;
        uint32_t* u32;
    } values[ DefNode_Last ];
    char* buf;
    size_t buf_sz;
    size_t* writ;
} DeflineData;


static bool CC Defline_Builder( SLNode *node, void *data )
{
    DefNode* n = ( DefNode* )node;
    DeflineData* d = ( DeflineData* )data;
    char s[ 256 ];
    size_t w;
    int x = 0;

    s[ 0 ] = '\0';
    switch ( n->type )
    {
        case DefNode_Optional :
            d->optional = true;
            w = *d->writ;
            *d->writ = 0;
            SLListDoUntil( n->data.optional, Defline_Builder, data );
            x = ( *d->writ == 0 ) ? 0 : 1;
            d->optional = false;
            *d->writ = w;
            if ( x > 0 )
            {
                SLListDoUntil( n->data.optional, Defline_Builder, data );
            }
            break;

        case DefNode_Text :
            if ( d->optional )
            {
                break;
            }
            d->values[n->type].str.s = n->data.text;
            d->values[n->type].str.sz = strlen( n->data.text );

        case DefNode_Accession :
        case DefNode_SpotName :
        case DefNode_SpotGroup :
        case DefNode_ReadName :
            if ( d->values[n->type].str.s != NULL )
            {
                x = d->values[ n->type ].str.sz;
                if ( x < sizeof( s ) )
                {
                    strncpy( s, d->values[ n->type ].str.s, x );
                    s[ x ] = '\0';
                    *d->writ = *d->writ + x;
                }
                else
                {
                    d->rc = RC( rcExe, rcNamelist, rcExecuting, rcBuffer, rcInsufficient );
                }
            }
            break;

        case DefNode_SpotId :
            if ( d->values[ n->type ].id != NULL &&
                ( !d->optional || *d->values[ n->type ].id > 0 ) )
            {
                x = snprintf( s, sizeof( s ), "%ld", *d->values[ n->type ].id );
                if ( x < 0 || x >= sizeof( s ) )
                {
                    d->rc = RC( rcExe, rcNamelist, rcExecuting, rcBuffer, rcInsufficient );
                }
                else
                {
                    *d->writ = *d->writ + x;
                }
            }
            break;

        case DefNode_ReadId :
        case DefNode_SpotLen :
        case DefNode_ReadLen :
            if ( d->values[ n->type] .u32 != NULL &&
                 ( !d->optional || *d->values[ n->type ].u32 > 0 ) )
            {
                x = snprintf( s, sizeof( s ), "%u", *d->values[ n->type ].u32 );
                if ( x < 0 || x >= sizeof( s ) )
                {
                    d->rc = RC( rcExe, rcNamelist, rcExecuting, rcBuffer, rcInsufficient );
                }
                else
                {
                    *d->writ = *d->writ + x;
                }
            }
            break;

        default:
            d->rc = RC( rcExe, rcNamelist, rcExecuting, rcId, rcInvalid );
    } /* switch */

    if ( d->rc == 0 && !d->optional && n->type != DefNode_Optional )
    {
        if ( *d->writ < d->buf_sz )
        {
            strcat( d->buf, s );
        }
        else
        {
            d->rc = RC( rcExe, rcNamelist, rcExecuting, rcBuffer, rcInsufficient );
        }
    }
    return d->rc != 0;
}


static rc_t Defline_Bind( DeflineData* data, const char* accession,
            spotid_t* spotId, const char* spot_name, size_t spotname_sz,
            const char* spot_group, size_t sgrp_sz, uint32_t* spot_len,
            uint32_t* readId, const char* read_name, INSDC_coord_len rlabel_sz,
            INSDC_coord_len* read_len )
{
    if ( data == NULL )
    {
        return RC( rcExe, rcNamelist, rcExecuting, rcMemory, rcInsufficient );
    }
    data->values[ DefNode_Unknown ].str.s = NULL;
    data->values[ DefNode_Text ].str.s = NULL;
    data->values[ DefNode_Optional ].str.s = NULL;
    data->values[ DefNode_Accession ].str.s = accession;
    data->values[ DefNode_Accession ].str.sz = strlen( accession );
    data->values[ DefNode_SpotId ].id = spotId;
    data->values[ DefNode_SpotName ].str.s = spot_name;
    data->values[ DefNode_SpotName ].str.sz = spotname_sz;
    data->values[ DefNode_SpotGroup ].str.s = spot_group;
    data->values[ DefNode_SpotGroup ].str.sz = sgrp_sz;
    data->values[ DefNode_SpotLen ].u32 = spot_len;
    data->values[ DefNode_ReadId ].u32 = readId;
    data->values[ DefNode_ReadName ].str.s = read_name;
    data->values[ DefNode_ReadName ].str.sz = rlabel_sz;
    data->values[ DefNode_ReadLen ].u32 = read_len;
    return 0;
}


static rc_t Defline_Build( const SLList* def, DeflineData* data, char* buf,
                           size_t buf_sz, size_t* writ )
{
    if ( data == NULL )
    {
        return RC( rcExe, rcNamelist, rcExecuting, rcMemory, rcInsufficient );
    }

    data->rc = 0;
    data->optional = false;
    data->buf = buf;
    data->buf_sz = buf_sz;
    data->writ = writ;

    data->buf[ 0 ] = '\0';
    *data->writ = 0;

    SLListDoUntil( def, Defline_Builder, data );
    return data->rc;
}


static rc_t DeflineNode_Add( SLList* list, DefNode** node,
                            DefNodeType type, const char* text, size_t text_sz )
{
    rc_t rc = 0;

    *node = calloc( 1, sizeof( **node ) );
    if ( *node == NULL )
    {
        rc = RC( rcExe, rcNamelist, rcConstructing, rcMemory, rcExhausted );
    }
    else if ( type == DefNode_Text && ( text == NULL || text_sz == 0 ) )
    {
        rc = RC( rcExe, rcNamelist, rcConstructing, rcParam, rcInvalid );
    }
    else
    {
        ( *node )->type = type;
        if ( type == DefNode_Text )
        {
            ( *node )->data.text = string_dup( text, text_sz );
            if ( ( *node )->data.text == NULL )
            {
                rc = RC( rcExe, rcNamelist, rcConstructing, rcMemory, rcExhausted );
                free( *node );
            }
        }
        else if ( type == DefNode_Optional )
        {
            ( *node )->data.optional = malloc( sizeof( SLList ) );
            if ( ( *node )->data.optional == NULL )
            {
                rc = RC( rcExe, rcNamelist, rcConstructing, rcMemory, rcExhausted );
                free( *node );
            }
            else
            {
                SLListInit( ( *node )->data.optional );
            }
        }
        if ( rc == 0 )
        {
            SLListPushTail( list, &( *node )->node );
        }
    }
    return rc;
}


static void Defline_Release( SLList* list );


static void CC DeflineNode_Whack( SLNode* node, void* data )
{
    if ( node != NULL )
    {
        DefNode* n = (DefNode*)node;
        if ( n->type == DefNode_Text )
        {
            free( n->data.text );
        }
        else if ( n->type == DefNode_Optional )
        {
            Defline_Release( n->data.optional );
        }
        free( node );
    }
}


static void Defline_Release( SLList* list )
{
    if ( list != NULL )
    {
        SLListForEach( list, DeflineNode_Whack, NULL );
        free( list );
    }
}


#if _DEBUGGING
static void CC Defline_Dump( SLNode* node, void* data )
{
    DefNode* n = ( DefNode* )node;
    const char* s = NULL, *t;
    if ( n->type == DefNode_Text )
    {
        s = n->data.text;
    }
    switch ( n->type )
    {
        case DefNode_Unknown :      t = "Unknown";   break;
        case DefNode_Text :         t = "Text";      break;
        case DefNode_Optional :     t = "Optional";  break;
        case DefNode_Accession :    t = "Accession"; break;
        case DefNode_SpotId :       t = "SpotId";    break;
        case DefNode_SpotName :     t = "SpotName";  break;
        case DefNode_SpotGroup :    t = "SpotGroup"; break;
        case DefNode_SpotLen :      t = "SpotLen";   break;
        case DefNode_ReadId :       t = "ReadId";    break;
        case DefNode_ReadName :     t = "ReadName";  break;
        case DefNode_ReadLen :      t = "ReadLen";   break;
        default :  t = "ERROR";
    }

    SRA_DUMP_DBG( 3, ( "%s type %s", data, t ) );
    if ( s )
    {
        SRA_DUMP_DBG( 3, ( ": '%s'", s ) );
    }
    SRA_DUMP_DBG( 3, ( "\n" ) );
    if ( n->type == DefNode_Optional )
    {
        SLListForEach( n->data.optional, Defline_Dump, "+-->" );
    }
}
#endif


static rc_t Defline_Parse( SLList** def, const char* line )
{
    rc_t rc = 0;
    size_t i, sz, text = 0, opt_vars = 0;
    DefNode* node;
    SLList* list = NULL;

    if ( def == NULL || line == NULL )
    {
        return RC( rcExe, rcNamelist, rcConstructing, rcParam, rcInvalid );
    }
    *def = malloc( sizeof( SLList ) );
    if ( *def  == NULL )
    {
        return RC( rcExe, rcNamelist, rcConstructing, rcMemory, rcExhausted );
    }
    sz = strlen( line );
    list = *def;
    SLListInit( list );

    for ( i = 0; rc == 0 && i < sz; i++ )
    {
        if ( line[ i ] == '[' )
        {
            if ( ( i + 1 ) < sz && line[ i + 1 ] == '[' )
            {
                i++;
            }
            else
            {
                if ( list != *def )
                {
                    rc = RC( rcExe, rcNamelist, rcConstructing, rcFormat, rcIncorrect );
                }
                else if ( i > text )
                {
                    rc = DeflineNode_Add( list, &node, DefNode_Text, &line[text], i - text );
                }
                if ( rc == 0 )
                {
                    rc = DeflineNode_Add( list, &node, DefNode_Optional, NULL, 0 );
                    if ( rc == 0 )
                    {
                        opt_vars = 0;
                        list = node->data.optional;
                        text = i + 1;
                    }
                }
            }
        }
        else if ( line[ i ] == ']' )
        {
            if ( ( i + 1 ) < sz && line[ i + 1 ] == ']' )
            {
                i++;
            }
            else
            {
                if ( list == *def )
                {
                    rc = RC( rcExe, rcNamelist, rcConstructing, rcFormat, rcIncorrect );
                }
                else
                {
                    if ( opt_vars < 1 )
                    {
                        rc = RC( rcExe, rcNamelist, rcConstructing, rcConstraint, rcEmpty );
                    }
                    else if ( i > text )
                    {
                        rc = DeflineNode_Add( list, &node, DefNode_Text, &line[text], i - text );
                    }
                    list = *def;
                    text = i + 1;
                }
            }
        }
        else if ( line[ i ] == '$' )
        {
            if ( ( i + 1 ) < sz && line[ i + 1 ] == '$' )
            {
                i++;
            }
            else
            {
                DefNodeType type = DefNode_Unknown;
                switch ( line[ ++i] )
                {
                    case 'a' :
                        switch( line[ ++i ] )
                        {
                            case 'c': type = DefNode_Accession; break;
                        }
                        break;

                    case 's' :
                        switch ( line[ ++i ] )
                        {
                            case 'i': type = DefNode_SpotId; break;
                            case 'n': type = DefNode_SpotName; break;
                            case 'g': type = DefNode_SpotGroup; break;
                            case 'l': type = DefNode_SpotLen; break;
                        }
                        break;
                    case 'r' :
                        switch( line[ ++i ] )
                        {
                            case 'i': type = DefNode_ReadId; break;
                            case 'n': type = DefNode_ReadName; break;
                            case 'l': type = DefNode_ReadLen; break;
                        }
                        break;
                }
                if ( type == DefNode_Unknown )
                {
                    rc = RC( rcExe, rcNamelist, rcConstructing, rcName, rcUnrecognized );
                }
                else
                {
                    if ( ( i - 2 ) > text )
                    {
                        rc = DeflineNode_Add( list, &node, DefNode_Text, &line[ text ], i - text - 2 );
                    }
                    if ( rc == 0 )
                    {
                        rc = DeflineNode_Add( list, &node, type, NULL, 0 );
                        if ( rc == 0 )
                        {
                            opt_vars++;
                            text = i + 1;
                        }
                    }
                }
            }
        }
    }
    if ( rc == 0 )
    {
        if ( list != *def )
        {
            rc = RC( rcExe, rcNamelist, rcConstructing, rcFormat, rcInvalid );
        }
        else if ( i > text )
        {
            rc = DeflineNode_Add( list, &node, DefNode_Text, &line[ text ], i - text );
        }
    }
    if ( rc != 0 )
    {
        i = i < sz ? i : sz;
        PLOGERR( klogErr, ( klogErr, rc, "$(l1) -->$(c)<-- $(l2)",
                 "l1=%.*s,c=%c,l2=%.*s", i - 1, line, line[ i - 1 ], sz - i, &line[ i ] ) );
    }
#if _DEBUGGING
    SRA_DUMP_DBG( 3, ( "| defline\n" ) );
    SLListForEach( *def, Defline_Dump, "+->" );
#endif
    return rc;
}

