/*===========================================================================
*
*                            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 <vdb/extern.h>

#include <sra/sradb.h>
#include <vdb/xform.h>
#include <vdb/table.h>
#include <klib/data-buffer.h>
#include <klib/text.h>
#include <klib/rc.h>
#include <sysalloc.h>

#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include <assert.h>

static
rc_t CC template_len_impl(void *data,const VXformInfo *info, int64_t row_id, VRowResult *rslt, uint32_t argc, const VRowData argv [] ) 
{
    rc_t 	rc;
    int32_t	*dst;
    const INSDC_coord_zero *p1 = argv[0].u.data.base;
    const INSDC_coord_zero *p2 = argv[1].u.data.base;
    const INSDC_coord_len  *l1 = argv[2].u.data.base;
    const INSDC_coord_len  *l2 = argv[3].u.data.base;
    const char             *n1 = argv[4].u.data.base;
    const char             *n2 = argv[5].u.data.base;
    const INSDC_coord_one  *r1 = argv[6].u.data.base;

    /** primary should have everything defines ***/
    assert(argv[0].u.data.elem_count == 1);
    assert(argv[2].u.data.elem_count == 1);
    assert(argv[4].u.data.elem_count > 0 );
    assert(argv[6].u.data.elem_count == 1);

    rc = KDataBufferResize(rslt->data, 1);
    if(rc != 0) return rc;
    rslt->elem_count=1;
    dst = rslt->data->base;
    dst[0] = 0;

    /*** check if the mate is mapped **/
    if(   argv[1].u.data.elem_count > 0
        && argv[3].u.data.elem_count > 0
        && argv[4].u.data.elem_count == argv[5].u.data.elem_count)
    {
        n1+=argv[4].u.data.first_elem;
        n2+=argv[5].u.data.first_elem;
        r1+=argv[6].u.data.first_elem;
        
        if(   argv[4].u.data.elem_count == argv[5].u.data.elem_count
            && memcmp(n1,n2,argv[4].u.data.elem_count)==0) /*** same reference name ***/
        {
#if 1
            unsigned const self_left  = p1[argv[0].u.data.first_elem];
            unsigned const mate_left  = p2[argv[1].u.data.first_elem];
            unsigned const self_right = self_left + l1[argv[2].u.data.first_elem];
            unsigned const mate_right = mate_left + l2[argv[3].u.data.first_elem];
            unsigned const  leftmost  = (self_left  < mate_left ) ? self_left  : mate_left;
            unsigned const rightmost  = (self_right > mate_right) ? self_right : mate_right;
            unsigned const tlen = rightmost - leftmost;
            
            /* The standard says, "The leftmost segment has a plus sign and the rightmost has a minus sign." */
            if (   (self_left <= mate_left && self_right >= mate_right)     /* mate fully contained within self or */
                || (mate_left <= self_left && mate_right >= self_right))    /* self fully contained within mate; */
            {
                if (self_left < mate_left || (r1[0] == 1 && self_left == mate_left))
                    dst[0] = tlen;
                else
                    dst[0] = -tlen;
            }
            else if (   (self_right == mate_right && mate_left == leftmost) /* both are rightmost, but mate is leftmost */
                     ||  self_right == rightmost)
            {
                dst[0] = -tlen;
            }
            else
                dst[0] = tlen;
#else
            dst[0] = p2[argv[1].u.data.first_elem] -  p1[argv[0].u.data.first_elem];
            if(dst[0] < 0){
                dst[0] -= l1[argv[2].u.data.first_elem];
            } else if (dst[0] > 0) {
                dst[0] += l2[argv[3].u.data.first_elem];
            } else if(r1[0]==1){/*** bam wants to give positive TLEN ***/
                dst[0] = l1[argv[2].u.data.first_elem];
            } else if(r1[0]==2){/*** bam wants to give negative TLEN ***/
                dst[0] = -l2[argv[3].u.data.first_elem];
            } 
#endif
        }
    }
    return 0;	
}

VTRANSFACT_IMPL ( NCBI_align_template_len, 1, 0, 0 ) ( const void *self, const VXfactInfo *info, VFuncDesc *rslt,
                                                 const VFactoryParams *cp, const VFunctionParams *dp )
{
    rslt->variant = vftRow;
    rslt->u.rf = template_len_impl;
    return 0;
}