/* ### ALIGNMENT_COUNT based filtering ##################################################### */

typedef struct AlignedFilter_struct
{
    const SRAColumn* col;
    uint64_t rejected_reads;
    bool aligned;
    bool unaligned;
} AlignedFilter;


static rc_t AlignedFilter_GetKey( const SRASplitter* cself, const char** key,
                                  spotid_t spot, readmask_t* readmask )
{
    rc_t rc = 0;
    AlignedFilter* self = ( AlignedFilter* )cself;

    if ( self == NULL || key == NULL )
    {
        rc = RC( rcSRA, rcNode, rcExecuting, rcParam, rcNull );
    }
    else
    {
        *key = "";
        if ( self->col != NULL )
        {
            const uint8_t* ac = NULL;
            bitsz_t o = 0, sz = 0;
            rc = SRAColumnRead( self->col, spot, (const void **)&ac, &o, &sz );
            if ( rc == 0 && sz > 0 )
            {
                sz = sz / 8 / sizeof( *ac );
                for( o = 0; o < sz; o++ )
                {
                    if ( ( self->aligned   && !self->unaligned && ac[ o ] == 0 ) ||
                         ( self->unaligned && !self->aligned   && ac[ o ] != 0 ) )
                    {
                        unset_readmask( readmask, o );
                        self->rejected_reads ++;
                    }
                }
            }
        }
    }
    return rc;
}


static rc_t AlignedFilter_Release( const SRASplitter* cself )
{
    rc_t rc = 0;
    AlignedFilter* self = ( AlignedFilter* )cself;
    if ( self == NULL )
    {
        rc = RC( rcSRA, rcNode, rcExecuting, rcParam, rcNull );
    }
    else
    {
        if ( self->rejected_reads > 0 && !g_legacy_report )
            rc = KOutMsg( "Rejected %lu READS because of aligned/unaligned filter\n", self->rejected_reads );
    }
    return rc;
}

typedef struct AlignedFilterFactory_struct
{
    const SRATable* table;
    const SRAColumn* col;
    bool aligned;
    bool unaligned;
} AlignedFilterFactory;


static rc_t AlignedFilterFactory_Init( const SRASplitterFactory* cself )
{
    rc_t rc = 0;
    AlignedFilterFactory* self = ( AlignedFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcSRA, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = SRATableOpenColumnRead( self->table, &self->col, "ALIGNMENT_COUNT", vdb_uint8_t );
        if ( rc != 0 )
        {
            if ( GetRCState( rc ) == rcNotFound )
            {
                LOGMSG( klogWarn, "Column ALIGNMENT_COUNT was not found, param ignored" );
                rc = 0;
            }
            else if ( GetRCState( rc ) == rcExists )
            {
                rc = 0;
            }
        }
    }
    return rc;
}


static rc_t AlignedFilterFactory_NewObj( const SRASplitterFactory* cself, const SRASplitter** splitter )
{
    rc_t rc = 0;
    AlignedFilterFactory* self = ( AlignedFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcSRA, rcType, rcExecuting, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitter_Make( splitter, sizeof( AlignedFilter ),
                               AlignedFilter_GetKey, NULL, NULL, AlignedFilter_Release );
        if ( rc == 0 )
        {
            AlignedFilter * filter = ( AlignedFilter * )( * splitter );
            filter->col = self->col;
            filter->aligned = self->aligned;
            filter->unaligned = self->unaligned;
            filter->rejected_reads = 0;
        }
    }
    return rc;
}


static void AlignedFilterFactory_Release( const SRASplitterFactory* cself )
{
    if ( cself != NULL )
    {
        AlignedFilterFactory* self = ( AlignedFilterFactory* )cself;
        SRAColumnRelease( self->col );
    }
}


static rc_t AlignedFilterFactory_Make( const SRASplitterFactory** cself,
                    const SRATable* table, bool aligned, bool unaligned )
{
    rc_t rc = 0;
    AlignedFilterFactory* obj = NULL;

    if ( cself == NULL || table == NULL )
    {
        rc = RC( rcSRA, rcType, rcAllocating, rcParam, rcNull );
    }
    else
    {
        SRASplitterFactory_Make( cself, eSplitterSpot, sizeof( *obj ),
                                 AlignedFilterFactory_Init,
                                 AlignedFilterFactory_NewObj,
                                 AlignedFilterFactory_Release );
        if ( rc == 0 )
        {
            obj = ( AlignedFilterFactory* )*cself;
            obj->table = table;
            obj->aligned = aligned;
            obj->unaligned = unaligned;
        }
    }
    return rc;
}


/* ### alignment region filtering ##################################################### */

typedef struct AlignRegionFilter_struct
{
    const SRAColumn* col_pos;
    const SRAColumn* col_name;
    const SRAColumn* col_seqid;
    const TAlignedRegion* alregion;
    uint64_t rejected_spots;
    uint32_t alregion_qty;
} AlignRegionFilter;


static rc_t AlignRegionFilter_GetKey( const SRASplitter* cself, const char** key,
                                      spotid_t spot, readmask_t* readmask )
{
    rc_t rc = 0;
    AlignRegionFilter* self = ( AlignRegionFilter* )cself;

    if ( self == NULL || key == NULL )
    {
        rc = RC( rcSRA, rcNode, rcExecuting, rcParam, rcNull );
    }
    else
    {
        *key = "";
        reset_readmask( readmask );
        if ( self->col_name || self->col_seqid )
        {
            bool match = false;
            uint32_t i;
            const char* nm, *si;
            bitsz_t o, nm_len = 0, si_len = 0;

            if ( self->col_name )
            {
                rc = SRAColumnRead( self->col_name, spot, (const void **)&nm, &o, &nm_len );
                if ( rc == 0 && nm_len > 0 )
                    nm_len /= 8;
            }
            if ( rc == 0 && self->col_seqid )
            {
                rc = SRAColumnRead( self->col_seqid, spot, (const void **)&si, &o, &si_len );
                if ( rc == 0 && si_len > 0 )
                    si_len /= 8;
            }
            for ( i = 0; rc == 0 && i < self->alregion_qty; i++ )
            {
                if ( ( self->alregion[i].name_len == nm_len && 
                       strncasecmp( self->alregion[ i ].name, nm, nm_len ) == 0 ) ||
                     ( self->alregion[i].name_len == si_len && 
                       strncasecmp(self->alregion[i].name, si, si_len) == 0 ) )
                {
                    if ( self->col_pos )
                    {
                        INSDC_coord_zero* pos;
                        bitsz_t nreads, j;
                        rc = SRAColumnRead( self->col_pos, spot, ( const void ** )&pos, &o, &nreads );
                        if ( rc == 0 && nreads > 0 )
                        {
                            nreads = nreads / sizeof(*pos) / 8;
                            for ( i = 0; !match && i < self->alregion_qty; i++ )
                            {
                                for ( j = 0; j < nreads; j++ )
                                {
                                    if ( self->alregion[i].from <= pos[j] &&
                                         pos[j] <= self->alregion[i].to )
                                    {
                                        match = true;
                                        break;
                                    }
                                }
                            }
                        }
                    }
                    else
                    {
                        match = true;
                    }
                    break;
                }
            }
            if ( !match )
            {
                clear_readmask( readmask );
                self->rejected_spots ++;
            }
        }
    }
    return rc;
}


static rc_t AlignRegionFilter_Release( const SRASplitter* cself )
{
    rc_t rc = 0;
    AlignRegionFilter* self = ( AlignRegionFilter* )cself;

    if ( self == NULL )
    {
        rc = RC( rcSRA, rcNode, rcExecuting, rcParam, rcNull );
    }
    else
    {
        if ( self->rejected_spots > 0 && !g_legacy_report )
            rc = KOutMsg( "Rejected %lu SPOTS because of AlignRegionFilter\n", self->rejected_spots );
    }
    return rc;
}


typedef struct AlignRegionFilterFactory_struct
{
    const SRATable* table;
    const SRAColumn* col_pos;
    const SRAColumn* col_name;
    const SRAColumn* col_seqid;
    TAlignedRegion* alregion;
    uint32_t alregion_qty;
} AlignRegionFilterFactory;


static rc_t AlignRegionFilterFactory_Init( const SRASplitterFactory* cself )
{
    rc_t rc = 0;
    AlignRegionFilterFactory* self = ( AlignRegionFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcSRA, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {

#define COLNF(v,n,t) (!(rc == 0 && ((rc = SRATableOpenColumnRead(self->table, &v, n, t)) == 0 || \
                       GetRCState(rc) == rcExists)) && GetRCState(rc) == rcNotFound)

        if ( COLNF( self->col_name, "REF_NAME", vdb_ascii_t ) )
        {
            SRAColumnRelease( self->col_name );
            self->col_name = NULL;
            rc = 0;
        }

        if ( COLNF( self->col_seqid, "REF_SEQ_ID", vdb_ascii_t ) )
        {
            SRAColumnRelease( self->col_seqid );
            self->col_seqid = NULL;
            rc = 0;
        }

        if ( self->col_name == NULL && self->col_seqid == NULL )
        {
            LOGMSG( klogWarn, "None of columns REF_NAME or REF_SEQ_ID was found, no region filtering" );
        }
        else
        {
            bool range_used = false;
            uint32_t i;
            /* see if there are any actual ranges set and open col only if yes */
            for ( i = 0; i < self->alregion_qty; i++ )
            {
                if ( self->alregion[ i ].from != 0 || self->alregion[ i ].to != 0 )
                {
                    range_used = true;
                    break;
                }
            }
            if ( range_used )
            {
                if ( COLNF( self->col_pos, "REF_POS", "INSDC:coord:zero" ) )
                {
                    LOGMSG( klogWarn, "Column REF_POS is not found, no region position filtering" );
                    rc = 0;
                }
                else
                {
                    for ( i = 0; i < self->alregion_qty; i++ )
                    {
                        if ( self->alregion[ i ].from > 0 )
                        {
                            self->alregion[ i ].from--;
                        }
                        if ( self->alregion[ i ].to > 0 )
                        {
                            self->alregion[ i ].to--;
                        }
                        else if ( self->alregion[ i ].to == 0 )
                        {
                            self->alregion[ i ].to = ~0;
                        }
                    }
                }
            }
        }
    }
#undef COLNF
    return rc;
}


static rc_t AlignRegionFilterFactory_NewObj( const SRASplitterFactory* cself, const SRASplitter** splitter )
{
    rc_t rc = 0;
    AlignRegionFilterFactory* self = ( AlignRegionFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcSRA, rcType, rcExecuting, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitter_Make( splitter, sizeof( AlignRegionFilter ),
                               AlignRegionFilter_GetKey, NULL, NULL, AlignRegionFilter_Release );
        if ( rc == 0 )
        {
            AlignRegionFilter * filter = ( AlignRegionFilter * )( * splitter );
            filter->col_pos = self->col_pos;
            filter->col_name = self->col_name;
            filter->col_seqid = self->col_seqid;
            filter->alregion = self->alregion;
            filter->alregion_qty = self->alregion_qty;
            filter->rejected_spots = 0;
        }
    }
    return rc;
}


static void AlignRegionFilterFactory_Release( const SRASplitterFactory* cself )
{
    if ( cself != NULL )
    {
        AlignRegionFilterFactory* self = ( AlignRegionFilterFactory* )cself;
        SRAColumnRelease( self->col_pos );
        SRAColumnRelease( self->col_name );
        SRAColumnRelease( self->col_seqid );
    }
}


static rc_t AlignRegionFilterFactory_Make( const SRASplitterFactory** cself,
            const SRATable* table, TAlignedRegion* alregion, uint32_t alregion_qty )
{
    rc_t rc = 0;
    AlignRegionFilterFactory* obj = NULL;

    if ( cself == NULL || table == NULL )
    {
        rc = RC( rcSRA, rcType, rcAllocating, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitterFactory_Make( cself, eSplitterSpot, sizeof( *obj ),
                                      AlignRegionFilterFactory_Init,
                                      AlignRegionFilterFactory_NewObj,
                                      AlignRegionFilterFactory_Release );
        if ( rc == 0 )
        {
            obj = ( AlignRegionFilterFactory* )*cself;
            obj->table = table;
            obj->alregion = alregion;
            obj->alregion_qty = alregion_qty;
        }
    }
    return rc;
}

/* ### alignment meta-pair distance filtering ##################################################### */

typedef struct AlignPairDistanceFilter_struct
{
    const SRAColumn* col_tlen;
    const TMatepairDistance* mp_dist;
    uint64_t rejected_reads;
    bool mp_dist_unknown;
    uint32_t mp_dist_qty;
} AlignPairDistanceFilter;


static rc_t AlignPairDistanceFilter_GetKey( const SRASplitter* cself,
                const char** key, spotid_t spot, readmask_t* readmask )
{
    rc_t rc = 0;
    AlignPairDistanceFilter* self = ( AlignPairDistanceFilter* )cself;

    if ( self == NULL || key == NULL )
    {
        rc = RC( rcSRA, rcNode, rcExecuting, rcParam, rcNull );
    }
    else
    {
        *key = "";
        reset_readmask( readmask );
        if ( self->col_tlen )
        {
            uint32_t i, j;
            bitsz_t o, nreads;
            int32_t* tlen;
            rc = SRAColumnRead( self->col_tlen, spot, (const void **)&tlen, &o, &nreads );
            if ( rc == 0 )
            {
                nreads = nreads / sizeof(*tlen) / 8;
                for ( i = 0; i < self->mp_dist_qty; i++ )
                {
                    for ( j = 0; j < nreads; j++ )
                    {
                        if ( ( tlen[ j ] == 0 && !self->mp_dist_unknown) ||
                             ( tlen[ j ] != 0 && 
                               ( tlen[ j ] < self->mp_dist[ i ].from || self->mp_dist[ i ].to < tlen[ j ] ) ) )
                        {
                            unset_readmask( readmask, j );
                            self->rejected_reads ++;
                        }
                    }
                }
            }
        }
    }
    return rc;
}


static rc_t AlignPairDistanceFilter_Release( const SRASplitter* cself )
{
    rc_t rc = 0;
    AlignPairDistanceFilter* self = ( AlignPairDistanceFilter* )cself;

    if ( self == NULL )
    {
        rc = RC( rcSRA, rcNode, rcExecuting, rcParam, rcNull );
    }
    else
    {
        if ( self->rejected_reads > 0 && !g_legacy_report )
            rc = KOutMsg( "Rejected %lu READS because of AlignPairDistanceFilter\n", self->rejected_reads );
    }
    return rc;
}

typedef struct AlignPairDistanceFilterFactory_struct
{
    const SRATable* table;
    const SRAColumn* col_tlen;
    bool mp_dist_unknown;
    TMatepairDistance* mp_dist;
    uint32_t mp_dist_qty;
} AlignPairDistanceFilterFactory;


static rc_t AlignPairDistanceFilterFactory_Init( const SRASplitterFactory* cself )
{
    rc_t rc = 0;
    AlignPairDistanceFilterFactory* self = ( AlignPairDistanceFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcSRA, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = SRATableOpenColumnRead( self->table, &self->col_tlen, "TEMPLATE_LEN", "I32" );
        if( !( rc == 0 || GetRCState( rc ) == rcExists ) && GetRCState( rc ) == rcNotFound )
        {
            LOGMSG( klogWarn, "Column TLEN was not found, no distance filtering" );
            self->col_tlen = NULL;
            rc = 0;
        }
        if ( rc == 0 )
        {
            uint32_t i;
            for ( i = 0; i < self->mp_dist_qty; i++ )
            {
                if ( self->mp_dist[ i ].to == 0 )
                {
                    self->mp_dist[ i ].to = ~0;
                }
            }
        }
    }
    return rc;
}


static rc_t AlignPairDistanceFilterFactory_NewObj( const SRASplitterFactory* cself,
                                                   const SRASplitter** splitter )
{
    rc_t rc = 0;
    AlignPairDistanceFilterFactory* self = ( AlignPairDistanceFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcSRA, rcType, rcExecuting, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitter_Make( splitter, sizeof( AlignPairDistanceFilter ),
                               AlignPairDistanceFilter_GetKey, NULL, NULL, AlignPairDistanceFilter_Release );
        if ( rc == 0 )
        {
            AlignPairDistanceFilter * filter = ( AlignPairDistanceFilter * )( * splitter );
            filter->col_tlen = self->col_tlen;
            filter->mp_dist_unknown = self->mp_dist_unknown;
            filter->mp_dist = self->mp_dist;
            filter->mp_dist_qty = self->mp_dist_qty;
            filter->rejected_reads = 0;
        }
    }
    return rc;
}


static void AlignPairDistanceFilterFactory_Release( const SRASplitterFactory* cself )
{
    if ( cself != NULL )
    {
        AlignPairDistanceFilterFactory* self = ( AlignPairDistanceFilterFactory* )cself;
        SRAColumnRelease( self->col_tlen );
    }
}


static rc_t AlignPairDistanceFilterFactory_Make( const SRASplitterFactory** cself,
        const SRATable* table, bool mp_dist_unknown, TMatepairDistance* mp_dist, uint32_t mp_dist_qty )
{
    rc_t rc = 0;
    AlignPairDistanceFilterFactory* obj = NULL;

    if ( cself == NULL || table == NULL )
    {
        rc = RC( rcSRA, rcType, rcAllocating, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitterFactory_Make( cself, eSplitterSpot, sizeof( *obj ),
                                      AlignPairDistanceFilterFactory_Init,
                                      AlignPairDistanceFilterFactory_NewObj,
                                      AlignPairDistanceFilterFactory_Release );
        if ( rc == 0 )
        {
            obj = ( AlignPairDistanceFilterFactory* ) *cself;
            obj->table = table;
            obj->mp_dist_unknown = mp_dist_unknown;
            obj->mp_dist = mp_dist;
            obj->mp_dist_qty = mp_dist_qty;
        }
    }
    return rc;
}


/* ============== FASTQ read type (bio/tech) filter ============================ */

typedef struct FastqBioFilter_struct
{
    const FastqReader* reader;
    uint64_t rejected_reads;
} FastqBioFilter;


/* filter out non-bio reads */
static rc_t FastqBioFilter_GetKey( const SRASplitter* cself, const char** key,
                                   spotid_t spot, readmask_t* readmask )
{
    rc_t rc = 0;
    FastqBioFilter* self = ( FastqBioFilter* )cself;

    if ( self == NULL || key == NULL )
    {
        rc = RC( rcExe, rcNode, rcExecuting, rcParam, rcInvalid );
    }
    else
    {
        uint32_t num_reads = 0;

        *key = NULL;
        rc = FastqReaderSeekSpot( self->reader, spot );
        if ( rc == 0 )
        {
            rc = FastqReader_SpotInfo( self->reader, NULL, NULL, NULL, NULL, NULL, &num_reads );
            if ( rc == 0 )
            {
                uint32_t readId;
                SRA_DUMP_DBG( 3, ( "%s %u row reads: ", __func__, spot ) );
                for (readId = 0; rc == 0 && readId < num_reads; readId++ )
                {
                    if ( isset_readmask( readmask, readId ) )
                    {
                        SRAReadTypes read_type;
                        rc = FastqReader_SpotReadInfo( self->reader, readId + 1, &read_type,
                                                       NULL, NULL, NULL, NULL);
                        if ( rc == 0 )
                        {
                            if ( !( read_type & SRA_READ_TYPE_BIOLOGICAL ) )
                            {
                                unset_readmask( readmask, readId );
                                self->rejected_reads ++;
                            }
                            else
                            {
                                SRA_DUMP_DBG( 3, ( " %u", readId ) );
                            }
                        }
                    }
                }
                *key = "";
                SRA_DUMP_DBG( 3, ( " key '%s'\n", *key ) );
            }
        }
        else if ( GetRCObject( rc ) == rcRow && GetRCState( rc ) == rcNotFound )
        {
            SRA_DUMP_DBG( 3, ( "%s skipped %u row\n", __func__, spot ) );
            rc = 0;
        }
    }
    return rc;
}


static rc_t FastqBioFilter_Release( const SRASplitter * cself )
{
    rc_t rc = 0;
    FastqBioFilter * self = ( FastqBioFilter * )cself;

    if ( self == NULL )
        rc = RC( rcExe, rcNode, rcExecuting, rcParam, rcInvalid );
    else
    {
        if ( self->rejected_reads > 0 && !g_legacy_report )
            rc = KOutMsg( "Rejected %lu READS because of filtering out non-biological READS\n", self->rejected_reads );
    }
    return rc;
}


typedef struct FastqBioFilterFactory_struct
{
    const char* accession;
    const SRATable* table;
    const FastqReader* reader;
} FastqBioFilterFactory;


static rc_t FastqBioFilterFactory_Init( const SRASplitterFactory* cself )
{
    rc_t rc = 0;
    FastqBioFilterFactory* self = ( FastqBioFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = FastqReaderMake( &self->reader, self->table, self->accession,
                              /* preserve orig spot format to save on conversions */
                              FastqArgs.is_platform_cs_native, false, FastqArgs.fasta > 0, false, 
                              false, !FastqArgs.applyClip, FastqArgs.SuppressQualForCSKey, 0,
                              FastqArgs.offset, '\0', 0, 0) ;
    }
    return rc;
}


static rc_t FastqBioFilterFactory_NewObj( const SRASplitterFactory* cself, const SRASplitter** splitter )
{
    rc_t rc = 0;
    FastqBioFilterFactory* self = ( FastqBioFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcExecuting, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitter_Make( splitter, sizeof( FastqBioFilter ),
                               FastqBioFilter_GetKey, NULL, NULL, FastqBioFilter_Release );
        if ( rc == 0 )
        {
            FastqBioFilter * filter = ( FastqBioFilter * )( * splitter );
            filter->reader = self->reader;
            filter->rejected_reads = 0;
        }
    }
    return rc;
}


static void FastqBioFilterFactory_Release( const SRASplitterFactory* cself )
{
    if ( cself != NULL )
    {
        FastqBioFilterFactory* self = ( FastqBioFilterFactory* )cself;
        FastqReaderWhack( self->reader );
    }
}


static rc_t FastqBioFilterFactory_Make( const SRASplitterFactory** cself,
                        const char* accession, const SRATable* table )
{
    rc_t rc = 0;
    FastqBioFilterFactory* obj = NULL;

    if ( cself == NULL || accession == NULL || table == NULL )
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitterFactory_Make( cself, eSplitterSpot, sizeof( *obj ),
                                      FastqBioFilterFactory_Init,
                                      FastqBioFilterFactory_NewObj,
                                      FastqBioFilterFactory_Release );

        if ( rc == 0 )
        {
            obj = ( FastqBioFilterFactory* )*cself;
            obj->accession = accession;
            obj->table = table;
        }
    }
    return rc;
}


/* ============== FASTQ number of reads filter ============================ */

typedef struct FastqRNumberFilter_struct
{
    const FastqReader* reader;
    uint64_t rejected_reads;
} FastqRNumberFilter;


static rc_t FastqRNumberFilter_GetKey( const SRASplitter* cself, const char** key,
                                       spotid_t spot, readmask_t* readmask )
{
    rc_t rc = 0;
    FastqRNumberFilter* self = ( FastqRNumberFilter* )cself;

    if ( self == NULL || key == NULL )
    {
        rc = RC( rcExe, rcNode, rcExecuting, rcParam, rcInvalid );
    }
    else
    {
        uint32_t num_reads = 0;

        *key = NULL;
        rc = FastqReaderSeekSpot( self->reader, spot );
        if ( rc == 0 )
        {
            rc = FastqReader_SpotInfo( self->reader, NULL, NULL, NULL, NULL, NULL, &num_reads );
            if ( rc == 0 )
            {
                int readId, q;

                SRA_DUMP_DBG( 3, ( "%s %u row reads: ", __func__, spot ) );
                for ( readId = 0, q = 0; readId < num_reads; readId++ )
                {
                    if ( isset_readmask( readmask, readId ) )
                    {
                        if ( ++q > FastqArgs.maxReads )
                        {
                            unset_readmask( readmask, 1 << readId );
                        }
                        else
                        {
                            SRA_DUMP_DBG( 3, ( " %u", readId ) );
                        }
                    }
                }
                *key = "";
                SRA_DUMP_DBG( 3, ( " key '%s'\n", *key ) );
            }
        }
        else if ( GetRCObject( rc ) == rcRow && GetRCState( rc ) == rcNotFound )
        {
            SRA_DUMP_DBG( 3, ( "%s skipped %u row\n", __func__, spot ) );
            rc = 0;
        }
    }
    return rc;
}


static rc_t FastqRNumberFilter_Release( const SRASplitter* cself )
{
    rc_t rc = 0;
    FastqRNumberFilter * self = ( FastqRNumberFilter * )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcNode, rcExecuting, rcParam, rcInvalid );
    }
    else
    {
        if ( self->rejected_reads > 0 && !g_legacy_report )
            rc = KOutMsg( "Rejected %lu READS because of max. number of READS = %u\n", self->rejected_reads, FastqArgs.maxReads );
    }
    return rc;
}

typedef struct FastqRNumberFilterFactory_struct
{
    const char* accession;
    const SRATable* table;
    const FastqReader* reader;
} FastqRNumberFilterFactory;


static rc_t FastqRNumberFilterFactory_Init( const SRASplitterFactory* cself )
{
    rc_t rc = 0;
    FastqRNumberFilterFactory* self = ( FastqRNumberFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = FastqReaderMake( &self->reader, self->table, self->accession,
                              /* preserve orig spot format to save on conversions */
                              FastqArgs.is_platform_cs_native, false, FastqArgs.fasta > 0, false, 
                              false, !FastqArgs.applyClip, FastqArgs.SuppressQualForCSKey, 0,
                              FastqArgs.offset, '\0', 0, 0 );
    }
    return rc;
}


static rc_t FastqRNumberFilterFactory_NewObj( const SRASplitterFactory* cself, const SRASplitter** splitter )
{
    rc_t rc = 0;
    FastqRNumberFilterFactory* self = ( FastqRNumberFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcExecuting, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitter_Make( splitter, sizeof( FastqRNumberFilter ),
                               FastqRNumberFilter_GetKey, NULL, NULL, FastqRNumberFilter_Release );
        if ( rc == 0 )
        {
            FastqRNumberFilter * filter = ( FastqRNumberFilter * )( * splitter );
            filter->reader = self->reader;
            filter->rejected_reads = 0;
        }
    }
    return rc;
}


static void FastqRNumberFilterFactory_Release( const SRASplitterFactory* cself )
{
    if ( cself != NULL )
    {
        FastqRNumberFilterFactory* self = ( FastqRNumberFilterFactory* )cself;
        FastqReaderWhack( self->reader );
    }
}


static rc_t FastqRNumberFilterFactory_Make( const SRASplitterFactory** cself,
                                const char* accession, const SRATable* table )
{
    rc_t rc = 0;
    FastqRNumberFilterFactory* obj = NULL;

    if ( cself == NULL || accession == NULL || table == NULL )
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitterFactory_Make( cself, eSplitterSpot, sizeof( *obj ),
                                      FastqRNumberFilterFactory_Init,
                                      FastqRNumberFilterFactory_NewObj,
                                      FastqRNumberFilterFactory_Release );
        if ( rc == 0 )
        {
            obj = ( FastqRNumberFilterFactory* )*cself;
            obj->accession = accession;
            obj->table = table;
        }
    }
    return rc;
}

/* ============== FASTQ quality filter ============================ */

typedef struct FastqQFilter_struct
{
    const FastqReader * reader;
    KDataBuffer * buffer_for_read_column;
    KDataBuffer * buffer_for_quality;
    uint64_t rejected_spots;
    uint64_t rejected_reads;
} FastqQFilter;


#define MIN_QUAL_FOR_RULE_3 ( 33 + 2 )

static bool QFilter_Test_new( const char * read, const char * quality, uint32_t readlen, uint32_t minlen, char N_char )
{
    uint32_t idx, cnt, cnt1, start;
    char b0;

    /* 1st criteria : READ has to be longer than the minlen */
    if ( readlen < minlen ) return false;

    /* 2nd criteria : READ does not contain any N's in the first minlen bases */
    for ( idx = 0; idx < minlen; ++idx )
    {
        if ( read[ idx ] == N_char ) return false;
    }

    start = ( N_char == '.' ) ? 1 : 0;
    /* 3rd criteria : QUALITY values are all 2 or higher in the first minlen values */
    for ( idx = start; idx < minlen; ++idx )
    {
        if ( quality[ idx ] < MIN_QUAL_FOR_RULE_3 ) return false;
    }

    /* 4th criteria : READ contains more than one type of base in the first minlen bases */
    b0 = read[ 0 ];
    for ( idx = 1, cnt = 1; idx < minlen; ++idx )
    {
        if ( read[ idx ] == b0 ) cnt++;
    }
    if ( cnt == minlen ) return false;

    /* 5th criteria : READ does not contain more than 50% N's in its whole length */
    cnt = ( readlen / 2 );
    for ( idx = 0, cnt1 = 0; idx < readlen; ++idx )
    {
        if ( read[ idx ] == N_char ) cnt1++;
    }
    if ( cnt1 > cnt ) return false;

    /* 6th criteria : READ does not contain values other than ACGTN in its whole length */
    if ( N_char != '.' )
    {
        for ( idx = 0; idx < readlen; ++idx )
        {
            if ( ! ( ( read[ idx ] == 'A' ) || ( read[ idx ] == 'C' ) || ( read[ idx ] == 'G' ) ||
                    ( read[ idx ] == 'T' ) || ( read[ idx ] == 'N' ) ) )
                return false;
        }
    }

    return true;
}


static bool QFilter_Test_old( const char * read, uint32_t readlen, bool cs_native )
{
    static char const* const baseStr = "NNNNNNNNNN";
    static char const* const colorStr = "..........";
    static const uint32_t strLen = 10;
    uint32_t xLen = readlen < strLen ? readlen : strLen;

    if ( cs_native )
    {
        if ( strncmp( &read[ 1 ], colorStr, xLen ) == 0 || strcmp( &read[ readlen - xLen + 1 ], colorStr ) == 0 )
            return false;
    }
    else
    {
        if ( strncmp( read, baseStr, xLen ) == 0 || strcmp( &read[ readlen - xLen ], baseStr ) == 0 )
            return false;
    }
    return true;
}


/* filter out reads by leading/trialing quality */
static rc_t FastqQFilter_GetKey( const SRASplitter* cself, const char** key,
                                 spotid_t spot, readmask_t* readmask )
{
    rc_t rc = 0;
    FastqQFilter* self = ( FastqQFilter* )cself;

    if ( self == NULL || key == NULL )
    {
        rc = RC( rcExe, rcNode, rcExecuting, rcParam, rcInvalid );
    }
    else
    {
        uint32_t num_reads = 0, spot_len;

        *key = NULL;
        rc = FastqReaderSeekSpot( self->reader, spot );
        if ( rc == 0 )
        {
            rc = FastqReader_SpotInfo( self->reader, NULL, NULL, NULL, NULL, &spot_len, &num_reads );
            if ( rc == 0 )
            {
                SRA_DUMP_DBG( 3, ( "%s %u row reads: ", __func__, spot ) );
                if ( FastqArgs.split_spot )
                {
                    uint32_t readId;
                    INSDC_coord_len read_len;
                    for ( readId = 0; rc == 0 && readId < num_reads; readId++ )
                    {
                        if ( isset_readmask( readmask, readId ) )
                        {
                            rc = FastqReader_SpotReadInfo( self->reader, readId + 1, NULL, NULL, NULL, NULL, &read_len );
                            if ( rc == 0 )
                            {
                                /* FastqReaderBase() in libsra! libs/sra/fastq.h 
                                   IF_BUF ... very, very bad macro defined in factory.h !!
                                   it combines reading from table with resizing of a KDatabuffer in a loop until rc == 0 is reached!
                                */
                                IF_BUF( ( FastqReaderBase( self->reader, readId + 1,
                                          self->buffer_for_read_column->base,
                                          KDataBufferBytes( self->buffer_for_read_column ), NULL) ),
                                          self->buffer_for_read_column, read_len )
                                {
                                    const char * b = self->buffer_for_read_column->base;
                                    bool filter_passed = true;

                                    if ( FastqArgs.qual_filter1 )
                                    {
                                        if ( quality_N_limit > 0 )
                                        {
                                            IF_BUF( ( FastqReaderQuality( self->reader, readId + 1,
                                                      self->buffer_for_quality->base,
                                                      KDataBufferBytes( self->buffer_for_quality ), NULL) ),
                                                      self->buffer_for_quality, read_len )
                                            {
                                                const char * q = self->buffer_for_quality->base;
                                                char N_char = FastqArgs.is_platform_cs_native ? '.' : 'N';
                                                filter_passed = QFilter_Test_new( b, q, read_len, quality_N_limit, N_char );
                                            }
                                        }
                                    }
                                    else
                                        filter_passed = QFilter_Test_old( b, read_len, FastqArgs.is_platform_cs_native );

                                    if ( filter_passed )
                                        SRA_DUMP_DBG( 3, ( " %u", readId ) );
                                    else
                                    {
                                        unset_readmask( readmask, readId );
                                        /* READ did not pass filter */
                                        self->rejected_reads ++;
                                    }
                                }
                            }
                        }
                    }
                    *key = "";
                }
                else
                {
                    IF_BUF( ( FastqReaderBase( self->reader, 0, self->buffer_for_read_column->base,
                              KDataBufferBytes( self->buffer_for_read_column ), NULL ) ), self->buffer_for_read_column, spot_len )
                    {
                        const char* b = self->buffer_for_read_column->base;
                        bool filter_passed = true;

                        if ( FastqArgs.qual_filter1 )
                        {
                            if ( quality_N_limit > 0 )
                            {
                                IF_BUF( ( FastqReaderQuality( self->reader, 0, self->buffer_for_quality->base,
                                          KDataBufferBytes( self->buffer_for_quality ), NULL ) ), self->buffer_for_quality, spot_len )
                                {
                                    const char * q = self->buffer_for_quality->base;
                                    char N_char = FastqArgs.is_platform_cs_native ? '.' : 'N';
                                    filter_passed = QFilter_Test_new( b, q, spot_len, quality_N_limit, N_char );
                                }
                            }
                        }
                        else
                            filter_passed = QFilter_Test_old( b, spot_len, FastqArgs.is_platform_cs_native );

                        if ( filter_passed )
                        {
                            *key = "";
                            SRA_DUMP_DBG( 3, ( " whole spot" ) );
                        }
                        else
                        {
                            /* SPOT did not pass filter */
                            self->rejected_spots ++;
                        }
                    }
                }
                SRA_DUMP_DBG( 3, ( " key '%s'\n", *key ) );
            }
        }
        else if ( GetRCObject( rc ) == rcRow && GetRCState( rc ) == rcNotFound )
        {
            SRA_DUMP_DBG( 3, ( "%s skipped %u row\n", __func__, spot ) );
            rc = 0;
        }
    }
    return rc;
}


static rc_t FastqQFilter_Release( const SRASplitter * cself )
{
    rc_t rc = 0;
    FastqQFilter* self = ( FastqQFilter* )cself;

    if ( self == NULL )
        rc = RC( rcExe, rcNode, rcExecuting, rcParam, rcInvalid );
    else if ( !g_legacy_report )
    {
        if ( self->rejected_reads > 0 )
            rc = KOutMsg( "Rejected %lu READS because of Quality-Filtering\n", self->rejected_reads );
        if ( rc == 0 && self->rejected_spots > 0 )
            rc = KOutMsg( "Rejected %lu SPOTS because of Quality-Filtering\n", self->rejected_spots );

    }
    return rc;
}


typedef struct FastqQFilterFactory_struct
{
    const char* accession;
    const SRATable* table;
    const FastqReader* reader;
    KDataBuffer kdbuf;
    KDataBuffer kdbuf2;
} FastqQFilterFactory;


static rc_t FastqQFilterFactory_Init( const SRASplitterFactory* cself )
{
    rc_t rc = 0;
    FastqQFilterFactory* self = ( FastqQFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = KDataBufferMakeBytes( &self->kdbuf, DATABUFFERINITSIZE );
        if ( rc == 0 )
        {
            rc = KDataBufferMakeBytes( &self->kdbuf2, DATABUFFERINITSIZE );
            if ( rc == 0 )
            {
                rc = FastqReaderMake( &self->reader, self->table, self->accession,
                             /* preserve orig spot format to save on conversions */
                             FastqArgs.is_platform_cs_native, false, FastqArgs.fasta > 0, false, 
                             false, !FastqArgs.applyClip, FastqArgs.SuppressQualForCSKey, 0,
                             FastqArgs.offset, '\0', 0, 0 );
            }
        }
    }
    return rc;
}


static rc_t FastqQFilterFactory_NewObj( const SRASplitterFactory* cself, const SRASplitter** splitter )
{
    rc_t rc = 0;
    FastqQFilterFactory* self = ( FastqQFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcExecuting, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitter_Make( splitter, sizeof( FastqQFilter ), FastqQFilter_GetKey, NULL, NULL, FastqQFilter_Release );
        if ( rc == 0 )
        {
            FastqQFilter * filter = ( FastqQFilter * )( * splitter );
            filter->reader = self->reader;
            filter->buffer_for_read_column = &self->kdbuf;
            filter->buffer_for_quality = &self->kdbuf2;
            filter->rejected_spots = 0;
            filter->rejected_reads = 0;
        }
    }
    return rc;
}


static void FastqQFilterFactory_Release( const SRASplitterFactory* cself )
{
    if ( cself != NULL )
    {
        FastqQFilterFactory* self = ( FastqQFilterFactory* )cself;
        KDataBufferWhack( &self->kdbuf );
        KDataBufferWhack( &self->kdbuf2 );
        FastqReaderWhack( self->reader );
    }
}


static rc_t FastqQFilterFactory_Make( const SRASplitterFactory** cself,
                                      const char* accession, const SRATable* table )
{
    rc_t rc = 0;
    FastqQFilterFactory* obj = NULL;

    if ( cself == NULL || accession == NULL || table == NULL )
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitterFactory_Make( cself, eSplitterSpot, sizeof( *obj ),
                                      FastqQFilterFactory_Init,
                                      FastqQFilterFactory_NewObj,
                                      FastqQFilterFactory_Release );
        if ( rc == 0 )
        {
            obj = ( FastqQFilterFactory* )*cself;
            obj->accession = accession;
            obj->table = table;
        }
    }
    return rc;
}


/* ============== FASTQ min read length filter ============================ */


typedef struct FastqReadLenFilter_struct
{
    const FastqReader* reader;
    uint64_t rejected_spots;
    uint64_t rejected_reads;
} FastqReadLenFilter;


static rc_t FastqReadLenFilter_GetKey( const SRASplitter* cself, const char** key,
                                       spotid_t spot, readmask_t* readmask )
{
    rc_t rc = 0;
    FastqReadLenFilter* self = ( FastqReadLenFilter* )cself;

    if ( self == NULL || key == NULL )
    {
        rc = RC( rcExe, rcNode, rcExecuting, rcParam, rcInvalid );
    }
    else
    {
        uint32_t num_reads = 0, spot_len = 0;

        *key = NULL;
        rc = FastqReaderSeekSpot( self->reader, spot );
        if ( rc == 0 )
        {
            rc = FastqReader_SpotInfo( self->reader, NULL, NULL, NULL, NULL, &spot_len, &num_reads );
            if ( rc == 0 )
            {
                SRA_DUMP_DBG( 3, ( "%s %u row reads:", __func__, spot ) );
                if ( FastqArgs.split_spot )
                {
                    uint32_t readId;
                    INSDC_coord_len read_len = 0;
                    for ( readId = 0; rc == 0 && readId < num_reads; readId++ )
                    {
                        if ( isset_readmask( readmask, readId ) )
                        {
                            rc = FastqReader_SpotReadInfo( self->reader, readId + 1, NULL, NULL, NULL, NULL, &read_len );
                            if ( rc == 0 )
                            {
                                if ( read_len < FastqArgs.minReadLen )
                                {
                                    unset_readmask( readmask, readId );
                                    self->rejected_reads ++;
                                }
                                else
                                {
                                    SRA_DUMP_DBG( 3, ( " %u", readId ) );
                                }
                            }
                        }
                    }
                    *key = "";
                }
                else
                {
                    if ( spot_len >= FastqArgs.minReadLen )
                    {
                        *key = "";
                        SRA_DUMP_DBG( 3, ( " whole spot" ) );
                    }
                    else
                        self->rejected_spots ++;
                }
                SRA_DUMP_DBG( 3, ( "\n" ) );
            }
        }
        else if ( GetRCObject( rc ) == rcRow && GetRCState( rc ) == rcNotFound )
        {
            SRA_DUMP_DBG( 3, ( "%s skipped %u row\n", __func__, spot ) );
            rc = 0;
        }
    }
    return rc;
}


static rc_t FastqReadLenFilter_Release( const SRASplitter * cself )
{
    rc_t rc = 0;
    FastqReadLenFilter * self = ( FastqReadLenFilter* )cself;

    if ( self == NULL )
        rc = RC( rcExe, rcNode, rcExecuting, rcParam, rcInvalid );
    else if ( !g_legacy_report )
    {
        if ( self->rejected_reads > 0 )
            rc = KOutMsg( "Rejected %lu READS because READLEN < %u\n", self->rejected_reads, FastqArgs.minReadLen );
        if ( self->rejected_spots > 0 && rc == 0 )
            rc = KOutMsg( "Rejected %lu SPOTS because SPOTLEN < %u\n", self->rejected_spots, FastqArgs.minReadLen );
    }
    return rc;
}


typedef struct FastqReadLenFilterFactory_struct
{
    const char* accession;
    const SRATable* table;
    const FastqReader* reader;
} FastqReadLenFilterFactory;


static rc_t FastqReadLenFilterFactory_Init( const SRASplitterFactory* cself )
{
    rc_t rc = 0;
    FastqReadLenFilterFactory* self = ( FastqReadLenFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = FastqReaderMake( &self->reader, self->table, self->accession,
                             /* preserve orig spot format to save on conversions */
                              FastqArgs.is_platform_cs_native, false, FastqArgs.fasta > 0, false, 
                              false, !FastqArgs.applyClip, FastqArgs.SuppressQualForCSKey, 0,
                              FastqArgs.offset, '\0', 0, 0 );
    }
    return rc;
}


static rc_t FastqReadLenFilterFactory_NewObj( const SRASplitterFactory* cself, const SRASplitter** splitter )
{
    rc_t rc = 0;
    FastqReadLenFilterFactory* self = ( FastqReadLenFilterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcExecuting, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitter_Make( splitter, sizeof( FastqReadLenFilter ),
                               FastqReadLenFilter_GetKey, NULL, NULL, FastqReadLenFilter_Release );
        if ( rc == 0 )
        {
            FastqReadLenFilter * filter = ( FastqReadLenFilter* )( *splitter );
            filter->reader = self->reader;
            filter->rejected_spots = 0;
            filter->rejected_reads = 0;
        }
    }
    return rc;
}


static void FastqReadLenFilterFactory_Release( const SRASplitterFactory* cself )
{
    if ( cself != NULL )
    {
        FastqReadLenFilterFactory* self = ( FastqReadLenFilterFactory* )cself;
        FastqReaderWhack( self->reader );
    }
}


static rc_t FastqReadLenFilterFactory_Make( const SRASplitterFactory** cself,
                            const char* accession, const SRATable* table )
{
    rc_t rc = 0;
    FastqReadLenFilterFactory* obj = NULL;

    if ( cself == NULL || accession == NULL || table == NULL )
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitterFactory_Make( cself, eSplitterSpot, sizeof( *obj ),
                                      FastqReadLenFilterFactory_Init,
                                      FastqReadLenFilterFactory_NewObj,
                                      FastqReadLenFilterFactory_Release );
        if ( rc == 0 )
        {
            obj = ( FastqReadLenFilterFactory* )*cself;
            obj->accession = accession;
            obj->table = table;
        }
    }
    return rc;
}


/* ============== FASTQ read splitter ============================ */

char* FastqReadSplitter_key_buf = NULL;


typedef struct FastqReadSplitter_struct
{
    const FastqReader* reader;
    SRASplitter_Keys* keys;
    uint32_t keys_max;
} FastqReadSplitter;


static rc_t FastqReadSplitter_GetKeySet( const SRASplitter* cself, const SRASplitter_Keys** key,
                    uint32_t* keys, spotid_t spot, const readmask_t* readmask )
{
    rc_t rc = 0;
    FastqReadSplitter* self = ( FastqReadSplitter* )cself;
    const size_t key_offset = 5;

    if ( self == NULL || key == NULL )
    {
        rc = RC( rcExe, rcNode, rcExecuting, rcParam, rcInvalid );
    }
    else
    {
        uint32_t num_reads = 0;

        *keys = 0;
        if ( FastqReadSplitter_key_buf == NULL )
        {
            /* initial alloc key_buf: "  1\0  2\0...\0  9\0 10\0 11\0...\03220..\08192\0" */
            if ( nreads_max > 9999 )
            {
                /* key_offset and sprintf format size are insufficient for keys longer than 4 digits */
                rc = RC( rcExe, rcNode, rcExecuting, rcBuffer, rcInsufficient );
            }
            else
            {
                FastqReadSplitter_key_buf = malloc( nreads_max * key_offset );
                if ( FastqReadSplitter_key_buf == NULL )
                {
                    rc = RC( rcExe, rcNode, rcExecuting, rcMemory, rcExhausted );
                }
                else
                {
                    /* fill buffer w/keys */
                    int i;
                    char* p = FastqReadSplitter_key_buf;
                    for ( i = 1; rc == 0 && i <= nreads_max; i++ )
                    {
                        if ( sprintf( p, "%4u", i ) <= 0 )
                        {
                            rc = RC( rcExe, rcNode, rcExecuting, rcTransfer, rcIncomplete );
                        }
                        p += key_offset;
                    }
                }
            }
        }

        if ( rc == 0 )
        {
            rc = FastqReaderSeekSpot( self->reader, spot );
            if ( rc == 0 )
            {
                rc = FastqReader_SpotInfo( self->reader, NULL, NULL, NULL, NULL, NULL, &num_reads );
                if ( rc == 0 )
                {
                    uint32_t readId, good = 0;

                    SRA_DUMP_DBG( 3, ( "%s %u row reads:", __func__, spot ) );
                    for ( readId = 0; rc == 0 && readId < num_reads; readId++ )
                    {
                        rc = FastqReader_SpotReadInfo( self->reader, readId + 1, NULL, NULL, NULL, NULL, NULL );
                        if ( !isset_readmask( readmask, readId ) )
                        {
                            continue;
                        }
                        if ( self->keys_max < ( good + 1 ) )
                        {
                            void* p = realloc( self->keys, sizeof( *self->keys ) * ( good + 1 ) );
                            if ( p == NULL )
                            {
                                rc = RC( rcExe, rcNode, rcExecuting, rcMemory, rcExhausted );
                                break;
                            }
                            else
                            {
                                self->keys = p;
                                self->keys_max = good + 1;
                            }
                        }
                        self->keys[ good ].key = &FastqReadSplitter_key_buf[ readId * key_offset ];
                        while ( self->keys[ good ].key[ 0 ] == ' ' && self->keys[ good ].key[0] != '\0' )
                        {
                            self->keys[ good ].key++;
                        }
                        clear_readmask( self->keys[ good ].readmask );
                        set_readmask( self->keys[good].readmask, readId );
                        SRA_DUMP_DBG( 3, ( " key['%s']+=%u", self->keys[ good ].key, readId ) );
                        good++;
                    }
                    if ( rc == 0 )
                    {
                        *key = self->keys;
                        *keys = good;
                    }
                    SRA_DUMP_DBG( 3, ( "\n" ) );
                }
            }
            else if ( GetRCObject( rc ) == rcRow && GetRCState( rc ) == rcNotFound )
            {
                SRA_DUMP_DBG( 3, ( "%s skipped %u row\n", __func__, spot ) );
                rc = 0;
            }
        }
        else if ( GetRCObject( rc ) == rcRow && GetRCState( rc ) == rcNotFound )
        {
                SRA_DUMP_DBG( 3, ( "%s skipped %u row\n", __func__, spot ) );
                rc = 0;
        }
    }
    return rc;
}


rc_t FastqReadSplitter_Release( const SRASplitter* cself )
{
    if ( cself != NULL )
    {
        FastqReadSplitter* self = ( FastqReadSplitter* )cself;
        free( self->keys );
    }
    return 0;
}


typedef struct FastqReadSplitterFactory_struct
{
    const char* accession;
    const SRATable* table;
    const FastqReader* reader;
} FastqReadSplitterFactory;


static rc_t FastqReadSplitterFactory_Init( const SRASplitterFactory* cself )
{
    rc_t rc = 0;
    FastqReadSplitterFactory* self = ( FastqReadSplitterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = FastqReaderMake( &self->reader, self->table, self->accession,
                              /* preserve orig spot format to save on conversions */
                              FastqArgs.is_platform_cs_native, false, FastqArgs.fasta > 0, false, 
                              false, !FastqArgs.applyClip, FastqArgs.SuppressQualForCSKey, 0,
                              FastqArgs.offset, '\0', 0, 0 );
    }
    return rc;
}


static rc_t FastqReadSplitterFactory_NewObj( const SRASplitterFactory* cself, const SRASplitter** splitter )
{
    rc_t rc = 0;
    FastqReadSplitterFactory* self = ( FastqReadSplitterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcExecuting, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitter_Make( splitter, sizeof( FastqReadSplitter ), NULL,
                               FastqReadSplitter_GetKeySet, NULL, FastqReadSplitter_Release );
        if ( rc == 0 )
        {
            ( (FastqReadSplitter*)(*splitter) )->reader = self->reader;
        }
    }
    return rc;
}


static void FastqReadSplitterFactory_Release( const SRASplitterFactory* cself )
{
    if ( cself != NULL )
    {
        FastqReadSplitterFactory* self = ( FastqReadSplitterFactory* )cself;
        FastqReaderWhack( self->reader );
        free( FastqReadSplitter_key_buf );
        FastqReadSplitter_key_buf = NULL;
    }
}


static rc_t FastqReadSplitterFactory_Make( const SRASplitterFactory** cself,
                const char* accession, const SRATable* table )
{
    rc_t rc = 0;
    FastqReadSplitterFactory* obj = NULL;

    if ( cself == NULL || accession == NULL || table == NULL )
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitterFactory_Make( cself, eSplitterRead, sizeof( *obj ),
                                      FastqReadSplitterFactory_Init,
                                      FastqReadSplitterFactory_NewObj,
                                      FastqReadSplitterFactory_Release );
        if ( rc == 0 )
        {
            obj = ( FastqReadSplitterFactory* )*cself;
            obj->accession = accession;
            obj->table = table;
        }
    }
    return rc;
}


/* ============== FASTQ 3 read splitter ============================ */

char* Fastq3ReadSplitter_key_buf = NULL;

typedef struct Fastq3ReadSplitter_struct
{
    const FastqReader* reader;
    SRASplitter_Keys keys[ 2 ];
} Fastq3ReadSplitter;


/* if all active reads len >= minreadlen, reads are splitted into separate files, otherwise on single key "" is returnded for all reads */
static rc_t Fastq3ReadSplitter_GetKeySet( const SRASplitter* cself, const SRASplitter_Keys** key,
            uint32_t* keys, spotid_t spot, const readmask_t* readmask )
{
    rc_t rc = 0;
    Fastq3ReadSplitter* self = ( Fastq3ReadSplitter* )cself;
    const size_t key_offset = 5;

    if ( self == NULL || key == NULL )
    {
        rc = RC( rcExe, rcNode, rcExecuting, rcParam, rcInvalid );
    }
    else
    {
        uint32_t num_reads = 0;

        *keys = 0;
        if ( Fastq3ReadSplitter_key_buf == NULL )
        {
            /* initial alloc key_buf: "  1\0  2\0...\0  9\0 10\0 11\0...\03220..\08192\0" */
            if ( nreads_max > 9999 )
            {
                /* key_offset and sprintf format size are insufficient for keys longer than 4 digits */
                rc = RC( rcExe, rcNode, rcExecuting, rcBuffer, rcInsufficient );
            }
            else
            {
                Fastq3ReadSplitter_key_buf = malloc( nreads_max * key_offset );
                if ( Fastq3ReadSplitter_key_buf == NULL )
                {
                    rc = RC( rcExe, rcNode, rcExecuting, rcMemory, rcExhausted );
                }
                else
                {
                    /* fill buffer w/keys */
                    int i;
                    char* p = Fastq3ReadSplitter_key_buf;
                    for ( i = 1; rc == 0 && i <= nreads_max; i++ )
                    {
                        if ( sprintf( p, "%4u", i ) <= 0 )
                        {
                            rc = RC( rcExe, rcNode, rcExecuting, rcTransfer, rcIncomplete );
                        }
                        p += key_offset;
                    }
                }
            }
        }

        if ( rc == 0 )
        {
            rc = FastqReaderSeekSpot( self->reader, spot );
            if ( rc == 0 )
            {
                rc = FastqReader_SpotInfo( self->reader, NULL, NULL, NULL, NULL, NULL, &num_reads );
                if ( rc == 0 )
                {
                    uint32_t readId, good  = 0;
                    const uint32_t max_reads = sizeof( self->keys ) /sizeof( self->keys[ 0 ] );

                    SRA_DUMP_DBG( 3, ( "%s %u row reads:", __func__, spot ) );
                    for ( readId = 0; rc == 0 && readId < num_reads && good < max_reads; readId++ )
                    {
                        rc = FastqReader_SpotReadInfo( self->reader, readId + 1, NULL, NULL, NULL, NULL, NULL );
                        if ( !isset_readmask( readmask, readId ) )
                        {
                            continue;
                        }
                        self->keys[ good ].key = &Fastq3ReadSplitter_key_buf[ good * key_offset ];
                        while ( self->keys[ good ].key[ 0 ] == ' ' && self->keys[good].key[ 0 ] != '\0' )
                        {
                            self->keys[ good ].key++;
                        }
                        clear_readmask( self->keys[ good ].readmask );
                        set_readmask( self->keys[ good ].readmask, readId );
                        SRA_DUMP_DBG( 3, ( " key['%s']+=%u", self->keys[ good ].key, readId ) );
                        good++;
                    }
                    if ( rc == 0 )
                    {
                        *key = self->keys;
                        *keys = good;
                        if ( good != max_reads )
                        {
                            /* some are short -> reset keys to same value for all valid reads */
                            /* run has just one read -> no suffix */
                            /* or single file was requested */
                            for ( readId = 0; readId < good; readId++ )
                            {
                                self->keys[ readId ].key = "";
                            }
                            SRA_DUMP_DBG( 3, ( " all keys joined to ''" ) );
                        }
                    }
                    SRA_DUMP_DBG( 3, ( "\n" ) );
                }
            }
            else if ( GetRCObject( rc ) == rcRow && GetRCState( rc ) == rcNotFound )
            {
                SRA_DUMP_DBG( 3, ( "%s skipped %u row\n", __func__, spot ) );
                rc = 0;
            }
        }
        else if ( GetRCObject( rc ) == rcRow && GetRCState( rc ) == rcNotFound )
        {
            SRA_DUMP_DBG( 3, ( "%s skipped %u row\n", __func__, spot ) );
            rc = 0;
        }
    }
    return rc;
}

typedef struct Fastq3ReadSplitterFactory_struct
{
    const char* accession;
    const SRATable* table;
    const FastqReader* reader;
} Fastq3ReadSplitterFactory;


static rc_t Fastq3ReadSplitterFactory_Init( const SRASplitterFactory* cself )
{
    rc_t rc = 0;
    Fastq3ReadSplitterFactory* self = ( Fastq3ReadSplitterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = FastqReaderMake( &self->reader, self->table, self->accession,
                              /* preserve orig spot format to save on conversions */
                              FastqArgs.is_platform_cs_native, false, FastqArgs.fasta > 0, false, 
                              false, !FastqArgs.applyClip, FastqArgs.SuppressQualForCSKey, 0,
                              FastqArgs.offset, '\0', 0, 0 );
    }
    return rc;
}


static rc_t Fastq3ReadSplitterFactory_NewObj( const SRASplitterFactory* cself, const SRASplitter** splitter )
{
    rc_t rc = 0;
    Fastq3ReadSplitterFactory* self = ( Fastq3ReadSplitterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcExecuting, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitter_Make( splitter, sizeof( Fastq3ReadSplitter ),
                               NULL, Fastq3ReadSplitter_GetKeySet, NULL, NULL );
        if ( rc == 0 )
        {
            ( (Fastq3ReadSplitter*)(*splitter) )->reader = self->reader;
        }
    }
    return rc;
}


static void Fastq3ReadSplitterFactory_Release( const SRASplitterFactory* cself )
{
    if ( cself != NULL )
    {
        Fastq3ReadSplitterFactory* self = ( Fastq3ReadSplitterFactory* )cself;
        FastqReaderWhack( self->reader );
        free( Fastq3ReadSplitter_key_buf );
    }
}


static rc_t Fastq3ReadSplitterFactory_Make( const SRASplitterFactory** cself,
                    const char* accession, const SRATable* table )
{
    rc_t rc = 0;
    Fastq3ReadSplitterFactory* obj = NULL;

    if ( cself == NULL || accession == NULL || table == NULL ) 
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitterFactory_Make( cself, eSplitterRead, sizeof( *obj ),
                                      Fastq3ReadSplitterFactory_Init,
                                      Fastq3ReadSplitterFactory_NewObj,
                                      Fastq3ReadSplitterFactory_Release );
        if ( rc == 0 )
        {
            obj = ( Fastq3ReadSplitterFactory* )*cself;
            obj->accession = accession;
            obj->table = table;
        }
    }
    return rc;
}


/* ============== FASTQ formatter object  ============================ */


typedef struct FastqFormatterSplitter_struct
{
    const char* accession;
    const FastqReader* reader;
    KDataBuffer* b[ 5 ];
    size_t bsz[ 5 ]; /* fifth is for fasta line wrap */
} FastqFormatterSplitter;


static rc_t FastqFormatterSplitter_WrapLine( const KDataBuffer* src, size_t src_sz,
                                             KDataBuffer* dst, size_t* dst_sz, const uint64_t width )
{
    rc_t rc = 0;
    size_t sz = src_sz + ( src_sz - 1 ) / width;

    if ( KDataBufferBytes( dst ) < sz )
    {
        SRA_DUMP_DBG( 10, ( "%s grow buffer from %u to %u\n", __func__, KDataBufferBytes( dst ), sz + 10 ) );
        rc = KDataBufferResize( dst, sz + 10 );
    }
    if ( rc == 0 )
    {
        const char* s = src->base;
        char* d = dst->base;
        *dst_sz = sz = src_sz;
        while ( sz > 0 )
        {
            memmove( d, s, sz > width ? width : sz );
            if ( sz <= width )
            {
                break;
            }
            d += width;
            *d++ = '\n';
            *dst_sz = *dst_sz + 1;
            s += width;
            sz -= width;
        }
    }
    return rc;
}


static rc_t FastqFormatterSplitter_DumpByRead( const SRASplitter* cself, spotid_t spot, const readmask_t* readmask )
{
    rc_t rc = 0;
    FastqFormatterSplitter* self = ( FastqFormatterSplitter* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcExecuting, rcParam, rcNull );
    }
    else 
    {
        rc = FastqReaderSeekSpot( self->reader, spot );
        if ( rc == 0 )
        {
            rc = SRASplitter_FileActivate( cself, FastqArgs.file_extension );
            if ( rc == 0 )
            {
                DeflineData def_data;
                const char* spot_name = NULL, *spot_group = NULL, *read_name = NULL;
                uint32_t readIdx, spot_len = 0;
                uint32_t num_reads, readId, k;
                size_t sname_sz, sgrp_sz;
                INSDC_coord_len rlabel_sz = 0, read_len = 0;

                if ( FastqArgs.b_defline || FastqArgs.q_defline )
                {
                    rc = FastqReader_SpotInfo( self->reader, &spot_name, &sname_sz, &spot_group, &sgrp_sz, &spot_len, &num_reads );
                }
                else
                {
                    rc = FastqReader_SpotInfo( self->reader, NULL, NULL, NULL, NULL, NULL, &num_reads );
                }

                for ( readId = 1, readIdx = 1; rc == 0 && readId <= num_reads; readId++, readIdx++ )
                {
                    if ( !isset_readmask( readmask, readId - 1 ) )
                    {
                        continue;
                    }
                    if ( FastqArgs.b_defline || FastqArgs.q_defline )
                    {
                        rc = FastqReader_SpotReadInfo( self->reader, readId, NULL, &read_name, &rlabel_sz, NULL, &read_len );
                        if ( rc == 0 )
                        {
                            rc = Defline_Bind( &def_data, self->accession, &spot, spot_name, sname_sz, spot_group, sgrp_sz,
                                               &spot_len, &readIdx, read_name, rlabel_sz, &read_len );
                        }
                    }
                    if ( rc == 0 )
                    {
                        if ( FastqArgs.b_defline )
                        {
                            IF_BUF( ( Defline_Build( FastqArgs.b_defline, &def_data, self->b[0]->base,
                                      KDataBufferBytes( self->b[0] ), &self->bsz[0] ) ), self->b[0], self->bsz[0] );
                        }
                        else
                        {
                            IF_BUF( ( FastqReaderBaseName( self->reader, readId, &FastqArgs.dumpCs, self->b[0]->base,
                                      KDataBufferBytes( self->b[0] ), &self->bsz[0] ) ), self->b[0], self->bsz[0] );
                        }
                    }
                    if ( rc == 0 )
                    {
                        if ( FastqArgs.fasta > 0 )
                        {
                            IF_BUF( ( FastqReaderBase( self->reader, readId, self->b[4]->base, KDataBufferBytes( self->b[4] ),
                                      &self->bsz[4] ) ), self->b[4], self->bsz[4] )
                            {
                                rc = FastqFormatterSplitter_WrapLine( self->b[4], self->bsz[4], self->b[1], &self->bsz[1], FastqArgs.fasta );
                            }
                        }
                        else
                        {
                            IF_BUF( ( FastqReaderBase( self->reader, readId, self->b[1]->base,
                                      KDataBufferBytes( self->b[1] ), &self->bsz[1] ) ), self->b[1], self->bsz[1] );
                        }
                    }
                    if ( !FastqArgs.fasta && rc == 0 )
                    {
                        if ( FastqArgs.q_defline )
                        {
                            IF_BUF( ( Defline_Build( FastqArgs.q_defline, &def_data, self->b[2]->base,
                                      KDataBufferBytes( self->b[2] ), &self->bsz[2] ) ), self->b[2], self->bsz[2] );
                        }
                        else
                        {
                            IF_BUF( ( FastqReaderQualityName( self->reader, readId, &FastqArgs.dumpCs, self->b[2]->base,
                                      KDataBufferBytes( self->b[2] ), &self->bsz[2] ) ), self->b[2], self->bsz[2] );
                        }
                        if ( rc == 0 )
                        {
                            IF_BUF( ( FastqReaderQuality( self->reader, readId, self->b[3]->base,
                                      KDataBufferBytes( self->b[3] ), &self->bsz[3] ) ), self->b[3], self->bsz[3] );
                        }
                    }
                    else if ( ( (char*)(self->b[0]->base))[0] == '@' )
                    {
                        ( (char*)(self->b[0]->base) )[0] = '>';
                    }
                    for ( k = 0; rc == 0 && k < ( FastqArgs.fasta ? 2 : 4); k++ )
                    {
                        rc = SRASplitter_FileWrite( cself, spot, self->b[ k ]->base, self->bsz[ k ] );
                        if ( rc == 0 )
                        {
                            rc = SRASplitter_FileWrite( cself, spot, "\n", 1 );
                        }
                    }
                }
            }
        }
        else if ( GetRCObject( rc ) == rcRow && GetRCState( rc ) == rcNotFound )
        {
            SRA_DUMP_DBG( 3, ( "%s skipped %u row\n", __func__, spot ) );
            rc = 0;
        }
    }
    return rc;
}


static rc_t Fasta_dump( const SRASplitter* cself, FastqFormatterSplitter* self, spotid_t spot, uint32_t columns )
{
    uint32_t readId;
    rc_t rc = FastqFormatterSplitter_WrapLine( self->b[4], self->bsz[4], self->b[1], &self->bsz[1], columns );
    for ( readId = 0; rc == 0 && readId < 2; readId++ )
    {
        rc = SRASplitter_FileWrite( cself, spot, self->b[readId]->base, self->bsz[ readId ] );
        if ( rc == 0 )
        {
            rc = SRASplitter_FileWrite( cself, spot, "\n", 1 );
        }
    }
    return rc;
}


static rc_t FastqFormatterSplitter_DumpBySpot( const SRASplitter* cself, spotid_t spot, const readmask_t* readmask )
{
    rc_t rc = 0;
    FastqFormatterSplitter* self = ( FastqFormatterSplitter* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcExecuting, rcParam, rcNull );
    }
    else
    {
        rc = FastqReaderSeekSpot( self->reader, spot );
        if ( rc == 0 )
        {
            uint32_t num_reads, readId;

            rc = FastqReader_SpotInfo( self->reader, NULL, NULL, NULL, NULL, NULL, &num_reads );
            for ( readId = 0; rc == 0 && readId < num_reads; readId++ )
            {
                /* if any read in readmask is not set - skip whole spot */
                if ( !isset_readmask( readmask, readId ) )
                {
                    return 0;
                }
            }
            if ( rc == 0 )
            {
                rc = SRASplitter_FileActivate( cself, FastqArgs.file_extension );
                if ( rc == 0 )
                {
                    DeflineData def_data;
                    const char* spot_name = NULL, *spot_group = NULL;
                    uint32_t spot_len = 0;
                    size_t writ, sname_sz, sgrp_sz;
                    const int base_i = FastqArgs.fasta ? 4 : 1;

                    if ( FastqArgs.b_defline || FastqArgs.q_defline )
                    {
                        rc = FastqReader_SpotInfo( self->reader, &spot_name, &sname_sz,
                                                   &spot_group, &sgrp_sz, &spot_len, NULL );
                        if ( rc == 0 )
                        {
                            rc = Defline_Bind( &def_data, self->accession, &spot, spot_name,
                                               sname_sz, spot_group, sgrp_sz, 
                                               &spot_len, &readId, NULL, 0, &spot_len );
                        }
                    }

                    if ( rc == 0 )
                    {
                        if ( FastqArgs.b_defline )
                        {
                            IF_BUF( ( Defline_Build( FastqArgs.b_defline, &def_data, self->b[0]->base,
                                      KDataBufferBytes( self->b[0] ), &self->bsz[0] ) ), self->b[0], self->bsz[0] );
                        }
                        else
                        {
                            IF_BUF( ( FastqReaderBaseName( self->reader, 0, &FastqArgs.dumpCs, self->b[0]->base,
                                      KDataBufferBytes( self->b[0] ), &self->bsz[0] ) ), self->b[0], self->bsz[0] );
                        }
                        self->bsz[ base_i ] = 0;
                        if ( !FastqArgs.fasta && rc == 0 )
                        {
                            if ( FastqArgs.q_defline )
                            {
                                IF_BUF( ( Defline_Build( FastqArgs.q_defline, &def_data, self->b[2]->base,
                                          KDataBufferBytes( self->b[2] ), &self->bsz[2] ) ), self->b[2], self->bsz[2] );
                            }
                            else
                            {
                                IF_BUF( ( FastqReaderQualityName( self->reader, 0, &FastqArgs.dumpCs, self->b[2]->base,
                                          KDataBufferBytes( self->b[2] ), &self->bsz[2] ) ), self->b[2], self->bsz[2] );
                            }
                            self->bsz[3] = 0;
                        }
                        else if ( ( (char*)(self->b[0]->base) )[0] == '@' )
                        {
                            ( (char*)(self->b[0]->base) )[0] = '>';
                        }
                    }

                    for ( readId = 1; rc == 0 && readId <= num_reads; readId++ )
                    {
                        IF_BUF( ( FastqReaderBase( self->reader, readId, &( (char*)(self->b[base_i]->base) )[ self->bsz[ base_i ] ],
                                  KDataBufferBytes( self->b[ base_i ] ) - self->bsz[ base_i ], &writ) ), self->b[ base_i ], self->bsz[ base_i ] + writ )
                        {
                            self->bsz[base_i] += writ;
                            if ( !FastqArgs.fasta )
                            {
                                IF_BUF( ( FastqReaderQuality( self->reader, readId, &( (char*)(self->b[3]->base) )[ self->bsz[3] ],
                                        KDataBufferBytes( self->b[3] ) - self->bsz[3], &writ ) ), self->b[3], self->bsz[3] + writ )
                                {
                                    self->bsz[ 3 ] += writ;
                                }
                            }
                        }
                    }

                    if ( rc == 0 )
                    {
                        if ( FastqArgs.fasta > 0 )
                        {
                            /* special printint of fasta-output ( line-wrap... ) */
                            rc = Fasta_dump( cself, self, spot, FastqArgs.fasta );
                        }
                        else
                        {
                            for ( readId = 0; rc == 0 && readId < 4; readId++ )
                            {
                                rc = SRASplitter_FileWrite( cself, spot, self->b[readId]->base, self->bsz[ readId ] );
                                if ( rc == 0 )
                                {
                                    rc = SRASplitter_FileWrite( cself, spot, "\n", 1 );
                                }
                            }
                        }
                    }
                }
            }
        }
        else if ( GetRCObject( rc ) == rcRow && GetRCState( rc ) == rcNotFound )
        {
            SRA_DUMP_DBG( 3, ( "%s skipped %u row\n", __func__, spot ) );
            rc = 0;
        }
    }
    return rc;
}


typedef struct FastqFormatterFactory_struct
{
    const char* accession;
    const SRATable* table;
    const FastqReader* reader;
    KDataBuffer buf[ 5 ]; /* fifth is for fasta line wrap */
} FastqFormatterFactory;


static rc_t FastqFormatterFactory_Init( const SRASplitterFactory* cself )
{
    rc_t rc = 0;
    FastqFormatterFactory* self = ( FastqFormatterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = FastqReaderMake( &self->reader, self->table, self->accession,
                     FastqArgs.dumpCs, FastqArgs.dumpOrigFmt, FastqArgs.fasta > 0, FastqArgs.dumpCs,
                     FastqArgs.readIds, !FastqArgs.applyClip, FastqArgs.SuppressQualForCSKey, 0,
                     FastqArgs.offset, FastqArgs.desiredCsKey[ 0 ], 0, 0 );
        if ( rc == 0 )
        {
            int i;
            for( i = 0; rc == 0 && i < sizeof( self->buf ) / sizeof( self->buf[ 0 ] ); i++ )
            {
                rc = KDataBufferMakeBytes( &self->buf[ i ], DATABUFFERINITSIZE );
            }
        }
    }
    return rc;
}


static rc_t FastqFormatterFactory_NewObj( const SRASplitterFactory* cself, const SRASplitter** splitter )
{
    rc_t rc = 0;
    FastqFormatterFactory* self = ( FastqFormatterFactory* )cself;

    if ( self == NULL )
    {
        rc = RC( rcExe, rcType, rcExecuting, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitter_Make ( splitter, sizeof( FastqFormatterSplitter ), NULL, NULL,
                                FastqArgs.split_spot ?
                                    FastqFormatterSplitter_DumpByRead :
                                    FastqFormatterSplitter_DumpBySpot, NULL );
        if ( rc == 0 )
        {
            int i;
            ( (FastqFormatterSplitter*)(*splitter) )->accession = self->accession;
            ( (FastqFormatterSplitter*)(*splitter) )->reader = self->reader;
            for ( i = 0; i < sizeof( self->buf ) / sizeof( self->buf[ 0 ] ); i++ )
            {
                ( (FastqFormatterSplitter*)(*splitter) )->b[ i ] = &self->buf[ i ];
            }
        }
    }
    return rc;
}


static void FastqFormatterFactory_Release( const SRASplitterFactory* cself )
{
    if ( cself != NULL )
    {
        int i;
        FastqFormatterFactory* self = ( FastqFormatterFactory* )cself;
        FastqReaderWhack( self->reader );
        for ( i = 0; i < sizeof( self->buf ) / sizeof( self->buf[ 0 ] ); i++ )
        {
            KDataBufferWhack( &self->buf[ i ] );
        }
    }
}


static rc_t FastqFormatterFactory_Make( const SRASplitterFactory** cself,
                const char* accession, const SRATable* table )
{
    rc_t rc = 0;
    FastqFormatterFactory* obj = NULL;

    if ( cself == NULL || accession == NULL || table == NULL )
    {
        rc = RC( rcExe, rcType, rcConstructing, rcParam, rcNull );
    }
    else
    {
        rc = SRASplitterFactory_Make( cself, eSplitterFormat, sizeof( *obj ),
                                      FastqFormatterFactory_Init,
                                      FastqFormatterFactory_NewObj,
                                      FastqFormatterFactory_Release );
        if ( rc == 0 )
        {
            obj = (FastqFormatterFactory*)*cself;
            obj->accession = accession;
            obj->table = table;
        }
    }
    return rc;
}


/* ### External entry points ##################################################### */


const char UsageDefaultName[] = "fastq-dump";


rc_t CC UsageSummary ( const char * progname )
{
    return 0;
}

#define H_splip_sot 0
#define H_clip 1
#define H_minReadLen 2
#define H_qual_filter 3
#define H_skip_tech 4
#define H_split_files 5
#define H_split_3 6
#define H_dumpcs 7
#define H_dumpbase 8
#define H_offset 9
#define H_fasta 10
#define H_origfmt 11
#define H_readids 12
#define H_helicos 13
#define H_defline_seq 14
#define H_defline_qual 15
#define H_aligned 16
#define H_unaligned 17
#define H_aligned_region 18
#define H_matepair_distance 19
#define H_qual_filter_1 20
#define H_SuppressQualForCSKey 21

rc_t FastqDumper_Usage( const SRADumperFmt* fmt, const SRADumperFmt_Arg* core_args, int first )
{
    int i, j;
    /* known core options */
    const SRADumperFmt_Arg* core[ 13 ];

    memset( (void*)core, 0, sizeof( core ) );
    for ( i = first; core_args[i].abbr != NULL || core_args[ i ].full != NULL; i++ )
    {
        const char* nm = core_args[ i ].abbr;
        nm = nm ? nm : core_args[ i ].full;
        if ( strcmp( nm, "A" ) == 0 )
        {
            core[ 0 ] = &core_args[ i ];
        }
        else if ( strcmp( nm, "O" ) == 0 )
        {
            core[ 1 ] = &core_args[ i ];
        }
        else if ( strcmp( nm, "N" ) == 0 )
        {
            core[ 2 ] = &core_args[ i ];
        }
        else if ( strcmp( nm, "X" ) == 0 )
        {
            core[ 3 ] = &core_args[ i ];
        }
        else if ( strcmp( nm, "G" ) == 0 )
        {
            core[ 4 ] = &core_args[ i ];
        }
        else if ( strcmp( nm, "spot-groups" ) == 0 )
        {
            core[ 5 ] = &core_args[ i ];
        }
        else if ( strcmp( nm, "R" ) == 0 )
        {
            core[ 6 ] = &core_args[ i ];
        }
        else if ( strcmp( nm, "T" ) == 0 )
        {
            core[ 7 ] = &core_args[ i ];
        }
        else if ( strcmp( nm, "K" ) == 0 )
        {
            core[ 8 ] = &core_args[ i ];
        }
        else if ( strcmp( nm, "table" ) == 0 )
        {
            core[ 9 ] = &core_args[ i ];
        }
        else if ( strcmp( nm, "Z" ) == 0 )
        {
            core[ 10 ] = &core_args[ i ];
        }
        else if ( strcmp( nm, "gzip" ) == 0 )
        {
            core[ 11 ] = &core_args[ i ];
        }
        else if ( strcmp( nm, "bzip2" ) == 0 )
        {
            core[ 12 ] = &core_args[ i ];
        }
    }

#define OARG(arg,msg) (arg ? HelpOptionLine((arg)->abbr, (arg)->full, (arg)->param, \
                       msg ? msg : (const char**)((arg)->descr)) : ((void)(0)))

    OUTMSG(( "INPUT\n" ));
    OARG( core[ 0 ], NULL );
    OARG( core[ 9 ], NULL );

    OUTMSG(( "\nPROCESSING\n" ));
    OUTMSG(( "\nRead Splitting                     Sequence data may be used in raw form or\n"));
    OUTMSG(( "                                     split into individual reads\n" ));
    OARG( &fmt->arg_desc[ 0 ], NULL);

    OUTMSG(( "\nFull Spot Filters                  Applied to the full spot independently\n" ));
    OUTMSG(( "                                     of --%s\n", fmt->arg_desc[0].full ));
    OARG( core[ 2 ], NULL );
    OARG( core[ 3 ], NULL );
    OARG( core[ 5 ], NULL );
    OARG( &fmt->arg_desc[ 1 ], NULL );

    OUTMSG(( "\nCommon Filters                     Applied to spots when --%s is not\n",
                                                  fmt->arg_desc[0].full ));
    OUTMSG(( "                                     set, otherwise - to individual reads\n" ));
    OARG( &fmt->arg_desc[ 2 ], NULL );
    OARG( core[ 6 ], NULL );
    OARG( &fmt->arg_desc[ 3 ], NULL );
    OARG( &fmt->arg_desc[ H_qual_filter_1 ], NULL );

    OUTMSG(( "\nFilters based on alignments        Filters are active when alignment\n" ));
    OUTMSG(( "                                     data are present\n" ));
    OARG( &fmt->arg_desc[ 16 ], NULL );
    OARG( &fmt->arg_desc[ 17 ], NULL );
    OARG( &fmt->arg_desc[ 18 ], NULL );
    OARG( &fmt->arg_desc[ 19 ], NULL );

    OUTMSG(( "\nFilters for individual reads       Applied only with --%s set\n",
                                                  fmt->arg_desc[0].full ));
    OARG( &fmt->arg_desc[ 4 ], NULL );

    OUTMSG(( "\nOUTPUT\n" ));
    OARG( core[ 1 ], NULL );
    OARG( core[ 10 ], NULL );
    OARG( core[ 11 ], NULL  );
    OARG( core[ 12 ], NULL);

    OUTMSG(( "\nMultiple File Options              Setting these options will produce more\n" ));
    OUTMSG(( "                                     than 1 file, each of which will be suffixed\n" ));
    OUTMSG(( "                                     according to splitting criteria.\n" ));
    OARG( &fmt->arg_desc[ 5 ], NULL );
    OARG( &fmt->arg_desc[ 6 ], NULL );
    OARG( core[ 4 ], NULL );
    OARG( core[ 6 ], NULL );
    OARG( core[ 7 ], NULL );
    OARG( core[ 8 ], NULL );

    OUTMSG(( "\nFORMATTING\n" ));
    OUTMSG(( "\nSequence\n" ));
    OARG( &fmt->arg_desc[ 7 ], NULL );
    OARG( &fmt->arg_desc[ 8 ], NULL );

    OUTMSG(( "\nQuality\n" ));
    OARG( &fmt->arg_desc[ 9 ], NULL );
    OARG( &fmt->arg_desc[ 10 ], NULL );
    OARG( &fmt->arg_desc[ H_SuppressQualForCSKey ], NULL ); /* added Jan 15th 2014 ( a new fastq-variation! ) */

    OUTMSG(( "\nDefline\n" ));
    OARG( &fmt->arg_desc[ 11 ], NULL );
    OARG( &fmt->arg_desc[ 12 ], NULL );
    OARG( &fmt->arg_desc[ 13 ], NULL );
    OARG( &fmt->arg_desc[ 14 ], NULL );
    OARG( &fmt->arg_desc[ 15 ], NULL );

    OUTMSG(( "OTHER:\n" ));
    for ( i = first; core_args[ i ].abbr != NULL || core_args[ i ].full != NULL; i++ )
    {
        bool print = true;
        for ( j = 0; j < sizeof( core ) / sizeof( core[ 0 ] ); j++ )
        {
            if ( core[ j ] == &core_args[ i ] )
            {
                print = false;
                break;
            }
        }
        if ( print )
        {
            OARG( &core_args[ i ], NULL );
        }
    }
    return 0;
}


rc_t FastqDumper_Release( const SRADumperFmt* fmt )
{
    if ( fmt == NULL )
    {
        return RC( rcExe, rcFormatter, rcDestroying, rcParam, rcInvalid );
    }
    else
    {
        Defline_Release( FastqArgs.b_defline );
        Defline_Release( FastqArgs.q_defline );
        free( FastqArgs.alregion );
    }
    return 0;
}


bool FastqDumper_AddArg( const SRADumperFmt* fmt, GetArg* f, int* i, int argc, char *argv[] )
{
    const char* arg = NULL;

    if ( fmt == NULL || f == NULL || i == NULL || argv == NULL )
    {
        LOGERR( klogErr, RC( rcExe, rcArgv, rcReading, rcParam, rcInvalid ), "null param" );
        return false;
    }
    else if ( f( fmt, "M", "minReadLen", i, argc, argv, &arg ) )
    {
        FastqArgs.minReadLen = AsciiToU32( arg, NULL, NULL );
    }
    else if ( f( fmt, "W", "clip", i, argc, argv, NULL ) )
    {
        FastqArgs.applyClip = true;
    }
    else if ( f( fmt, "SU", "suppress-qual-for-cskey", i, argc, argv, NULL ) )
    {
        FastqArgs.SuppressQualForCSKey = true;
    }
    else if ( f( fmt, "F", "origfmt", i, argc, argv, NULL ) )
    {
        FastqArgs.dumpOrigFmt = true;
    }
    else if ( f( fmt, "C", "dumpcs", i, argc, argv, NULL ) )
    {
        int k = ( *i ) + 1;
        FastqArgs.dumpCs = true;
        if ( k < argc && strlen( argv[ k ] ) == 1 && strchr( "acgtACGT", argv[ k ][ 0 ] ) != NULL )
        {
            FastqArgs.desiredCsKey = argv[ k ];
            *i = k;
        }
    }
    else if ( f( fmt, "B", "dumpbase", i, argc, argv, NULL ) )
    {
        FastqArgs.dumpBase = true;
    }
    else if ( f( fmt, "Q", "offset", i, argc, argv, &arg ) )
    {
        FastqArgs.offset = AsciiToU32( arg, NULL, NULL );
    }
    else if ( f( fmt, "I", "readids", i, argc, argv, NULL ) )
    {
        FastqArgs.readIds = true;
    }
    else if ( f( fmt, "E", "qual-filter", i, argc, argv, NULL ) )
    {
        FastqArgs.qual_filter = true;
    }
    else if ( f( fmt, "E1", "qual-filter-1", i, argc, argv, NULL ) )
    {
        FastqArgs.qual_filter1 = true;
    }
    else if ( f( fmt, "DB", "defline-seq", i, argc, argv, &arg ) )
    {
        FastqArgs.b_deffmt = arg;
    }
    else if ( f( fmt, "DQ", "defline-qual", i, argc, argv, &arg ) )
    {
        FastqArgs.q_deffmt = arg;
    }
    else if ( f( fmt, "TR", "skip-technical", i, argc, argv, NULL ) )
    {
        FastqArgs.skipTechnical = true;
    }
    else if ( f( fmt, "SF", "split-files", i, argc, argv, NULL ) )
    {
        SRADumperFmt * nc_fmt = ( SRADumperFmt * )fmt;
        FastqArgs.split_spot = true;
        FastqArgs.split_files = true;
        nc_fmt->split_files = true;
    }
    else if ( f( fmt, NULL, "split-3", i, argc, argv, NULL ) )
    {
        FastqArgs.split_3 = true;
        FastqArgs.split_spot = true;
        FastqArgs.maxReads = 2;
        FastqArgs.skipTechnical = true;
    }
    else if ( f( fmt, "SL", "split-spot", i, argc, argv, NULL ) )
    {
        FastqArgs.split_spot = true;
    }
    else if ( f( fmt, "HS", "helicos", i, argc, argv, NULL ) )
    {
        FastqArgs.b_deffmt = "@$sn";
        FastqArgs.q_deffmt =  "+";
    }
    else if ( f( fmt, "FA", "fasta", i, argc, argv, NULL ) )
    {
        int k = (*i) + 1;
        FastqArgs.fasta = 70;
        if ( k < argc && isdigit( argv[ k ][ 0 ] ) )
        {
            char* endp = NULL;
            errno = 0;
            FastqArgs.fasta = strtou64( argv[ k ], &endp, 10 );
            if ( errno != 0 || endp == NULL || *endp != '\0' )
            {
                return false;
            }
            *i = k;
            if ( FastqArgs.fasta == 0 )
            {
                FastqArgs.fasta = ~0;
            }
        }
        FastqArgs.file_extension = ".fasta";
    }
    else if ( f( fmt, NULL, "aligned", i, argc, argv, NULL ) )
    {
        FastqArgs.aligned = true;
    }
    else if ( f( fmt, NULL, "unaligned", i, argc, argv, NULL ) )
    {
        FastqArgs.unaligned = true;
    }
    else if ( f( fmt, NULL, "aligned-region", i, argc, argv, &arg ) )
    {
        /* name[:[from][-[to]]] */
        TAlignedRegion* r = realloc( FastqArgs.alregion, sizeof( *FastqArgs.alregion ) * ++FastqArgs.alregion_qty );
        if ( r == NULL )
        {
            return false;
        }
        FastqArgs.alregion = r;
        r = &FastqArgs.alregion[ FastqArgs.alregion_qty - 1 ];
        r->name = strchr( arg, ':' );
        r->from = 0;
        r->to = 0;
        if ( r->name == NULL )
        {
            r->name = arg;
            r->name_len = strlen( arg );
        }
        else
        {
            const char* c;
            uint64_t* v;

            r->name_len = r->name - arg;
            c = r->name;
            r->name = arg;

            v = &r->from;
            while ( *++c != '\0')
            {
                if ( *c == '-' )
                {
                    v = &r->to;
                }
                else if ( *c == '+' )
                {
                    if ( *v != 0 )
                    {
                        return false;
                    }
                }
                else if ( !isdigit( *c ) )
                {
                    return false;
                }
                else
                {
                    *v = *v * 10 + ( *c - '0' );
                }
            }
            if ( r->from > r->to && r->to != 0 )
            {
                uint64_t x = r->from;
                r->from = r->to;
                r->to = x;
            }
        }
    }
    else if ( f( fmt, NULL, "matepair-distance", i, argc, argv, &arg ) )
    {
        /* from[-to] | [from]-to | unknown */
        if ( strcmp( arg, "unknown" ) == 0 )
        {
            FastqArgs.mp_dist_unknown = true;
        }
        else
        {
            uint64_t* v;
            TMatepairDistance* p = realloc( FastqArgs.mp_dist, sizeof( *FastqArgs.mp_dist ) * ++FastqArgs.mp_dist_qty );
            if ( p == NULL )
            {
                return false;
            }
            FastqArgs.mp_dist = p;
            p = &FastqArgs.mp_dist[ FastqArgs.mp_dist_qty - 1 ];
            p->from = 0;
            p->to = 0;

            v = &p->from;
            while ( *++arg != '\0' )
            {
                if ( *arg == '-' )
                {
                    v = &p->to;
                }
                else if ( *arg == '+' )
                {
                    if ( *v != 0 )
                    {
                        return false;
                    }
                }
                else if ( !isdigit( *arg ) )
                {
                    return false;
                }
                else
                {
                    *v = *v * 10 + ( *arg - '0' );
                }
            }
            if ( p->from > p->to && p->to != 0 )
            {
                uint64_t x = p->from;
                p->from = p->to;
                p->to = x;
            }
            if ( p->from == 0 && p->to == 0 )
            {
                FastqArgs.mp_dist_qty--;
            }
        }
    }
    else
    {
        return false;
    }
    return true;
}


rc_t FastqDumper_Factories( const SRADumperFmt* fmt, const SRASplitterFactory** factory )
{
    rc_t rc = 0;
    const SRASplitterFactory* parent = NULL, *child = NULL;

    if ( fmt == NULL || factory == NULL )
    {
        return RC( rcExe, rcFormatter, rcReading, rcParam, rcInvalid );
    }
    *factory = NULL;
    {
        const SRAColumn* c = NULL;
        rc = SRATableOpenColumnRead( fmt->table, &c, "PLATFORM", sra_platform_id_t );
        if ( rc == 0 )
        {
            const INSDC_SRA_platform_id * platform;
            bitsz_t o, z;
            rc = SRAColumnRead( c, 1, ( const void ** )&platform, &o, &z );
            if ( rc == 0 )
            {
                if ( !FastqArgs.dumpCs && !FastqArgs.dumpBase )
                {
                    if ( platform != NULL && *platform == SRA_PLATFORM_ABSOLID )
                    {
                        FastqArgs.dumpCs = true;
                    }
                    else
                    {
                        FastqArgs.dumpBase = true;
                    }
                }
                if ( platform != NULL && *platform == SRA_PLATFORM_ABSOLID )
                {
                    FastqArgs.is_platform_cs_native = true;
                }
            }
            SRAColumnRelease( c );
        }
        else if ( GetRCState( rc ) == rcNotFound && GetRCObject( rc ) == ( enum RCObject )rcColumn )
        {
            rc = 0;
        }
    }

    if ( ( FastqArgs.aligned || FastqArgs.unaligned ) && !( FastqArgs.aligned && FastqArgs.unaligned ) )
    {
        rc = AlignedFilterFactory_Make( &child, fmt->table, FastqArgs.aligned, FastqArgs.unaligned );
        if ( rc == 0 )
        {
            if ( parent != NULL )
            {
                rc = SRASplitterFactory_AddNext( parent, child );
                if ( rc != 0 )
                {
                    SRASplitterFactory_Release(child);
                }
                else
                {
                    parent = child;
                }
            }
            else
            {
                parent = child;
                *factory = parent;
            }
        }
    }

    if ( FastqArgs.alregion_qty > 0 )
    {
        rc = AlignRegionFilterFactory_Make( &child, fmt->table, FastqArgs.alregion, FastqArgs.alregion_qty );
        if ( rc == 0 )
        {
            if ( parent != NULL )
            {
                rc = SRASplitterFactory_AddNext( parent, child );
                if ( rc != 0 )
                {
                    SRASplitterFactory_Release( child );
                }
                else
                {
                    parent = child;
                }
            }
            else
            {
                parent = child;
                *factory = parent;
            }
        }
    }

    if ( FastqArgs.mp_dist_unknown || FastqArgs.mp_dist_qty > 0 )
    {
        rc = AlignPairDistanceFilterFactory_Make( &child, fmt->table,
                FastqArgs.mp_dist_unknown, FastqArgs.mp_dist, FastqArgs.mp_dist_qty);
        if ( rc == 0 )
        {
            if ( parent != NULL )
            {
                rc = SRASplitterFactory_AddNext( parent, child );
                if ( rc != 0 )
                {
                    SRASplitterFactory_Release(child);
                }
                else
                {
                    parent = child;
                }
            }
            else
            {
                parent = child;
                *factory = parent;
            }
        }
    }

    if ( rc == 0 && FastqArgs.skipTechnical && FastqArgs.split_spot )
    {
        rc = FastqBioFilterFactory_Make( &child, fmt->accession, fmt->table );
        if ( rc == 0 )
        {
            if ( parent != NULL )
            {
                rc = SRASplitterFactory_AddNext( parent, child );
                if ( rc != 0 )
                {
                    SRASplitterFactory_Release( child );
                }
                else
                {
                    parent = child;
                }
            }
            else
            {
                parent = child;
                *factory = parent;
            }
        }
    }

    if ( rc == 0 && FastqArgs.maxReads > 0 )
    {
        rc = FastqRNumberFilterFactory_Make( &child, fmt->accession, fmt->table );
        if ( rc == 0 )
        {
            if ( parent != NULL )
            {
                rc = SRASplitterFactory_AddNext( parent, child );
                if ( rc != 0 )
                {
                    SRASplitterFactory_Release( child );
                }
                else
                {
                    parent = child;
                }
            }
            else
            {
                parent = child;
                *factory = parent;
            }
        }
    }

    if ( rc == 0 && ( FastqArgs.qual_filter || FastqArgs.qual_filter1 ) )
    {
        rc = FastqQFilterFactory_Make( &child, fmt->accession, fmt->table );
        if ( rc == 0 )
        {
            if ( parent != NULL )
            {
                rc = SRASplitterFactory_AddNext( parent, child );
                if ( rc != 0 )
                {
                    SRASplitterFactory_Release( child );
                }
                else
                {
                    parent = child;
                }
            }
            else
            {
                parent = child;
                *factory = parent;
            }
        }
    }

    if ( rc == 0 )
    {
        rc = FastqReadLenFilterFactory_Make( &child, fmt->accession, fmt->table );
        if ( rc == 0 )
        {
            if ( parent != NULL )
            {
                rc = SRASplitterFactory_AddNext( parent, child );
                if ( rc != 0 )
                {
                    SRASplitterFactory_Release( child );
                }
                else
                {
                    parent = child;
                }
            }
            else
            {
                parent = child;
                *factory = parent;
            }
        }
    }

    if ( rc == 0 )
    {
        if ( FastqArgs.split_3 )
        {
            rc = Fastq3ReadSplitterFactory_Make( &child, fmt->accession, fmt->table );
            if ( rc == 0 )
            {
                if ( parent != NULL )
                {
                    rc = SRASplitterFactory_AddNext( parent, child );
                    if ( rc != 0 )
                    {
                        SRASplitterFactory_Release( child );
                    }
                    else
                    {
                        parent = child;
                    }
                }
                else
                {
                    parent = child;
                    *factory = parent;
                }
            }
        }
        else if ( FastqArgs.split_files )
        {
            rc = FastqReadSplitterFactory_Make( &child, fmt->accession, fmt->table );
            if ( rc == 0 )
            {
                if ( parent != NULL )
                {
                    rc = SRASplitterFactory_AddNext( parent, child );
                    if ( rc != 0 )
                    {
                        SRASplitterFactory_Release(child);
                    }
                    else
                    {
                        parent = child;
                    }
                }
                else
                {
                    parent = child;
                    *factory = parent;
                }
            }
        }
    }

    if ( rc == 0 )
    {
        if ( FastqArgs.b_deffmt != NULL )
        {
            rc = Defline_Parse( &FastqArgs.b_defline, FastqArgs.b_deffmt );
        }
        if ( FastqArgs.q_deffmt != NULL )
        {
            rc = Defline_Parse( &FastqArgs.q_defline, FastqArgs.q_deffmt );
        }
        if ( rc == 0 )
        {
            rc = FastqFormatterFactory_Make( &child, fmt->accession, fmt->table );
            if ( rc == 0 )
            {
                if ( parent != NULL )
                {
                    rc = SRASplitterFactory_AddNext( parent, child );
                    if ( rc != 0 ) 
                    {
                        SRASplitterFactory_Release( child );
                    }
                }
                else
                {
                    *factory = child;
                }
            }
        }
    }
    return rc;
}

/* main entry point of the file */
rc_t SRADumper_Init( SRADumperFmt* fmt )
{
    static const SRADumperFmt_Arg arg[] =
        {

            /* DO NOT ADD IN THE MIDDLE ORDER IS IMPORTANT IN USAGE FUNCTION ABOVE!!! */
            {NULL, "split-spot", NULL, {"Split spots into individual reads", NULL}},            /* H_splip_sot = 0 */

            {"W", "clip", NULL, {"Clip adapter sequences", NULL}},                          /* H_clip = 1 */

            {"M", "minReadLen", "len", {"Filter by sequence length >= <len>", NULL}},           /* H_minReadLen = 2 */
            {"E", "qual-filter", NULL, {"Filter used in early 1000 Genomes data:",              /* H_qual_filter = 3 */
                                        "no sequences starting or ending with >= 10N", NULL}},

            {NULL, "skip-technical", NULL, {"Dump only biological reads", NULL}},               /* H_skip_tech = 4 */

            {NULL, "split-files", NULL, {"Dump each read into a separate file."                 /* H_split_files = 5 */
                                         "Files will receive suffix corresponding to read number", NULL}},

            /* DO NOT ADD IN THE MIDDLE ORDER IS IMPORTANT IN USAGE FUNCTION ABOVE!!! */
            {NULL, "split-3", NULL, {"Legacy 3-file splitting for mate-pairs:",                 /* H_split_3 = 6 */
                                     "First 2 biological reads satisfying dumping conditions",
                                     "are placed in files *_1.fastq and *_2.fastq",
                                     "If only one biological read is present - it is placed in *.fastq",
                                     "Biological reads 3 and above are ignored.", NULL}},
            
            {"C", "dumpcs", "[cskey]", {"Formats sequence using color space (default for SOLiD),"   /* H_dumpcs = 7 */
                                        "\"cskey\" may be specified for translation", NULL}},
            {"B", "dumpbase", NULL, {"Formats sequence using base space (default for other than SOLiD).", NULL}}, /* H_dumpbase = 8 */

            /* DO NOT ADD IN THE MIDDLE ORDER IS IMPORTANT IN USAGE FUNCTION ABOVE!!! */
            {"Q", "offset", "integer", {"Offset to use for quality conversion, default is 33", NULL}},  /* H_offset = 9 */
            {NULL, "fasta", "[line width]", {"FASTA only, no qualities, optional line wrap width (set to zero for no wrapping)", NULL}}, /* H_fasta = 10 */

            {"F", "origfmt", NULL, {"Defline contains only original sequence name", NULL}}, /* H_origfmt = 11 */
            {"I", "readids", NULL, {"Append read id after spot id as 'accession.spot.readid' on defline", NULL}}, /* H_readids = 12 */
            {NULL, "helicos", NULL, {"Helicos style defline", NULL}}, /* H_helicos = 13 */
            {NULL, "defline-seq", "fmt", {"Defline format specification for sequence.", NULL}}, /* H_defline_seq = 14 */
            {NULL, "defline-qual", "fmt", {"Defline format specification for quality.", /* H_defline_qual = 15 */
                              "<fmt> is a string of characters and/or variables. The variables can be one of:",
                              "$ac - accession, $si - spot id, $sn - spot name, $sg - spot group (barcode),",
                              "$sl - spot length in bases, $ri - read number, $rn - read name, $rl - read length in bases.",
                              "'[]' could be used for an optional output: if all vars in [] yield empty values whole group is not printed.",
                              "Empty value is empty string or 0 for numeric variables.",
                              "Ex: @$sn[_$rn]/$ri - '_$rn' is omitted if name is empty\n", NULL}},

            {NULL, "aligned", NULL, {"Dump only aligned sequences", NULL}}, /* H_aligned = 16 */
            {NULL, "unaligned", NULL, {"Dump only unaligned sequences", NULL}}, /* H_unaligned = 17 */

            /* DO NOT ADD IN THE MIDDLE ORDER IS IMPORTANT IN USAGE FUNCTION ABOVE!!! */
            {NULL, "aligned-region", "name[:from-to]", {"Filter by position on genome.", /* H_aligned_region = 18 */
                            "Name can either be accession.version (ex: NC_000001.10) or",
                            "file specific name (ex: \"chr1\" or \"1\").",
                            "\"from\" and \"to\" are 1-based coordinates", NULL}},
            {NULL, "matepair-distance", "from-to|unknown", {"Filter by distance between matepairs.", /* H_matepair-distance = 19 */
                            "Use \"unknown\" to find matepairs split between the references.",
                            "Use from-to to limit matepair distance on the same reference", NULL}},

            {NULL, "qual-filter-1", NULL, {"Filter used in current 1000 Genomes data", NULL}}, /* H_qual_filter_1 = 20 */

            {NULL, "suppress-qual-for-cskey", NULL, {"suppress quality-value for cskey", NULL}}, /* H_SuppressQualForCSKey = 21 */

            {NULL, NULL, NULL, {NULL}}
        };

    if ( fmt == NULL )
    {
        return RC( rcExe, rcFileFormat, rcConstructing, rcParam, rcNull );
    }

    memset( &FastqArgs, 0, sizeof( FastqArgs ) );
    FastqArgs.is_platform_cs_native = false;
    FastqArgs.maxReads = 0;
    FastqArgs.skipTechnical = false;
    FastqArgs.minReadLen = 1;
    FastqArgs.applyClip = false;
    FastqArgs.SuppressQualForCSKey = false;     /* added Jan 15th 2014 ( a new fastq-variation! ) */
    FastqArgs.dumpOrigFmt = false;
    FastqArgs.dumpBase = false;
    FastqArgs.dumpCs = false;
    FastqArgs.readIds = false;
    FastqArgs.offset = 33;
    FastqArgs.desiredCsKey = "";
    FastqArgs.qual_filter = false;
    FastqArgs.b_deffmt = NULL;
    FastqArgs.b_defline = NULL;
    FastqArgs.q_deffmt = NULL;
    FastqArgs.q_defline = NULL;
    FastqArgs.split_files = false;
    FastqArgs.split_3 = false;
    FastqArgs.split_spot = false;
    FastqArgs.fasta = 0;
    FastqArgs.file_extension = ".fastq";
    FastqArgs.aligned = false;
    FastqArgs.unaligned = false;
    FastqArgs.alregion = NULL;
    FastqArgs.alregion_qty = 0;
    FastqArgs.mp_dist = NULL;
    FastqArgs.mp_dist_unknown = false;
    FastqArgs.mp_dist_qty = 0;

    fmt->usage = FastqDumper_Usage;
    fmt->release = FastqDumper_Release;
    fmt->arg_desc = arg;
    fmt->add_arg = FastqDumper_AddArg;
    fmt->get_factory = FastqDumper_Factories;
    fmt->gzip = true;
    fmt->bzip2 = true;
    fmt->split_files = false;

    return 0;
}
